diff --git a/.travis.yml b/.travis.yml
index 03e319f6b16..b31d1f10da0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,6 +1,7 @@
 language: node_js
 
 node_js:
+  - 'stable'
   - '4'
   - '0.10'
 
diff --git a/Jakefile.js b/Jakefile.js
index 14bf047cf21..5dfbcc26d74 100644
--- a/Jakefile.js
+++ b/Jakefile.js
@@ -228,7 +228,7 @@ var builtLocalCompiler = path.join(builtLocalDirectory, compilerFilename);
 function compileFile(outFile, sources, prereqs, prefixes, useBuiltCompiler, noOutFile, generateDeclarations, outDir, preserveConstEnums, keepComments, noResolve, stripInternal, callback) {
     file(outFile, prereqs, function() {
         var compilerPath = useBuiltCompiler ? builtLocalCompiler : LKGCompiler;
-        var options = "--module commonjs --noImplicitAny --noEmitOnError --pretty";
+        var options = "--noImplicitAny --noEmitOnError --pretty";
 
         // Keep comments when specifically requested
         // or when in debug mode.
@@ -251,6 +251,9 @@ function compileFile(outFile, sources, prereqs, prefixes, useBuiltCompiler, noOu
         if (!noOutFile) {
             options += " --out " + outFile;
         }
+        else {
+            options += " --module commonjs"
+        }
 
         if(noResolve) {
             options += " --noResolve";
diff --git a/src/compiler/checker.ts b/src/compiler/checker.ts
index fe406c00180..b73543e14de 100644
--- a/src/compiler/checker.ts
+++ b/src/compiler/checker.ts
@@ -3003,7 +3003,7 @@ namespace ts {
                     (<GenericType>type).typeArguments = type.typeParameters;
                     type.thisType = <TypeParameter>createType(TypeFlags.TypeParameter | TypeFlags.ThisType);
                     type.thisType.symbol = symbol;
-                    type.thisType.constraint = getTypeWithThisArgument(type);
+                    type.thisType.constraint = type;
                 }
             }
             return <InterfaceType>links.declaredType;
@@ -3546,6 +3546,21 @@ namespace ts {
             return type.flags & TypeFlags.UnionOrIntersection ? getPropertiesOfUnionOrIntersectionType(<UnionType>type) : getPropertiesOfObjectType(type);
         }
 
+        /**
+         * The apparent type of a type parameter is the base constraint instantiated with the type parameter
+         * as the type argument for the 'this' type.
+         */
+        function getApparentTypeOfTypeParameter(type: TypeParameter) {
+            if (!type.resolvedApparentType) {
+                let constraintType = getConstraintOfTypeParameter(type);
+                while (constraintType && constraintType.flags & TypeFlags.TypeParameter) {
+                    constraintType = getConstraintOfTypeParameter(<TypeParameter>constraintType);
+                }
+                type.resolvedApparentType = getTypeWithThisArgument(constraintType || emptyObjectType, type);
+            }
+            return type.resolvedApparentType;
+        }
+
         /**
          * For a type parameter, return the base constraint of the type parameter. For the string, number,
          * boolean, and symbol primitive types, return the corresponding object types. Otherwise return the
@@ -3553,12 +3568,7 @@ namespace ts {
          */
         function getApparentType(type: Type): Type {
             if (type.flags & TypeFlags.TypeParameter) {
-                do {
-                    type = getConstraintOfTypeParameter(<TypeParameter>type);
-                } while (type && type.flags & TypeFlags.TypeParameter);
-                if (!type) {
-                    type = emptyObjectType;
-                }
+                type = getApparentTypeOfTypeParameter(<TypeParameter>type);
             }
             if (type.flags & TypeFlags.StringLike) {
                 type = globalStringType;
@@ -5099,9 +5109,6 @@ namespace ts {
             }
 
             function typeParameterIdenticalTo(source: TypeParameter, target: TypeParameter): Ternary {
-                if (source.symbol.name !== target.symbol.name) {
-                    return Ternary.False;
-                }
                 // covers case when both type parameters does not have constraint (both equal to noConstraintType)
                 if (source.constraint === target.constraint) {
                     return Ternary.True;
@@ -6462,9 +6469,10 @@ namespace ts {
 
             function narrowTypeByInstanceof(type: Type, expr: BinaryExpression, assumeTrue: boolean): Type {
                 // Check that type is not any, assumed result is true, and we have variable symbol on the left
-                if (isTypeAny(type) || !assumeTrue || expr.left.kind !== SyntaxKind.Identifier || getResolvedSymbol(<Identifier>expr.left) !== symbol) {
+                if (isTypeAny(type) || expr.left.kind !== SyntaxKind.Identifier || getResolvedSymbol(<Identifier>expr.left) !== symbol) {
                     return type;
                 }
+
                 // Check that right operand is a function type with a prototype property
                 const rightType = checkExpression(expr.right);
                 if (!isTypeSubtypeOf(rightType, globalFunctionType)) {
@@ -6496,6 +6504,13 @@ namespace ts {
                 }
 
                 if (targetType) {
+                    if (!assumeTrue) {
+                        if (type.flags & TypeFlags.Union) {
+                            return getUnionType(filter((<UnionType>type).types, t => !isTypeSubtypeOf(t, targetType)));
+                        }
+                        return type;
+                    }
+
                     return getNarrowedType(type, targetType);
                 }
 
@@ -14944,10 +14959,20 @@ namespace ts {
                 getReferencedValueDeclaration,
                 getTypeReferenceSerializationKind,
                 isOptionalParameter,
-                isArgumentsLocalBinding
+                isArgumentsLocalBinding,
+                getExternalModuleFileFromDeclaration
             };
         }
 
+        function getExternalModuleFileFromDeclaration(declaration: ImportEqualsDeclaration | ImportDeclaration | ExportDeclaration): SourceFile {
+                const specifier = getExternalModuleName(declaration);
+                const moduleSymbol = getSymbolAtLocation(specifier);
+                if (!moduleSymbol) {
+                    return undefined;
+                }
+                return getDeclarationOfKind(moduleSymbol, SyntaxKind.SourceFile) as SourceFile;
+        }
+
         function initializeTypeChecker() {
             // Bind all source files and propagate errors
             forEach(host.getSourceFiles(), file => {
diff --git a/src/compiler/core.ts b/src/compiler/core.ts
index a51f62e0d65..c866cf41a92 100644
--- a/src/compiler/core.ts
+++ b/src/compiler/core.ts
@@ -780,7 +780,8 @@ namespace ts {
     };
 
     export interface ObjectAllocator {
-        getNodeConstructor(kind: SyntaxKind): new (pos?: number, end?: number) => Node;
+        getNodeConstructor(): new (kind: SyntaxKind, pos?: number, end?: number) => Node;
+        getSourceFileConstructor(): new (kind: SyntaxKind, pos?: number, end?: number) => SourceFile;
         getSymbolConstructor(): new (flags: SymbolFlags, name: string) => Symbol;
         getTypeConstructor(): new (checker: TypeChecker, flags: TypeFlags) => Type;
         getSignatureConstructor(): new (checker: TypeChecker) => Signature;
@@ -799,17 +800,17 @@ namespace ts {
     function Signature(checker: TypeChecker) {
     }
 
+    function Node(kind: SyntaxKind, pos: number, end: number) {
+        this.kind = kind;
+        this.pos = pos;
+        this.end = end;
+        this.flags = NodeFlags.None;
+        this.parent = undefined;
+    }
+
     export let objectAllocator: ObjectAllocator = {
-        getNodeConstructor: kind => {
-            function Node(pos: number, end: number) {
-                this.pos = pos;
-                this.end = end;
-                this.flags = NodeFlags.None;
-                this.parent = undefined;
-            }
-            Node.prototype = { kind };
-            return <any>Node;
-        },
+        getNodeConstructor: () => <any>Node,
+        getSourceFileConstructor: () => <any>Node,
         getSymbolConstructor: () => <any>Symbol,
         getTypeConstructor: () => <any>Type,
         getSignatureConstructor: () => <any>Signature
diff --git a/src/compiler/declarationEmitter.ts b/src/compiler/declarationEmitter.ts
index ac91a39a78b..669cbcbcf0c 100644
--- a/src/compiler/declarationEmitter.ts
+++ b/src/compiler/declarationEmitter.ts
@@ -45,18 +45,22 @@ namespace ts {
         let writeLine: () => void;
         let increaseIndent: () => void;
         let decreaseIndent: () => void;
-        let writeTextOfNode: (sourceFile: SourceFile, node: Node) => void;
+        let writeTextOfNode: (text: string, node: Node) => void;
 
         let writer = createAndSetNewTextWriterWithSymbolWriter();
 
         let enclosingDeclaration: Node;
-        let currentSourceFile: SourceFile;
+        let currentText: string;
+        let currentLineMap: number[];
+        let currentIdentifiers: Map<string>;
+        let isCurrentFileExternalModule: boolean;
         let reportedDeclarationError = false;
         let errorNameNode: DeclarationName;
         const emitJsDocComments = compilerOptions.removeComments ? function (declaration: Node) { } : writeJsDocComments;
         const emit = compilerOptions.stripInternal ? stripInternal : emitNode;
+        let noDeclare = !root;
 
-        const moduleElementDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[] = [];
+        let moduleElementDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[] = [];
         let asynchronousSubModuleDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[];
 
         // Contains the reference paths that needs to go in the declaration file.
@@ -104,15 +108,16 @@ namespace ts {
         else {
             // Emit references corresponding to this file
             const emittedReferencedFiles: SourceFile[] = [];
+            let prevModuleElementDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[] = [];
             forEach(host.getSourceFiles(), sourceFile => {
-                if (!isExternalModuleOrDeclarationFile(sourceFile)) {
+                if (!isDeclarationFile(sourceFile)) {
                     // Check what references need to be added
                     if (!compilerOptions.noResolve) {
                         forEach(sourceFile.referencedFiles, fileReference => {
                             const referencedFile = tryResolveScriptReference(host, sourceFile, fileReference);
 
-                            // If the reference file is a declaration file or an external module, emit that reference
-                            if (referencedFile && (isExternalModuleOrDeclarationFile(referencedFile) &&
+                            // If the reference file is a declaration file, emit that reference
+                            if (referencedFile && (isDeclarationFile(referencedFile) &&
                                 !contains(emittedReferencedFiles, referencedFile))) { // If the file reference was not already emitted
 
                                 writeReferencePath(referencedFile);
@@ -120,10 +125,43 @@ namespace ts {
                             }
                         });
                     }
+                }
 
+                if (!isExternalModuleOrDeclarationFile(sourceFile)) {
+                    noDeclare = false;
                     emitSourceFile(sourceFile);
                 }
+                else if (isExternalModule(sourceFile)) {
+                    noDeclare = true;
+                    write(`declare module "${getResolvedExternalModuleName(host, sourceFile)}" {`);
+                    writeLine();
+                    increaseIndent();
+                    emitSourceFile(sourceFile);
+                    decreaseIndent();
+                    write("}");
+                    writeLine();
+
+                    // create asynchronous output for the importDeclarations
+                    if (moduleElementDeclarationEmitInfo.length) {
+                        const oldWriter = writer;
+                        forEach(moduleElementDeclarationEmitInfo, aliasEmitInfo => {
+                            if (aliasEmitInfo.isVisible && !aliasEmitInfo.asynchronousOutput) {
+                                Debug.assert(aliasEmitInfo.node.kind === SyntaxKind.ImportDeclaration);
+                                createAndSetNewTextWriterWithSymbolWriter();
+                                Debug.assert(aliasEmitInfo.indent === 1);
+                                increaseIndent();
+                                writeImportDeclaration(<ImportDeclaration>aliasEmitInfo.node);
+                                aliasEmitInfo.asynchronousOutput = writer.getText();
+                                decreaseIndent();
+                            }
+                        });
+                        setWriter(oldWriter);
+                    }
+                    prevModuleElementDeclarationEmitInfo = prevModuleElementDeclarationEmitInfo.concat(moduleElementDeclarationEmitInfo);
+                    moduleElementDeclarationEmitInfo = [];
+                }
             });
+            moduleElementDeclarationEmitInfo = moduleElementDeclarationEmitInfo.concat(prevModuleElementDeclarationEmitInfo);
         }
 
         return {
@@ -134,14 +172,13 @@ namespace ts {
         };
 
         function hasInternalAnnotation(range: CommentRange) {
-            const text = currentSourceFile.text;
-            const comment = text.substring(range.pos, range.end);
+            const comment = currentText.substring(range.pos, range.end);
             return comment.indexOf("@internal") >= 0;
         }
 
         function stripInternal(node: Node) {
             if (node) {
-                const leadingCommentRanges = getLeadingCommentRanges(currentSourceFile.text, node.pos);
+                const leadingCommentRanges = getLeadingCommentRanges(currentText, node.pos);
                 if (forEach(leadingCommentRanges, hasInternalAnnotation)) {
                     return;
                 }
@@ -243,7 +280,7 @@ namespace ts {
                     if (errorInfo.typeName) {
                         diagnostics.push(createDiagnosticForNode(symbolAccesibilityResult.errorNode || errorInfo.errorNode,
                             errorInfo.diagnosticMessage,
-                            getSourceTextOfNodeFromSourceFile(currentSourceFile, errorInfo.typeName),
+                            getTextOfNodeFromSourceText(currentText, errorInfo.typeName),
                             symbolAccesibilityResult.errorSymbolName,
                             symbolAccesibilityResult.errorModuleName));
                     }
@@ -321,10 +358,10 @@ namespace ts {
 
         function writeJsDocComments(declaration: Node) {
             if (declaration) {
-                const jsDocComments = getJsDocComments(declaration, currentSourceFile);
-                emitNewLineBeforeLeadingComments(currentSourceFile, writer, declaration, jsDocComments);
+                const jsDocComments = getJsDocCommentsFromText(declaration, currentText);
+                emitNewLineBeforeLeadingComments(currentLineMap, writer, declaration, jsDocComments);
                 // jsDoc comments are emitted at /*leading comment1 */space/*leading comment*/space
-                emitComments(currentSourceFile, writer, jsDocComments, /*trailingSeparator*/ true, newLine, writeCommentRange);
+                emitComments(currentText, currentLineMap, writer, jsDocComments, /*trailingSeparator*/ true, newLine, writeCommentRange);
             }
         }
 
@@ -343,7 +380,7 @@ namespace ts {
                 case SyntaxKind.VoidKeyword:
                 case SyntaxKind.ThisKeyword:
                 case SyntaxKind.StringLiteral:
-                    return writeTextOfNode(currentSourceFile, type);
+                    return writeTextOfNode(currentText, type);
                 case SyntaxKind.ExpressionWithTypeArguments:
                     return emitExpressionWithTypeArguments(<ExpressionWithTypeArguments>type);
                 case SyntaxKind.TypeReference:
@@ -375,14 +412,14 @@ namespace ts {
 
             function writeEntityName(entityName: EntityName | Expression) {
                 if (entityName.kind === SyntaxKind.Identifier) {
-                    writeTextOfNode(currentSourceFile, entityName);
+                    writeTextOfNode(currentText, entityName);
                 }
                 else {
                     const left = entityName.kind === SyntaxKind.QualifiedName ? (<QualifiedName>entityName).left : (<PropertyAccessExpression>entityName).expression;
                     const right = entityName.kind === SyntaxKind.QualifiedName ? (<QualifiedName>entityName).right : (<PropertyAccessExpression>entityName).name;
                     writeEntityName(left);
                     write(".");
-                    writeTextOfNode(currentSourceFile, right);
+                    writeTextOfNode(currentText, right);
                 }
             }
 
@@ -417,7 +454,7 @@ namespace ts {
             }
 
             function emitTypePredicate(type: TypePredicateNode) {
-                writeTextOfNode(currentSourceFile, type.parameterName);
+                writeTextOfNode(currentText, type.parameterName);
                 write(" is ");
                 emitType(type.type);
             }
@@ -466,9 +503,12 @@ namespace ts {
         }
 
         function emitSourceFile(node: SourceFile) {
-            currentSourceFile = node;
+            currentText = node.text;
+            currentLineMap = getLineStarts(node);
+            currentIdentifiers = node.identifiers;
+            isCurrentFileExternalModule = isExternalModule(node);
             enclosingDeclaration = node;
-            emitDetachedComments(currentSourceFile, writer, writeCommentRange, node, newLine, true /* remove comments */);
+            emitDetachedComments(currentText, currentLineMap, writer, writeCommentRange, node, newLine, true /* remove comments */);
             emitLines(node.statements);
         }
 
@@ -478,13 +518,13 @@ namespace ts {
         // do not need to keep track of created temp names.
         function getExportDefaultTempVariableName(): string {
             const baseName = "_default";
-            if (!hasProperty(currentSourceFile.identifiers, baseName)) {
+            if (!hasProperty(currentIdentifiers, baseName)) {
                 return baseName;
             }
             let count = 0;
             while (true) {
                 const name = baseName + "_" + (++count);
-                if (!hasProperty(currentSourceFile.identifiers, name)) {
+                if (!hasProperty(currentIdentifiers, name)) {
                     return name;
                 }
             }
@@ -493,7 +533,7 @@ namespace ts {
         function emitExportAssignment(node: ExportAssignment) {
             if (node.expression.kind === SyntaxKind.Identifier) {
                 write(node.isExportEquals ? "export = " : "export default ");
-                writeTextOfNode(currentSourceFile, node.expression);
+                writeTextOfNode(currentText, node.expression);
             }
             else {
                 // Expression
@@ -537,7 +577,7 @@ namespace ts {
             }
             // Import equals declaration in internal module can become visible as part of any emit so lets make sure we add these irrespective
             else if (node.kind === SyntaxKind.ImportEqualsDeclaration ||
-                (node.parent.kind === SyntaxKind.SourceFile && isExternalModule(currentSourceFile))) {
+                (node.parent.kind === SyntaxKind.SourceFile && isCurrentFileExternalModule)) {
                 let isVisible: boolean;
                 if (asynchronousSubModuleDeclarationEmitInfo && node.parent.kind !== SyntaxKind.SourceFile) {
                     // Import declaration of another module that is visited async so lets put it in right spot
@@ -593,7 +633,7 @@ namespace ts {
 
         function emitModuleElementDeclarationFlags(node: Node) {
             // If the node is parented in the current source file we need to emit export declare or just export
-            if (node.parent === currentSourceFile) {
+            if (node.parent.kind === SyntaxKind.SourceFile) {
                 // If the node is exported
                 if (node.flags & NodeFlags.Export) {
                     write("export ");
@@ -602,7 +642,7 @@ namespace ts {
                 if (node.flags & NodeFlags.Default) {
                     write("default ");
                 }
-                else if (node.kind !== SyntaxKind.InterfaceDeclaration) {
+                else if (node.kind !== SyntaxKind.InterfaceDeclaration && !noDeclare) {
                     write("declare ");
                 }
             }
@@ -632,7 +672,7 @@ namespace ts {
                 write("export ");
             }
             write("import ");
-            writeTextOfNode(currentSourceFile, node.name);
+            writeTextOfNode(currentText, node.name);
             write(" = ");
             if (isInternalModuleImportEqualsDeclaration(node)) {
                 emitTypeWithNewGetSymbolAccessibilityDiagnostic(<EntityName>node.moduleReference, getImportEntityNameVisibilityError);
@@ -640,7 +680,7 @@ namespace ts {
             }
             else {
                 write("require(");
-                writeTextOfNode(currentSourceFile, getExternalModuleImportEqualsDeclarationExpression(node));
+                writeTextOfNode(currentText, getExternalModuleImportEqualsDeclarationExpression(node));
                 write(");");
             }
             writer.writeLine();
@@ -678,7 +718,7 @@ namespace ts {
             if (node.importClause) {
                 const currentWriterPos = writer.getTextPos();
                 if (node.importClause.name && resolver.isDeclarationVisible(node.importClause)) {
-                    writeTextOfNode(currentSourceFile, node.importClause.name);
+                    writeTextOfNode(currentText, node.importClause.name);
                 }
                 if (node.importClause.namedBindings && isVisibleNamedBinding(node.importClause.namedBindings)) {
                     if (currentWriterPos !== writer.getTextPos()) {
@@ -687,7 +727,7 @@ namespace ts {
                     }
                     if (node.importClause.namedBindings.kind === SyntaxKind.NamespaceImport) {
                         write("* as ");
-                        writeTextOfNode(currentSourceFile, (<NamespaceImport>node.importClause.namedBindings).name);
+                        writeTextOfNode(currentText, (<NamespaceImport>node.importClause.namedBindings).name);
                     }
                     else {
                         write("{ ");
@@ -697,17 +737,31 @@ namespace ts {
                 }
                 write(" from ");
             }
-            writeTextOfNode(currentSourceFile, node.moduleSpecifier);
+            emitExternalModuleSpecifier(node.moduleSpecifier);
             write(";");
             writer.writeLine();
         }
 
+        function emitExternalModuleSpecifier(moduleSpecifier: Expression) {
+            if (moduleSpecifier.kind === SyntaxKind.StringLiteral && (!root) && (compilerOptions.out || compilerOptions.outFile)) {
+                const moduleName = getExternalModuleNameFromDeclaration(host, resolver, moduleSpecifier.parent as (ImportEqualsDeclaration | ImportDeclaration | ExportDeclaration));
+                if (moduleName) {
+                    write("\"");
+                    write(moduleName);
+                    write("\"");
+                    return;
+                }
+            }
+
+            writeTextOfNode(currentText, moduleSpecifier);
+        }
+
         function emitImportOrExportSpecifier(node: ImportOrExportSpecifier) {
             if (node.propertyName) {
-                writeTextOfNode(currentSourceFile, node.propertyName);
+                writeTextOfNode(currentText, node.propertyName);
                 write(" as ");
             }
-            writeTextOfNode(currentSourceFile, node.name);
+            writeTextOfNode(currentText, node.name);
         }
 
         function emitExportSpecifier(node: ExportSpecifier) {
@@ -733,7 +787,7 @@ namespace ts {
             }
             if (node.moduleSpecifier) {
                 write(" from ");
-                writeTextOfNode(currentSourceFile, node.moduleSpecifier);
+                emitExternalModuleSpecifier(node.moduleSpecifier);
             }
             write(";");
             writer.writeLine();
@@ -748,11 +802,11 @@ namespace ts {
             else {
                 write("module ");
             }
-            writeTextOfNode(currentSourceFile, node.name);
+            writeTextOfNode(currentText, node.name);
             while (node.body.kind !== SyntaxKind.ModuleBlock) {
                 node = <ModuleDeclaration>node.body;
                 write(".");
-                writeTextOfNode(currentSourceFile, node.name);
+                writeTextOfNode(currentText, node.name);
             }
             const prevEnclosingDeclaration = enclosingDeclaration;
             enclosingDeclaration = node;
@@ -772,7 +826,7 @@ namespace ts {
             emitJsDocComments(node);
             emitModuleElementDeclarationFlags(node);
             write("type ");
-            writeTextOfNode(currentSourceFile, node.name);
+            writeTextOfNode(currentText, node.name);
             emitTypeParameters(node.typeParameters);
             write(" = ");
             emitTypeWithNewGetSymbolAccessibilityDiagnostic(node.type, getTypeAliasDeclarationVisibilityError);
@@ -796,7 +850,7 @@ namespace ts {
                 write("const ");
             }
             write("enum ");
-            writeTextOfNode(currentSourceFile, node.name);
+            writeTextOfNode(currentText, node.name);
             write(" {");
             writeLine();
             increaseIndent();
@@ -808,7 +862,7 @@ namespace ts {
 
         function emitEnumMemberDeclaration(node: EnumMember) {
             emitJsDocComments(node);
-            writeTextOfNode(currentSourceFile, node.name);
+            writeTextOfNode(currentText, node.name);
             const enumMemberValue = resolver.getConstantValue(node);
             if (enumMemberValue !== undefined) {
                 write(" = ");
@@ -827,7 +881,7 @@ namespace ts {
                 increaseIndent();
                 emitJsDocComments(node);
                 decreaseIndent();
-                writeTextOfNode(currentSourceFile, node.name);
+                writeTextOfNode(currentText, node.name);
                 // If there is constraint present and this is not a type parameter of the private method emit the constraint
                 if (node.constraint && !isPrivateMethodTypeParameter(node)) {
                     write(" extends ");
@@ -958,7 +1012,7 @@ namespace ts {
             }
 
             write("class ");
-            writeTextOfNode(currentSourceFile, node.name);
+            writeTextOfNode(currentText, node.name);
             const prevEnclosingDeclaration = enclosingDeclaration;
             enclosingDeclaration = node;
             emitTypeParameters(node.typeParameters);
@@ -982,7 +1036,7 @@ namespace ts {
             emitJsDocComments(node);
             emitModuleElementDeclarationFlags(node);
             write("interface ");
-            writeTextOfNode(currentSourceFile, node.name);
+            writeTextOfNode(currentText, node.name);
             const prevEnclosingDeclaration = enclosingDeclaration;
             enclosingDeclaration = node;
             emitTypeParameters(node.typeParameters);
@@ -1020,7 +1074,7 @@ namespace ts {
                     // If this node is a computed name, it can only be a symbol, because we've already skipped
                     // it if it's not a well known symbol. In that case, the text of the name will be exactly
                     // what we want, namely the name expression enclosed in brackets.
-                    writeTextOfNode(currentSourceFile, node.name);
+                    writeTextOfNode(currentText, node.name);
                     // If optional property emit ?
                     if ((node.kind === SyntaxKind.PropertyDeclaration || node.kind === SyntaxKind.PropertySignature) && hasQuestionToken(node)) {
                         write("?");
@@ -1107,7 +1161,7 @@ namespace ts {
                         emitBindingPattern(<BindingPattern>bindingElement.name);
                     }
                     else {
-                        writeTextOfNode(currentSourceFile, bindingElement.name);
+                        writeTextOfNode(currentText, bindingElement.name);
                         writeTypeOfDeclaration(bindingElement, /*type*/ undefined, getBindingElementTypeVisibilityError);
                     }
                 }
@@ -1157,7 +1211,7 @@ namespace ts {
                 emitJsDocComments(accessors.getAccessor);
                 emitJsDocComments(accessors.setAccessor);
                 emitClassMemberDeclarationFlags(node);
-                writeTextOfNode(currentSourceFile, node.name);
+                writeTextOfNode(currentText, node.name);
                 if (!(node.flags & NodeFlags.Private)) {
                     accessorWithTypeAnnotation = node;
                     let type = getTypeAnnotationFromAccessor(node);
@@ -1247,13 +1301,13 @@ namespace ts {
                 }
                 if (node.kind === SyntaxKind.FunctionDeclaration) {
                     write("function ");
-                    writeTextOfNode(currentSourceFile, node.name);
+                    writeTextOfNode(currentText, node.name);
                 }
                 else if (node.kind === SyntaxKind.Constructor) {
                     write("constructor");
                 }
                 else {
-                    writeTextOfNode(currentSourceFile, node.name);
+                    writeTextOfNode(currentText, node.name);
                     if (hasQuestionToken(node)) {
                         write("?");
                     }
@@ -1393,7 +1447,7 @@ namespace ts {
                 emitBindingPattern(<BindingPattern>node.name);
             }
             else {
-                writeTextOfNode(currentSourceFile, node.name);
+                writeTextOfNode(currentText, node.name);
             }
             if (resolver.isOptionalParameter(node)) {
                 write("?");
@@ -1519,7 +1573,7 @@ namespace ts {
                         // Example:
                         //      original: function foo({y: [a,b,c]}) {}
                         //      emit    : declare function foo({y: [a, b, c]}: { y: [any, any, any] }) void;
-                        writeTextOfNode(currentSourceFile, bindingElement.propertyName);
+                        writeTextOfNode(currentText, bindingElement.propertyName);
                         write(": ");
                     }
                     if (bindingElement.name) {
@@ -1542,7 +1596,7 @@ namespace ts {
                             if (bindingElement.dotDotDotToken) {
                                 write("...");
                             }
-                            writeTextOfNode(currentSourceFile, bindingElement.name);
+                            writeTextOfNode(currentText, bindingElement.name);
                         }
                     }
                 }
diff --git a/src/compiler/diagnosticMessages.json b/src/compiler/diagnosticMessages.json
index e6008ce3c1e..ad71d646b7b 100644
--- a/src/compiler/diagnosticMessages.json
+++ b/src/compiler/diagnosticMessages.json
@@ -2310,7 +2310,6 @@
         "category": "Message",
         "code": 6078
     },
-
     "Specify JSX code generation: 'preserve' or 'react'": {
         "category": "Message",
         "code": 6080
@@ -2319,7 +2318,10 @@
         "category": "Message",
         "code": 6081
     },
-
+    "Only 'amd' and 'system' modules are supported alongside --{0}.": {
+        "category": "Error",
+        "code": 6082
+    },
     "Variable '{0}' implicitly has an '{1}' type.": {
         "category": "Error",
         "code": 7005
diff --git a/src/compiler/emitter.ts b/src/compiler/emitter.ts
index 464bd51a91d..ce92150f9fd 100644
--- a/src/compiler/emitter.ts
+++ b/src/compiler/emitter.ts
@@ -7,6 +7,18 @@ namespace ts {
         return isExternalModule(sourceFile) || isDeclarationFile(sourceFile);
     }
 
+    export function getResolvedExternalModuleName(host: EmitHost, file: SourceFile): string {
+        return file.moduleName || getExternalModuleNameFromPath(host, file.fileName);
+    }
+
+    export function getExternalModuleNameFromDeclaration(host: EmitHost, resolver: EmitResolver, declaration: ImportEqualsDeclaration | ImportDeclaration | ExportDeclaration): string {
+        const file = resolver.getExternalModuleFileFromDeclaration(declaration);
+        if (!file || isDeclarationFile(file)) {
+            return undefined;
+        }
+        return getResolvedExternalModuleName(host, file);
+    }
+
     type DependencyGroup = Array<ImportDeclaration | ImportEqualsDeclaration | ExportDeclaration>;
 
     const enum Jump {
@@ -332,17 +344,21 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
         const newLine = host.getNewLine();
         const jsxDesugaring = host.getCompilerOptions().jsx !== JsxEmit.Preserve;
         const shouldEmitJsx = (s: SourceFile) => (s.languageVariant === LanguageVariant.JSX && !jsxDesugaring);
+        const outFile = compilerOptions.outFile || compilerOptions.out;
+
+        const emitJavaScript = createFileEmitter();
 
         if (targetSourceFile === undefined) {
-            forEach(host.getSourceFiles(), sourceFile => {
-                if (shouldEmitToOwnFile(sourceFile, compilerOptions)) {
-                    const jsFilePath = getOwnEmitOutputFilePath(sourceFile, host, shouldEmitJsx(sourceFile) ? ".jsx" : ".js");
-                    emitFile(jsFilePath, sourceFile);
-                }
-            });
-
-            if (compilerOptions.outFile || compilerOptions.out) {
-                emitFile(compilerOptions.outFile || compilerOptions.out);
+            if (outFile) {
+                emitFile(outFile);
+            }
+            else {
+                forEach(host.getSourceFiles(), sourceFile => {
+                    if (shouldEmitToOwnFile(sourceFile, compilerOptions)) {
+                        const jsFilePath = getOwnEmitOutputFilePath(sourceFile, host, shouldEmitJsx(sourceFile) ? ".jsx" : ".js");
+                        emitFile(jsFilePath, sourceFile);
+                    }
+                });
             }
         }
         else {
@@ -351,8 +367,8 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 const jsFilePath = getOwnEmitOutputFilePath(targetSourceFile, host, shouldEmitJsx(targetSourceFile) ? ".jsx" : ".js");
                 emitFile(jsFilePath, targetSourceFile);
             }
-            else if (!isDeclarationFile(targetSourceFile) && (compilerOptions.outFile || compilerOptions.out)) {
-                emitFile(compilerOptions.outFile || compilerOptions.out);
+            else if (!isDeclarationFile(targetSourceFile) && outFile) {
+                emitFile(outFile);
             }
         }
 
@@ -470,11 +486,18 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
         }
 
-        function emitJavaScript(jsFilePath: string, root?: SourceFile) {
-            const writer = createTextWriter(newLine);
+        function createFileEmitter(): (jsFilePath: string, root?: SourceFile) => void {
+            const writer: EmitTextWriter = createTextWriter(newLine);
             const { write, writeTextOfNode, writeLine, increaseIndent, decreaseIndent } = writer;
 
             let currentSourceFile: SourceFile;
+            let currentText: string;
+            let currentLineMap: number[];
+            let currentFileIdentifiers: Map<string>;
+            let renamedDependencies: Map<string>;
+            let isEs6Module: boolean;
+            let isCurrentFileExternalModule: boolean;
+
             // name of an exporter function if file is a System external module
             // System.register([...], function (<exporter>) {...})
             // exporting in System modules looks like:
@@ -483,17 +506,17 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             // var x;... exporter("x", x = 1)
             let exportFunctionForFile: string;
 
-            const generatedNameSet: Map<string> = {};
-            const nodeToGeneratedName: string[] = [];
+            let generatedNameSet: Map<string>;
+            let nodeToGeneratedName: string[];
             let computedPropertyNamesToGeneratedNames: string[];
 
             let convertedLoopState: ConvertedLoopState;
 
-            let extendsEmitted = false;
-            let decorateEmitted = false;
-            let paramEmitted = false;
-            let awaiterEmitted = false;
-            let tempFlags = 0;
+            let extendsEmitted: boolean;
+            let decorateEmitted: boolean;
+            let paramEmitted: boolean;
+            let awaiterEmitted: boolean;
+            let tempFlags: TempFlags;
             let tempVariables: Identifier[];
             let tempParameters: Identifier[];
             let externalImports: (ImportDeclaration | ImportEqualsDeclaration | ExportDeclaration)[];
@@ -536,10 +559,13 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             /** Sourcemap data that will get encoded */
             let sourceMapData: SourceMapData;
 
+            /** The root file passed to the emit function (if present) */
+            let root: SourceFile;
+
             /** If removeComments is true, no leading-comments needed to be emitted **/
             const emitLeadingCommentsOfPosition = compilerOptions.removeComments ? function (pos: number) { } : emitLeadingCommentsOfPositionWorker;
 
-            const moduleEmitDelegates: Map<(node: SourceFile) => void> = {
+            const moduleEmitDelegates: Map<(node: SourceFile, emitRelativePathAsModuleName?: boolean) => void> = {
                 [ModuleKind.ES6]: emitES6Module,
                 [ModuleKind.AMD]: emitAMDModule,
                 [ModuleKind.System]: emitSystemModule,
@@ -547,35 +573,86 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 [ModuleKind.CommonJS]: emitCommonJSModule,
             };
 
-            if (compilerOptions.sourceMap || compilerOptions.inlineSourceMap) {
-                initializeEmitterWithSourceMaps();
-            }
+            const bundleEmitDelegates: Map<(node: SourceFile, emitRelativePathAsModuleName?: boolean) => void> = {
+                [ModuleKind.ES6]() {},
+                [ModuleKind.AMD]: emitAMDModule,
+                [ModuleKind.System]: emitSystemModule,
+                [ModuleKind.UMD]() {},
+                [ModuleKind.CommonJS]() {},
+            };
 
-            if (root) {
-                // Do not call emit directly. It does not set the currentSourceFile.
-                emitSourceFile(root);
-            }
-            else {
-                forEach(host.getSourceFiles(), sourceFile => {
-                    if (!isExternalModuleOrDeclarationFile(sourceFile)) {
-                        emitSourceFile(sourceFile);
+            return doEmit;
+
+            function doEmit(jsFilePath: string, rootFile?: SourceFile) {
+                // reset the state
+                writer.reset();
+                currentSourceFile = undefined;
+                currentText = undefined;
+                currentLineMap = undefined;
+                exportFunctionForFile = undefined;
+                generatedNameSet = {};
+                nodeToGeneratedName = [];
+                computedPropertyNamesToGeneratedNames = undefined;
+                convertedLoopState = undefined;
+
+                extendsEmitted = false;
+                decorateEmitted = false;
+                paramEmitted = false;
+                awaiterEmitted = false;
+                tempFlags = 0;
+                tempVariables = undefined;
+                tempParameters = undefined;
+                externalImports = undefined;
+                exportSpecifiers = undefined;
+                exportEquals = undefined;
+                hasExportStars = undefined;
+                detachedCommentsInfo = undefined;
+                sourceMapData = undefined;
+                isEs6Module = false;
+                renamedDependencies = undefined;
+                isCurrentFileExternalModule = false;
+                root = rootFile;
+
+                if (compilerOptions.sourceMap || compilerOptions.inlineSourceMap) {
+                    initializeEmitterWithSourceMaps(jsFilePath, root);
+                }
+
+                if (root) {
+                    // Do not call emit directly. It does not set the currentSourceFile.
+                    emitSourceFile(root);
+                }
+                else {
+                    if (modulekind) {
+                        forEach(host.getSourceFiles(), emitEmitHelpers);
                     }
-                });
-            }
+                    forEach(host.getSourceFiles(), sourceFile => {
+                        if ((!isExternalModuleOrDeclarationFile(sourceFile)) || (modulekind && isExternalModule(sourceFile))) {
+                            emitSourceFile(sourceFile);
+                        }
+                    });
+                }
 
-            writeLine();
-            writeEmittedFiles(writer.getText(), /*writeByteOrderMark*/ compilerOptions.emitBOM);
-            return;
+                writeLine();
+                writeEmittedFiles(writer.getText(), jsFilePath, /*writeByteOrderMark*/ compilerOptions.emitBOM);
+            }
 
             function emitSourceFile(sourceFile: SourceFile): void {
                 currentSourceFile = sourceFile;
+
+                currentText = sourceFile.text;
+                currentLineMap = getLineStarts(sourceFile);
                 exportFunctionForFile = undefined;
+                isEs6Module = sourceFile.symbol && sourceFile.symbol.exports && !!sourceFile.symbol.exports["___esModule"];
+                renamedDependencies = sourceFile.renamedDependencies;
+                currentFileIdentifiers = sourceFile.identifiers;
+                isCurrentFileExternalModule = isExternalModule(sourceFile);
+
                 emit(sourceFile);
             }
 
             function isUniqueName(name: string): boolean {
                 return !resolver.hasGlobalName(name) &&
-                    !hasProperty(currentSourceFile.identifiers, name) &&
+                    !hasProperty(currentFileIdentifiers, name) &&
                     !hasProperty(generatedNameSet, name);
             }
 
@@ -667,7 +744,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 return nodeToGeneratedName[id] || (nodeToGeneratedName[id] = unescapeIdentifier(generateNameForNode(node)));
             }
 
-            function initializeEmitterWithSourceMaps() {
+            function initializeEmitterWithSourceMaps(jsFilePath: string, root?: SourceFile) {
                 let sourceMapDir: string; // The directory in which sourcemap will be
 
                 // Current source map file and its index in the sources list
@@ -771,7 +848,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 }
 
                 function recordSourceMapSpan(pos: number) {
-                    const sourceLinePos = getLineAndCharacterOfPosition(currentSourceFile, pos);
+                    const sourceLinePos = computeLineAndCharacterOfPosition(currentLineMap, pos);
 
                     // Convert the location to be one-based.
                     sourceLinePos.line++;
@@ -810,7 +887,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
 
                 function recordEmitNodeStartSpan(node: Node) {
                     // Get the token pos after skipping to the token (ignoring the leading trivia)
-                    recordSourceMapSpan(skipTrivia(currentSourceFile.text, node.pos));
+                    recordSourceMapSpan(skipTrivia(currentText, node.pos));
                 }
 
                 function recordEmitNodeEndSpan(node: Node) {
@@ -818,7 +895,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 }
 
                 function writeTextWithSpanRecord(tokenKind: SyntaxKind, startPos: number, emitFn?: () => void) {
-                    const tokenStartPos = ts.skipTrivia(currentSourceFile.text, startPos);
+                    const tokenStartPos = ts.skipTrivia(currentText, startPos);
                     recordSourceMapSpan(tokenStartPos);
                     const tokenEndPos = emitTokenText(tokenKind, tokenStartPos, emitFn);
                     recordSourceMapSpan(tokenEndPos);
@@ -912,9 +989,9 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     sourceMapNameIndices.pop();
                 };
 
-                function writeCommentRangeWithMap(curentSourceFile: SourceFile, writer: EmitTextWriter, comment: CommentRange, newLine: string) {
+                function writeCommentRangeWithMap(currentText: string, currentLineMap: number[], writer: EmitTextWriter, comment: CommentRange, newLine: string) {
                     recordSourceMapSpan(comment.pos);
-                    writeCommentRange(currentSourceFile, writer, comment, newLine);
+                    writeCommentRange(currentText, currentLineMap, writer, comment, newLine);
                     recordSourceMapSpan(comment.end);
                 }
 
@@ -950,7 +1027,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     }
                 }
 
-                function writeJavaScriptAndSourceMapFile(emitOutput: string, writeByteOrderMark: boolean) {
+                function writeJavaScriptAndSourceMapFile(emitOutput: string, jsFilePath: string, writeByteOrderMark: boolean) {
                     encodeLastRecordedSourceMapSpan();
 
                     const sourceMapText = serializeSourceMapContents(
@@ -977,7 +1054,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     }
 
                     // Write sourcemap url to the js file and write the js file
-                    writeJavaScriptFile(emitOutput + sourceMapUrl, writeByteOrderMark);
+                    writeJavaScriptFile(emitOutput + sourceMapUrl, jsFilePath, writeByteOrderMark);
                 }
 
                 // Initialize source map data
@@ -1059,7 +1136,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 writeComment = writeCommentRangeWithMap;
             }
 
-            function writeJavaScriptFile(emitOutput: string, writeByteOrderMark: boolean) {
+            function writeJavaScriptFile(emitOutput: string, jsFilePath: string, writeByteOrderMark: boolean) {
                 writeFile(host, diagnostics, jsFilePath, emitOutput, writeByteOrderMark);
             }
 
@@ -1269,7 +1346,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 // If we don't need to downlevel and we can reach the original source text using
                 // the node's parent reference, then simply get the text as it was originally written.
                 if (node.parent) {
-                    return getSourceTextOfNodeFromSourceFile(currentSourceFile, node);
+                    return getTextOfNodeFromSourceText(currentText, node);
                 }
 
                 // If we can't reach the original source text, use the canonical form if it's a number,
@@ -1300,7 +1377,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 // Find original source text, since we need to emit the raw strings of the tagged template.
                 // The raw strings contain the (escaped) strings of what the user wrote.
                 // Examples: `\n` is converted to "\\n", a template string with a newline to "\n".
-                let text = getSourceTextOfNodeFromSourceFile(currentSourceFile, node);
+                let text = getTextOfNodeFromSourceText(currentText, node);
 
                 // text contains the original source, it will also contain quotes ("`"), dolar signs and braces ("${" and "}"),
                 // thus we need to remove those characters.
@@ -1772,7 +1849,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                         write((<LiteralExpression>node).text);
                     }
                     else {
-                        writeTextOfNode(currentSourceFile, node);
+                        writeTextOfNode(currentText, node);
                     }
 
                     write("\"");
@@ -1876,7 +1953,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                                 // Identifier references named import
                                 write(getGeneratedNameForNode(<ImportDeclaration>declaration.parent.parent.parent));
                                 const name =  (<ImportSpecifier>declaration).propertyName || (<ImportSpecifier>declaration).name;
-                                const identifier = getSourceTextOfNodeFromSourceFile(currentSourceFile, name);
+                                const identifier = getTextOfNodeFromSourceText(currentText, name);
                                 if (languageVersion === ScriptTarget.ES3 && identifier === "default") {
                                     write(`["default"]`);
                                 }
@@ -1902,7 +1979,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     write(node.text);
                 }
                 else {
-                    writeTextOfNode(currentSourceFile, node);
+                    writeTextOfNode(currentText, node);
                 }
             }
 
@@ -1943,7 +2020,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     write(node.text);
                 }
                 else {
-                    writeTextOfNode(currentSourceFile, node);
+                    writeTextOfNode(currentText, node);
                 }
             }
 
@@ -2403,7 +2480,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             function emitShorthandPropertyAssignment(node: ShorthandPropertyAssignment) {
                 // The name property of a short-hand property assignment is considered an expression position, so here
                 // we manually emit the identifier to avoid rewriting.
-                writeTextOfNode(currentSourceFile, node.name);
+                writeTextOfNode(currentText, node.name);
                 // If emitting pre-ES6 code, or if the name requires rewriting when resolved as an expression identifier,
                 // we emit a normal property assignment. For example:
                 //   module m {
@@ -2480,11 +2557,11 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
 
                 // 1 .toString is a valid property access, emit a space after the literal
                 // Also emit a space if expression is a integer const enum value - it will appear in generated code as numeric literal
-                let shouldEmitSpace: boolean;
+                let shouldEmitSpace = false;
                 if (!indentedBeforeDot) {
                     if (node.expression.kind === SyntaxKind.NumericLiteral) {
                         // check if numeric literal was originally written with a dot
-                        const text = getSourceTextOfNodeFromSourceFile(currentSourceFile, node.expression);
+                        const text = getTextOfNodeFromSourceText(currentText, node.expression);
                         shouldEmitSpace = text.indexOf(tokenToString(SyntaxKind.DotToken)) < 0;
                     }
                     else {
@@ -3815,18 +3892,18 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
 
             function nodeStartPositionsAreOnSameLine(node1: Node, node2: Node) {
-                return getLineOfLocalPosition(currentSourceFile, skipTrivia(currentSourceFile.text, node1.pos)) ===
-                    getLineOfLocalPosition(currentSourceFile, skipTrivia(currentSourceFile.text, node2.pos));
+                return getLineOfLocalPositionFromLineMap(currentLineMap, skipTrivia(currentText, node1.pos)) ===
+                    getLineOfLocalPositionFromLineMap(currentLineMap, skipTrivia(currentText, node2.pos));
             }
 
             function nodeEndPositionsAreOnSameLine(node1: Node, node2: Node) {
-                return getLineOfLocalPosition(currentSourceFile, node1.end) ===
-                    getLineOfLocalPosition(currentSourceFile, node2.end);
+                return getLineOfLocalPositionFromLineMap(currentLineMap, node1.end) ===
+                    getLineOfLocalPositionFromLineMap(currentLineMap, node2.end);
             }
 
             function nodeEndIsOnSameLineAsNodeStart(node1: Node, node2: Node) {
-                return getLineOfLocalPosition(currentSourceFile, node1.end) ===
-                    getLineOfLocalPosition(currentSourceFile, skipTrivia(currentSourceFile.text, node2.pos));
+                return getLineOfLocalPositionFromLineMap(currentLineMap, node1.end) ===
+                    getLineOfLocalPositionFromLineMap(currentLineMap, skipTrivia(currentText, node2.pos));
             }
 
             function emitCaseOrDefaultClause(node: CaseOrDefaultClause) {
@@ -3948,7 +4025,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     Debug.assert(!!(node.flags & NodeFlags.Default) || node.kind === SyntaxKind.ExportAssignment);
                     // only allow export default at a source file level
                     if (modulekind === ModuleKind.CommonJS || modulekind === ModuleKind.AMD || modulekind === ModuleKind.UMD) {
-                        if (!currentSourceFile.symbol.exports["___esModule"]) {
+                        if (!isEs6Module) {
                             if (languageVersion === ScriptTarget.ES5) {
                                 // default value of configurable, enumerable, writable are `false`.
                                 write("Object.defineProperty(exports, \"__esModule\", { value: true });");
@@ -6304,8 +6381,8 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
              * Here we check if alternative name was provided for a given moduleName and return it if possible.
              */
             function tryRenameExternalModule(moduleName: LiteralExpression): string {
-                if (currentSourceFile.renamedDependencies && hasProperty(currentSourceFile.renamedDependencies, moduleName.text)) {
-                    return `"${currentSourceFile.renamedDependencies[moduleName.text]}"`;
+                if (renamedDependencies && hasProperty(renamedDependencies, moduleName.text)) {
+                    return `"${renamedDependencies[moduleName.text]}"`;
                 }
                 return undefined;
             }
@@ -6467,7 +6544,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 // - current file is not external module
                 // - import declaration is top level and target is value imported by entity name
                 if (resolver.isReferencedAliasDeclaration(node) ||
-                    (!isExternalModule(currentSourceFile) && resolver.isTopLevelValueImportEqualsWithEntityName(node))) {
+                    (!isCurrentFileExternalModule && resolver.isTopLevelValueImportEqualsWithEntityName(node))) {
                     emitLeadingComments(node);
                     emitStart(node);
 
@@ -6708,7 +6785,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             function getLocalNameForExternalImport(node: ImportDeclaration | ExportDeclaration | ImportEqualsDeclaration): string {
                 const namespaceDeclaration = getNamespaceDeclarationNode(node);
                 if (namespaceDeclaration && !isDefaultImport(node)) {
-                    return getSourceTextOfNodeFromSourceFile(currentSourceFile, namespaceDeclaration.name);
+                    return getTextOfNodeFromSourceText(currentText, namespaceDeclaration.name);
                 }
                 if (node.kind === SyntaxKind.ImportDeclaration && (<ImportDeclaration>node).importClause) {
                     return getGeneratedNameForNode(node);
@@ -7064,7 +7141,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
 
             function isCurrentFileSystemExternalModule() {
-                return modulekind === ModuleKind.System && isExternalModule(currentSourceFile);
+                return modulekind === ModuleKind.System && isCurrentFileExternalModule;
             }
 
             function emitSystemModuleBody(node: SourceFile, dependencyGroups: DependencyGroup[], startIndex: number): void {
@@ -7249,7 +7326,14 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 write("}"); // execute
             }
 
-            function emitSystemModule(node: SourceFile): void {
+            function writeModuleName(node: SourceFile, emitRelativePathAsModuleName?: boolean): void {
+                let moduleName = node.moduleName;
+                if (moduleName || (emitRelativePathAsModuleName && (moduleName = getResolvedExternalModuleName(host, node)))) {
+                    write(`"${moduleName}", `);
+                }
+            }
+
+            function emitSystemModule(node: SourceFile,  emitRelativePathAsModuleName?: boolean): void {
                 collectExternalModuleInfo(node);
                 // System modules has the following shape
                 // System.register(['dep-1', ... 'dep-n'], function(exports) {/* module body function */})
@@ -7264,16 +7348,14 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 exportFunctionForFile = makeUniqueName("exports");
                 writeLine();
                 write("System.register(");
-                if (node.moduleName) {
-                    write(`"${node.moduleName}", `);
-                }
+                writeModuleName(node, emitRelativePathAsModuleName);
                 write("[");
 
                 const groupIndices: Map<number> = {};
                 const dependencyGroups: DependencyGroup[] = [];
 
                 for (let i = 0; i < externalImports.length; ++i) {
-                    const text = getExternalModuleNameText(externalImports[i]);
+                    let text = getExternalModuleNameText(externalImports[i]);
                     if (hasProperty(groupIndices, text)) {
                         // deduplicate/group entries in dependency list by the dependency name
                         const groupIndex = groupIndices[text];
@@ -7289,6 +7371,12 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                         write(", ");
                     }
 
+                    if (emitRelativePathAsModuleName) {
+                        const name = getExternalModuleNameFromDeclaration(host, resolver, externalImports[i]);
+                        if (name) {
+                            text = `"${name}"`;
+                        }
+                    }
                     write(text);
                 }
                 write(`], function(${exportFunctionForFile}) {`);
@@ -7309,7 +7397,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 importAliasNames: string[];
             }
 
-            function getAMDDependencyNames(node: SourceFile, includeNonAmdDependencies: boolean): AMDDependencyNames {
+            function getAMDDependencyNames(node: SourceFile, includeNonAmdDependencies: boolean, emitRelativePathAsModuleName?: boolean): AMDDependencyNames {
                 // names of modules with corresponding parameter in the factory function
                 const aliasedModuleNames: string[] = [];
                 // names of modules with no corresponding parameters in factory function
@@ -7331,7 +7419,14 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
 
                 for (const importNode of externalImports) {
                     // Find the name of the external module
-                    const externalModuleName = getExternalModuleNameText(importNode);
+                    let externalModuleName = getExternalModuleNameText(importNode);
+
+                    if (emitRelativePathAsModuleName) {
+                        const name = getExternalModuleNameFromDeclaration(host, resolver, importNode);
+                        if (name) {
+                            externalModuleName = `"${name}"`;
+                        }
+                    }
 
                     // Find the name of the module alias, if there is one
                     const importAliasName = getLocalNameForExternalImport(importNode);
@@ -7347,7 +7442,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 return { aliasedModuleNames, unaliasedModuleNames, importAliasNames };
             }
 
-            function emitAMDDependencies(node: SourceFile, includeNonAmdDependencies: boolean) {
+            function emitAMDDependencies(node: SourceFile, includeNonAmdDependencies: boolean, emitRelativePathAsModuleName?: boolean) {
                 // An AMD define function has the following shape:
                 //     define(id?, dependencies?, factory);
                 //
@@ -7360,7 +7455,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 // `import "module"` or `<amd-dependency path= "a.css" />`
                 // we need to add modules without alias names to the end of the dependencies list
 
-                const dependencyNames = getAMDDependencyNames(node, includeNonAmdDependencies);
+                const dependencyNames = getAMDDependencyNames(node, includeNonAmdDependencies, emitRelativePathAsModuleName);
                 emitAMDDependencyList(dependencyNames);
                 write(", ");
                 emitAMDFactoryHeader(dependencyNames);
@@ -7388,16 +7483,14 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 write(") {");
             }
 
-            function emitAMDModule(node: SourceFile) {
+            function emitAMDModule(node: SourceFile, emitRelativePathAsModuleName?: boolean) {
                 emitEmitHelpers(node);
                 collectExternalModuleInfo(node);
 
                 writeLine();
                 write("define(");
-                if (node.moduleName) {
-                    write("\"" + node.moduleName + "\", ");
-                }
-                emitAMDDependencies(node, /*includeNonAmdDependencies*/ true);
+                writeModuleName(node, emitRelativePathAsModuleName);
+                emitAMDDependencies(node, /*includeNonAmdDependencies*/ true, emitRelativePathAsModuleName);
                 increaseIndent();
                 const startIndex = emitDirectivePrologues(node.statements, /*startWithNewLine*/ true);
                 emitExportStarHelper();
@@ -7646,8 +7739,13 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 emitDetachedCommentsAndUpdateCommentsInfo(node);
 
                 if (isExternalModule(node) || compilerOptions.isolatedModules) {
-                    const emitModule = moduleEmitDelegates[modulekind] || moduleEmitDelegates[ModuleKind.CommonJS];
-                    emitModule(node);
+                    if (root || (!isExternalModule(node) && compilerOptions.isolatedModules)) {
+                        const emitModule = moduleEmitDelegates[modulekind] || moduleEmitDelegates[ModuleKind.CommonJS];
+                        emitModule(node);
+                    }
+                    else {
+                        bundleEmitDelegates[modulekind](node, /*emitRelativePathAsModuleName*/true);
+                    }
                 }
                 else {
                     // emit prologue directives prior to __extends
@@ -7927,7 +8025,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
 
             function getLeadingCommentsWithoutDetachedComments() {
                 // get the leading comments from detachedPos
-                const leadingComments = getLeadingCommentRanges(currentSourceFile.text,
+                const leadingComments = getLeadingCommentRanges(currentText,
                     lastOrUndefined(detachedCommentsInfo).detachedCommentEndPos);
                 if (detachedCommentsInfo.length - 1) {
                     detachedCommentsInfo.pop();
@@ -7947,10 +8045,10 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             function isTripleSlashComment(comment: CommentRange) {
                 // Verify this is /// comment, but do the regexp match only when we first can find /// in the comment text
                 // so that we don't end up computing comment string and doing match for all // comments
-                if (currentSourceFile.text.charCodeAt(comment.pos + 1) === CharacterCodes.slash &&
+                if (currentText.charCodeAt(comment.pos + 1) === CharacterCodes.slash &&
                     comment.pos + 2 < comment.end &&
-                    currentSourceFile.text.charCodeAt(comment.pos + 2) === CharacterCodes.slash) {
-                    const textSubStr = currentSourceFile.text.substring(comment.pos, comment.end);
+                    currentText.charCodeAt(comment.pos + 2) === CharacterCodes.slash) {
+                    const textSubStr = currentText.substring(comment.pos, comment.end);
                     return textSubStr.match(fullTripleSlashReferencePathRegEx) ||
                         textSubStr.match(fullTripleSlashAMDReferencePathRegEx) ?
                         true : false;
@@ -7968,7 +8066,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                         }
                         else {
                             // get the leading comments from the node
-                            return getLeadingCommentRangesOfNode(node, currentSourceFile);
+                            return getLeadingCommentRangesOfNodeFromText(node, currentText);
                         }
                     }
                 }
@@ -7978,7 +8076,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 // Emit the trailing comments only if the parent's pos doesn't match because parent should take care of emitting these comments
                 if (node.parent) {
                     if (node.parent.kind === SyntaxKind.SourceFile || node.end !== node.parent.end) {
-                        return getTrailingCommentRanges(currentSourceFile.text, node.end);
+                        return getTrailingCommentRanges(currentText, node.end);
                     }
                 }
             }
@@ -8017,10 +8115,10 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     }
                 }
 
-                emitNewLineBeforeLeadingComments(currentSourceFile, writer, node, leadingComments);
+                emitNewLineBeforeLeadingComments(currentLineMap, writer, node, leadingComments);
 
                 // Leading comments are emitted at /*leading comment1 */space/*leading comment*/space
-                emitComments(currentSourceFile, writer, leadingComments, /*trailingSeparator:*/ true, newLine, writeComment);
+                emitComments(currentText, currentLineMap, writer, leadingComments, /*trailingSeparator:*/ true, newLine, writeComment);
             }
 
             function emitTrailingComments(node: Node) {
@@ -8032,7 +8130,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 const trailingComments = getTrailingCommentsToEmit(node);
 
                 // trailing comments are emitted at space/*trailing comment1 */space/*trailing comment*/
-                emitComments(currentSourceFile, writer, trailingComments, /*trailingSeparator*/ false, newLine, writeComment);
+                emitComments(currentText, currentLineMap, writer, trailingComments, /*trailingSeparator*/ false, newLine, writeComment);
             }
 
             /**
@@ -8045,10 +8143,10 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     return;
                 }
 
-                const trailingComments = getTrailingCommentRanges(currentSourceFile.text, pos);
+                const trailingComments = getTrailingCommentRanges(currentText, pos);
 
                 // trailing comments are emitted at space/*trailing comment1 */space/*trailing comment*/
-                emitComments(currentSourceFile, writer, trailingComments, /*trailingSeparator*/ true, newLine, writeComment);
+                emitComments(currentText, currentLineMap, writer, trailingComments, /*trailingSeparator*/ true, newLine, writeComment);
             }
 
             function emitLeadingCommentsOfPositionWorker(pos: number) {
@@ -8063,17 +8161,17 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 }
                 else {
                     // get the leading comments from the node
-                    leadingComments = getLeadingCommentRanges(currentSourceFile.text, pos);
+                    leadingComments = getLeadingCommentRanges(currentText, pos);
                 }
 
-                emitNewLineBeforeLeadingComments(currentSourceFile, writer, { pos: pos, end: pos }, leadingComments);
+                emitNewLineBeforeLeadingComments(currentLineMap, writer, { pos: pos, end: pos }, leadingComments);
 
                 // Leading comments are emitted at /*leading comment1 */space/*leading comment*/space
-                emitComments(currentSourceFile, writer, leadingComments, /*trailingSeparator*/ true, newLine, writeComment);
+                emitComments(currentText, currentLineMap, writer, leadingComments, /*trailingSeparator*/ true, newLine, writeComment);
             }
 
             function emitDetachedCommentsAndUpdateCommentsInfo(node: TextRange) {
-                const currentDetachedCommentInfo = emitDetachedComments(currentSourceFile, writer, writeComment, node, newLine, compilerOptions.removeComments);
+                const currentDetachedCommentInfo = emitDetachedComments(currentText, currentLineMap, writer, writeComment, node, newLine, compilerOptions.removeComments);
 
                 if (currentDetachedCommentInfo) {
                     if (detachedCommentsInfo) {
@@ -8086,7 +8184,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
 
             function emitShebang() {
-                const shebang = getShebang(currentSourceFile.text);
+                const shebang = getShebang(currentText);
                 if (shebang) {
                     write(shebang);
                 }
diff --git a/src/compiler/parser.ts b/src/compiler/parser.ts
index 5c57bfb5501..ea7fec65b5b 100644
--- a/src/compiler/parser.ts
+++ b/src/compiler/parser.ts
@@ -2,15 +2,18 @@
 /// <reference path="scanner.ts"/>
 
 namespace ts {
-    const nodeConstructors = new Array<new (pos: number, end: number) => Node>(SyntaxKind.Count);
     /* @internal */ export let parseTime = 0;
 
-    export function getNodeConstructor(kind: SyntaxKind): new (pos?: number, end?: number) => Node {
-        return nodeConstructors[kind] || (nodeConstructors[kind] = objectAllocator.getNodeConstructor(kind));
-    }
+    let NodeConstructor: new (kind: SyntaxKind, pos: number, end: number) => Node;
+    let SourceFileConstructor: new (kind: SyntaxKind, pos: number, end: number) => Node;
 
     export function createNode(kind: SyntaxKind, pos?: number, end?: number): Node {
-        return new (getNodeConstructor(kind))(pos, end);
+        if (kind === SyntaxKind.SourceFile) {
+            return new (SourceFileConstructor || (SourceFileConstructor = objectAllocator.getSourceFileConstructor()))(kind, pos, end);
+        }
+        else {
+            return new (NodeConstructor || (NodeConstructor = objectAllocator.getNodeConstructor()))(kind, pos, end);
+        }
     }
 
     function visitNode<T>(cbNode: (node: Node) => T, node: Node): T {
@@ -437,6 +440,10 @@ namespace ts {
         const scanner = createScanner(ScriptTarget.Latest, /*skipTrivia*/ true);
         const disallowInAndDecoratorContext = ParserContextFlags.DisallowIn | ParserContextFlags.Decorator;
 
+        // capture constructors in 'initializeState' to avoid null checks
+        let NodeConstructor: new (kind: SyntaxKind, pos: number, end: number) => Node;
+        let SourceFileConstructor: new (kind: SyntaxKind, pos: number, end: number) => Node;
+
         let sourceFile: SourceFile;
         let parseDiagnostics: Diagnostic[];
         let syntaxCursor: IncrementalParser.SyntaxCursor;
@@ -538,6 +545,9 @@ namespace ts {
         }
 
         function initializeState(fileName: string, _sourceText: string, languageVersion: ScriptTarget, isJavaScriptFile: boolean, _syntaxCursor: IncrementalParser.SyntaxCursor) {
+            NodeConstructor = objectAllocator.getNodeConstructor();
+            SourceFileConstructor = objectAllocator.getSourceFileConstructor();
+
             sourceText = _sourceText;
             syntaxCursor = _syntaxCursor;
 
@@ -662,10 +672,11 @@ namespace ts {
         }
 
         function createSourceFile(fileName: string, languageVersion: ScriptTarget): SourceFile {
-            const sourceFile = <SourceFile>createNode(SyntaxKind.SourceFile, /*pos*/ 0);
+            // code from createNode is inlined here so createNode won't have to deal with special case of creating source files
+            // this is quite rare comparing to other nodes and createNode should be as fast as possible
+            const sourceFile = <SourceFile>new SourceFileConstructor(SyntaxKind.SourceFile, /*pos*/ 0, /* end */ sourceText.length);
+            nodeCount++;
 
-            sourceFile.pos = 0;
-            sourceFile.end = sourceText.length;
             sourceFile.text = sourceText;
             sourceFile.bindDiagnostics = [];
             sourceFile.languageVersion = languageVersion;
@@ -676,7 +687,7 @@ namespace ts {
             return sourceFile;
         }
 
-        function setContextFlag(val: Boolean, flag: ParserContextFlags) {
+        function setContextFlag(val: boolean, flag: ParserContextFlags) {
             if (val) {
                 contextFlags |= flag;
             }
@@ -996,12 +1007,14 @@ namespace ts {
             }
         }
 
+        // note: this function creates only node
         function createNode(kind: SyntaxKind, pos?: number): Node {
             nodeCount++;
             if (!(pos >= 0)) {
                 pos = scanner.getStartPos();
             }
-            return new (nodeConstructors[kind] || (nodeConstructors[kind] = objectAllocator.getNodeConstructor(kind)))(pos, pos);
+
+            return new NodeConstructor(kind, pos, pos);
         }
 
         function finishNode<T extends Node>(node: T, end?: number): T {
diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index 496dcbd0d7c..a72e41521e6 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -939,6 +939,10 @@ namespace ts {
                 }
             });
 
+            if (!commonPathComponents) { // Can happen when all input files are .d.ts files
+                return currentDirectory;
+            }
+
             return getNormalizedPathFromPathComponents(commonPathComponents);
         }
 
@@ -1040,12 +1044,16 @@ namespace ts {
                 programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_compile_modules_into_es2015_when_targeting_ES5_or_lower));
             }
 
+            // Cannot specify module gen that isn't amd or system with --out
+            if (outFile && options.module && !(options.module === ModuleKind.AMD || options.module === ModuleKind.System)) {
+                programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Only_amd_and_system_modules_are_supported_alongside_0, options.out ? "out" : "outFile"));
+            }
+
             // there has to be common source directory if user specified --outdir || --sourceRoot
             // if user specified --mapRoot, there needs to be common source directory if there would be multiple files being emitted
             if (options.outDir || // there is --outDir specified
                 options.sourceRoot || // there is --sourceRoot specified
-                (options.mapRoot &&  // there is --mapRoot specified and there would be multiple js files generated
-                    (!outFile || firstExternalModuleSourceFile !== undefined))) {
+                options.mapRoot) { // there is --mapRoot specified
 
                 if (options.rootDir && checkSourceFilesBelongToPath(files, options.rootDir)) {
                     // If a rootDir is specified and is valid use it as the commonSourceDirectory
diff --git a/src/compiler/scanner.ts b/src/compiler/scanner.ts
index 4e11e0d6b99..9703ef8517b 100644
--- a/src/compiler/scanner.ts
+++ b/src/compiler/scanner.ts
@@ -580,7 +580,7 @@ namespace ts {
     function getCommentRanges(text: string, pos: number, trailing: boolean): CommentRange[] {
         let result: CommentRange[];
         let collecting = trailing || pos === 0;
-        while (true) {
+        while (pos < text.length) {
             const ch = text.charCodeAt(pos);
             switch (ch) {
                 case CharacterCodes.carriageReturn:
@@ -650,6 +650,8 @@ namespace ts {
             }
             return result;
         }
+
+        return result;
     }
 
     export function getLeadingCommentRanges(text: string, pos: number): CommentRange[] {
@@ -741,7 +743,7 @@ namespace ts {
             }
         }
 
-        function scanNumber(): number {
+        function scanNumber(): string {
             const start = pos;
             while (isDigit(text.charCodeAt(pos))) pos++;
             if (text.charCodeAt(pos) === CharacterCodes.dot) {
@@ -761,7 +763,7 @@ namespace ts {
                     error(Diagnostics.Digit_expected);
                 }
             }
-            return +(text.substring(start, end));
+            return "" + +(text.substring(start, end));
         }
 
         function scanOctalDigits(): number {
@@ -1229,7 +1231,7 @@ namespace ts {
                         return pos++, token = SyntaxKind.MinusToken;
                     case CharacterCodes.dot:
                         if (isDigit(text.charCodeAt(pos + 1))) {
-                            tokenValue = "" + scanNumber();
+                            tokenValue = scanNumber();
                             return token = SyntaxKind.NumericLiteral;
                         }
                         if (text.charCodeAt(pos + 1) === CharacterCodes.dot && text.charCodeAt(pos + 2) === CharacterCodes.dot) {
@@ -1343,7 +1345,7 @@ namespace ts {
                     case CharacterCodes._7:
                     case CharacterCodes._8:
                     case CharacterCodes._9:
-                        tokenValue = "" + scanNumber();
+                        tokenValue = scanNumber();
                         return token = SyntaxKind.NumericLiteral;
                     case CharacterCodes.colon:
                         return pos++, token = SyntaxKind.ColonToken;
diff --git a/src/compiler/types.ts b/src/compiler/types.ts
index e7791bb579e..f722783976a 100644
--- a/src/compiler/types.ts
+++ b/src/compiler/types.ts
@@ -1625,6 +1625,7 @@ namespace ts {
         getTypeReferenceSerializationKind(typeName: EntityName): TypeReferenceSerializationKind;
         isOptionalParameter(node: ParameterDeclaration): boolean;
         isArgumentsLocalBinding(node: Identifier): boolean;
+        getExternalModuleFileFromDeclaration(declaration: ImportEqualsDeclaration | ImportDeclaration | ExportDeclaration): SourceFile;
     }
 
     export const enum SymbolFlags {
@@ -1959,6 +1960,8 @@ namespace ts {
         target?: TypeParameter;  // Instantiation target
         /* @internal */
         mapper?: TypeMapper;     // Instantiation mapper
+        /* @internal */
+        resolvedApparentType: Type;
     }
 
     export const enum SignatureKind {
diff --git a/src/compiler/utilities.ts b/src/compiler/utilities.ts
index a1f649f3cf8..7fdab45c2ed 100644
--- a/src/compiler/utilities.ts
+++ b/src/compiler/utilities.ts
@@ -424,18 +424,26 @@ namespace ts {
         return getLeadingCommentRanges(sourceFileOfNode.text, node.pos);
     }
 
+    export function getLeadingCommentRangesOfNodeFromText(node: Node, text: string) {
+        return getLeadingCommentRanges(text, node.pos);
+    }
+
     export function getJsDocComments(node: Node, sourceFileOfNode: SourceFile) {
+        return getJsDocCommentsFromText(node, sourceFileOfNode.text);
+    }
+
+    export function getJsDocCommentsFromText(node: Node, text: string) {
         const commentRanges = (node.kind === SyntaxKind.Parameter || node.kind === SyntaxKind.TypeParameter) ?
-            concatenate(getTrailingCommentRanges(sourceFileOfNode.text, node.pos),
-                getLeadingCommentRanges(sourceFileOfNode.text, node.pos)) :
-            getLeadingCommentRangesOfNode(node, sourceFileOfNode);
+            concatenate(getTrailingCommentRanges(text, node.pos),
+                getLeadingCommentRanges(text, node.pos)) :
+            getLeadingCommentRangesOfNodeFromText(node, text);
         return filter(commentRanges, isJsDocComment);
 
         function isJsDocComment(comment: CommentRange) {
             // True if the comment starts with '/**' but not if it is '/**/'
-            return sourceFileOfNode.text.charCodeAt(comment.pos + 1) === CharacterCodes.asterisk &&
-                sourceFileOfNode.text.charCodeAt(comment.pos + 2) === CharacterCodes.asterisk &&
-                sourceFileOfNode.text.charCodeAt(comment.pos + 3) !== CharacterCodes.slash;
+            return text.charCodeAt(comment.pos + 1) === CharacterCodes.asterisk &&
+                text.charCodeAt(comment.pos + 2) === CharacterCodes.asterisk &&
+                text.charCodeAt(comment.pos + 3) !== CharacterCodes.slash;
         }
     }
 
@@ -1437,8 +1445,8 @@ namespace ts {
     export function getFileReferenceFromReferencePath(comment: string, commentRange: CommentRange): ReferencePathMatchResult {
         const simpleReferenceRegEx = /^\/\/\/\s*<reference\s+/gim;
         const isNoDefaultLibRegEx = /^(\/\/\/\s*<reference\s+no-default-lib\s*=\s*)('|")(.+?)\2\s*\/>/gim;
-        if (simpleReferenceRegEx.exec(comment)) {
-            if (isNoDefaultLibRegEx.exec(comment)) {
+        if (simpleReferenceRegEx.test(comment)) {
+            if (isNoDefaultLibRegEx.test(comment)) {
                 return {
                     isNoDefaultLib: true
                 };
@@ -1706,6 +1714,7 @@ namespace ts {
         "\u0085": "\\u0085"  // nextLine
     };
 
+
     /**
      * Based heavily on the abstract 'Quote'/'QuoteJSONString' operation from ECMA-262 (24.3.2.2),
      * but augmented for a few select characters (e.g. lineSeparator, paragraphSeparator, nextLine)
@@ -1743,7 +1752,7 @@ namespace ts {
 
     export interface EmitTextWriter {
         write(s: string): void;
-        writeTextOfNode(sourceFile: SourceFile, node: Node): void;
+        writeTextOfNode(text: string, node: Node): void;
         writeLine(): void;
         increaseIndent(): void;
         decreaseIndent(): void;
@@ -1754,6 +1763,7 @@ namespace ts {
         getLine(): number;
         getColumn(): number;
         getIndent(): number;
+        reset(): void;
     }
 
     const indentStrings: string[] = ["", "    "];
@@ -1769,11 +1779,11 @@ namespace ts {
     }
 
     export function createTextWriter(newLine: String): EmitTextWriter {
-        let output = "";
-        let indent = 0;
-        let lineStart = true;
-        let lineCount = 0;
-        let linePos = 0;
+        let output: string;
+        let indent: number;
+        let lineStart: boolean;
+        let lineCount: number;
+        let linePos: number;
 
         function write(s: string) {
             if (s && s.length) {
@@ -1785,6 +1795,14 @@ namespace ts {
             }
         }
 
+        function reset(): void {
+            output = "";
+            indent = 0;
+            lineStart = true;
+            lineCount = 0;
+            linePos = 0;
+        }
+
         function rawWrite(s: string) {
             if (s !== undefined) {
                 if (lineStart) {
@@ -1814,10 +1832,12 @@ namespace ts {
             }
         }
 
-        function writeTextOfNode(sourceFile: SourceFile, node: Node) {
-            write(getSourceTextOfNodeFromSourceFile(sourceFile, node));
+        function writeTextOfNode(text: string, node: Node) {
+            write(getTextOfNodeFromSourceText(text, node));
         }
 
+        reset();
+
         return {
             write,
             rawWrite,
@@ -1831,9 +1851,19 @@ namespace ts {
             getLine: () => lineCount + 1,
             getColumn: () => lineStart ? indent * getIndentSize() + 1 : output.length - linePos + 1,
             getText: () => output,
+            reset
         };
     }
 
+    /**
+     * Resolves a local path to a path which is absolute to the base of the emit
+     */
+    export function getExternalModuleNameFromPath(host: EmitHost, fileName: string): string {
+        const dir = host.getCurrentDirectory();
+        const relativePath = getRelativePathToDirectoryOrUrl(dir, fileName, dir, f => host.getCanonicalFileName(f), /*isAbsolutePathAnUrl*/ false);
+        return removeFileExtension(relativePath);
+    }
+
     export function getOwnEmitOutputFilePath(sourceFile: SourceFile, host: EmitHost, extension: string) {
         const compilerOptions = host.getCompilerOptions();
         let emitOutputFilePathWithoutExtension: string;
@@ -1863,6 +1893,10 @@ namespace ts {
         return getLineAndCharacterOfPosition(currentSourceFile, pos).line;
     }
 
+    export function getLineOfLocalPositionFromLineMap(lineMap: number[], pos: number) {
+        return computeLineAndCharacterOfPosition(lineMap, pos).line;
+    }
+
     export function getFirstConstructorWithBody(node: ClassLikeDeclaration): ConstructorDeclaration {
         return forEach(node.members, member => {
             if (member.kind === SyntaxKind.Constructor && nodeIsPresent((<ConstructorDeclaration>member).body)) {
@@ -1937,23 +1971,23 @@ namespace ts {
         };
     }
 
-    export function emitNewLineBeforeLeadingComments(currentSourceFile: SourceFile, writer: EmitTextWriter, node: TextRange, leadingComments: CommentRange[]) {
+    export function emitNewLineBeforeLeadingComments(lineMap: number[], writer: EmitTextWriter, node: TextRange, leadingComments: CommentRange[]) {
         // If the leading comments start on different line than the start of node, write new line
         if (leadingComments && leadingComments.length && node.pos !== leadingComments[0].pos &&
-            getLineOfLocalPosition(currentSourceFile, node.pos) !== getLineOfLocalPosition(currentSourceFile, leadingComments[0].pos)) {
+            getLineOfLocalPositionFromLineMap(lineMap, node.pos) !== getLineOfLocalPositionFromLineMap(lineMap, leadingComments[0].pos)) {
             writer.writeLine();
         }
     }
 
-    export function emitComments(currentSourceFile: SourceFile, writer: EmitTextWriter, comments: CommentRange[], trailingSeparator: boolean, newLine: string,
-        writeComment: (currentSourceFile: SourceFile, writer: EmitTextWriter, comment: CommentRange, newLine: string) => void) {
+    export function emitComments(text: string, lineMap: number[], writer: EmitTextWriter, comments: CommentRange[], trailingSeparator: boolean, newLine: string,
+        writeComment: (text: string, lineMap: number[], writer: EmitTextWriter, comment: CommentRange, newLine: string) => void) {
         let emitLeadingSpace = !trailingSeparator;
         forEach(comments, comment => {
             if (emitLeadingSpace) {
                 writer.write(" ");
                 emitLeadingSpace = false;
             }
-            writeComment(currentSourceFile, writer, comment, newLine);
+            writeComment(text, lineMap, writer, comment, newLine);
             if (comment.hasTrailingNewLine) {
                 writer.writeLine();
             }
@@ -1971,8 +2005,8 @@ namespace ts {
      * Detached comment is a comment at the top of file or function body that is separated from
      * the next statement by space.
      */
-    export function emitDetachedComments(currentSourceFile: SourceFile, writer: EmitTextWriter,
-        writeComment: (currentSourceFile: SourceFile, writer: EmitTextWriter, comment: CommentRange, newLine: string) => void,
+    export function emitDetachedComments(text: string, lineMap: number[], writer: EmitTextWriter,
+        writeComment: (text: string, lineMap: number[], writer: EmitTextWriter, comment: CommentRange, newLine: string) => void,
         node: TextRange, newLine: string, removeComments: boolean) {
         let leadingComments: CommentRange[];
         let currentDetachedCommentInfo: {nodePos: number, detachedCommentEndPos: number};
@@ -1983,12 +2017,12 @@ namespace ts {
             //
             //      var x = 10;
             if (node.pos === 0) {
-                leadingComments = filter(getLeadingCommentRanges(currentSourceFile.text, node.pos), isPinnedComment);
+                leadingComments = filter(getLeadingCommentRanges(text, node.pos), isPinnedComment);
             }
         }
         else {
             // removeComments is false, just get detached as normal and bypass the process to filter comment
-            leadingComments = getLeadingCommentRanges(currentSourceFile.text, node.pos);
+            leadingComments = getLeadingCommentRanges(text, node.pos);
         }
 
         if (leadingComments) {
@@ -1997,8 +2031,8 @@ namespace ts {
 
             for (const comment of leadingComments) {
                 if (lastComment) {
-                    const lastCommentLine = getLineOfLocalPosition(currentSourceFile, lastComment.end);
-                    const commentLine = getLineOfLocalPosition(currentSourceFile, comment.pos);
+                    const lastCommentLine = getLineOfLocalPositionFromLineMap(lineMap, lastComment.end);
+                    const commentLine = getLineOfLocalPositionFromLineMap(lineMap, comment.pos);
 
                     if (commentLine >= lastCommentLine + 2) {
                         // There was a blank line between the last comment and this comment.  This
@@ -2016,12 +2050,12 @@ namespace ts {
                 // All comments look like they could have been part of the copyright header.  Make
                 // sure there is at least one blank line between it and the node.  If not, it's not
                 // a copyright header.
-                const lastCommentLine = getLineOfLocalPosition(currentSourceFile, lastOrUndefined(detachedComments).end);
-                const nodeLine = getLineOfLocalPosition(currentSourceFile, skipTrivia(currentSourceFile.text, node.pos));
+                const lastCommentLine = getLineOfLocalPositionFromLineMap(lineMap, lastOrUndefined(detachedComments).end);
+                const nodeLine = getLineOfLocalPositionFromLineMap(lineMap, skipTrivia(text, node.pos));
                 if (nodeLine >= lastCommentLine + 2) {
                     // Valid detachedComments
-                    emitNewLineBeforeLeadingComments(currentSourceFile, writer, node, leadingComments);
-                    emitComments(currentSourceFile, writer, detachedComments, /*trailingSeparator*/ true, newLine, writeComment);
+                    emitNewLineBeforeLeadingComments(lineMap, writer, node, leadingComments);
+                    emitComments(text, lineMap, writer, detachedComments, /*trailingSeparator*/ true, newLine, writeComment);
                     currentDetachedCommentInfo = { nodePos: node.pos, detachedCommentEndPos: lastOrUndefined(detachedComments).end };
                 }
             }
@@ -2030,25 +2064,26 @@ namespace ts {
         return currentDetachedCommentInfo;
 
         function isPinnedComment(comment: CommentRange) {
-            return currentSourceFile.text.charCodeAt(comment.pos + 1) === CharacterCodes.asterisk &&
-                currentSourceFile.text.charCodeAt(comment.pos + 2) === CharacterCodes.exclamation;
+            return text.charCodeAt(comment.pos + 1) === CharacterCodes.asterisk &&
+                text.charCodeAt(comment.pos + 2) === CharacterCodes.exclamation;
         }
+
     }
 
-    export function writeCommentRange(currentSourceFile: SourceFile, writer: EmitTextWriter, comment: CommentRange, newLine: string) {
-        if (currentSourceFile.text.charCodeAt(comment.pos + 1) === CharacterCodes.asterisk) {
-            const firstCommentLineAndCharacter = getLineAndCharacterOfPosition(currentSourceFile, comment.pos);
-            const lineCount = getLineStarts(currentSourceFile).length;
+    export function writeCommentRange(text: string, lineMap: number[], writer: EmitTextWriter, comment: CommentRange, newLine: string) {
+        if (text.charCodeAt(comment.pos + 1) === CharacterCodes.asterisk) {
+            const firstCommentLineAndCharacter = computeLineAndCharacterOfPosition(lineMap, comment.pos);
+            const lineCount = lineMap.length;
             let firstCommentLineIndent: number;
             for (let pos = comment.pos, currentLine = firstCommentLineAndCharacter.line; pos < comment.end; currentLine++) {
                 const nextLineStart = (currentLine + 1) === lineCount
-                    ? currentSourceFile.text.length + 1
-                    : getStartPositionOfLine(currentLine + 1, currentSourceFile);
+                    ? text.length + 1
+                    : lineMap[currentLine + 1];
 
                 if (pos !== comment.pos) {
                     // If we are not emitting first line, we need to write the spaces to adjust the alignment
                     if (firstCommentLineIndent === undefined) {
-                        firstCommentLineIndent = calculateIndent(getStartPositionOfLine(firstCommentLineAndCharacter.line, currentSourceFile), comment.pos);
+                        firstCommentLineIndent = calculateIndent(text, lineMap[firstCommentLineAndCharacter.line], comment.pos);
                     }
 
                     // These are number of spaces writer is going to write at current indent
@@ -2068,7 +2103,7 @@ namespace ts {
                     //            More right indented comment */                  --4 = 8 - 4 + 11
                     //     class c { }
                     // }
-                    const spacesToEmit = currentWriterIndentSpacing - firstCommentLineIndent + calculateIndent(pos, nextLineStart);
+                    const spacesToEmit = currentWriterIndentSpacing - firstCommentLineIndent + calculateIndent(text, pos, nextLineStart);
                     if (spacesToEmit > 0) {
                         let numberOfSingleSpacesToEmit = spacesToEmit % getIndentSize();
                         const indentSizeSpaceString = getIndentString((spacesToEmit - numberOfSingleSpacesToEmit) / getIndentSize());
@@ -2089,47 +2124,47 @@ namespace ts {
                 }
 
                 // Write the comment line text
-                writeTrimmedCurrentLine(pos, nextLineStart);
+                writeTrimmedCurrentLine(text, comment, writer, newLine, pos, nextLineStart);
 
                 pos = nextLineStart;
             }
         }
         else {
             // Single line comment of style //....
-            writer.write(currentSourceFile.text.substring(comment.pos, comment.end));
+            writer.write(text.substring(comment.pos, comment.end));
         }
+    }
 
-        function writeTrimmedCurrentLine(pos: number, nextLineStart: number) {
-            const end = Math.min(comment.end, nextLineStart - 1);
-            const currentLineText = currentSourceFile.text.substring(pos, end).replace(/^\s+|\s+$/g, "");
-            if (currentLineText) {
-                // trimmed forward and ending spaces text
-                writer.write(currentLineText);
-                if (end !== comment.end) {
-                    writer.writeLine();
-                }
+    function writeTrimmedCurrentLine(text: string, comment: CommentRange, writer: EmitTextWriter, newLine: string, pos: number, nextLineStart: number) {
+        const end = Math.min(comment.end, nextLineStart - 1);
+        const currentLineText = text.substring(pos, end).replace(/^\s+|\s+$/g, "");
+        if (currentLineText) {
+            // trimmed forward and ending spaces text
+            writer.write(currentLineText);
+            if (end !== comment.end) {
+                writer.writeLine();
+            }
+        }
+        else {
+            // Empty string - make sure we write empty line
+            writer.writeLiteral(newLine);
+        }
+    }
+
+    function calculateIndent(text: string, pos: number, end: number) {
+        let currentLineIndent = 0;
+        for (; pos < end && isWhiteSpace(text.charCodeAt(pos)); pos++) {
+            if (text.charCodeAt(pos) === CharacterCodes.tab) {
+                // Tabs = TabSize = indent size and go to next tabStop
+                currentLineIndent += getIndentSize() - (currentLineIndent % getIndentSize());
             }
             else {
-                // Empty string - make sure we write empty line
-                writer.writeLiteral(newLine);
+                // Single space
+                currentLineIndent++;
             }
         }
 
-        function calculateIndent(pos: number, end: number) {
-            let currentLineIndent = 0;
-            for (; pos < end && isWhiteSpace(currentSourceFile.text.charCodeAt(pos)); pos++) {
-                if (currentSourceFile.text.charCodeAt(pos) === CharacterCodes.tab) {
-                    // Tabs = TabSize = indent size and go to next tabStop
-                    currentLineIndent += getIndentSize() - (currentLineIndent % getIndentSize());
-                }
-                else {
-                    // Single space
-                    currentLineIndent++;
-                }
-            }
-
-            return currentLineIndent;
-        }
+        return currentLineIndent;
     }
 
     export function modifierToFlag(token: SyntaxKind): NodeFlags {
diff --git a/src/harness/harness.ts b/src/harness/harness.ts
index 934b7a0a36b..16c3b2d3488 100644
--- a/src/harness/harness.ts
+++ b/src/harness/harness.ts
@@ -1169,7 +1169,7 @@ namespace Harness {
                     }
                     else if (isTS(file.unitName)) {
                         const declFile = findResultCodeFile(file.unitName);
-                        if (!findUnit(declFile.fileName, declInputFiles) && !findUnit(declFile.fileName, declOtherFiles)) {
+                        if (declFile && !findUnit(declFile.fileName, declInputFiles) && !findUnit(declFile.fileName, declOtherFiles)) {
                             dtsFiles.push({ unitName: declFile.fileName, content: declFile.code });
                         }
                     }
diff --git a/src/harness/projectsRunner.ts b/src/harness/projectsRunner.ts
index 88bcfa7ddcc..f48822f1220 100644
--- a/src/harness/projectsRunner.ts
+++ b/src/harness/projectsRunner.ts
@@ -306,7 +306,10 @@ class ProjectRunner extends RunnerBase {
                     }
 
                     const outputDtsFileName = emitOutputFilePathWithoutExtension + ".d.ts";
-                    allInputFiles.unshift(findOutpuDtsFile(outputDtsFileName));
+                    const file = findOutpuDtsFile(outputDtsFileName);
+                    if (file) {
+                        allInputFiles.unshift(file);
+                    }
                 }
                 else {
                     const outputDtsFileName = ts.removeFileExtension(compilerOptions.outFile || compilerOptions.out) + ".d.ts";
@@ -346,7 +349,7 @@ class ProjectRunner extends RunnerBase {
             const inputFiles = ts.map(ts.filter(compilerResult.program.getSourceFiles(),
                 sourceFile => sourceFile.fileName !== "lib.d.ts"),
                 sourceFile => {
-                    return { unitName: sourceFile.fileName, content: sourceFile.text };
+                    return { unitName: RunnerBase.removeFullPaths(sourceFile.fileName), content: sourceFile.text };
                 });
 
             return Harness.Compiler.getErrorBaseline(inputFiles, compilerResult.errors);
@@ -387,7 +390,7 @@ class ProjectRunner extends RunnerBase {
                         return resolutionInfo;
                     }
 
-                    it(name + ": " + moduleNameToString(moduleKind) , () => {
+                    it(name + ": " + moduleNameToString(moduleKind), () => {
                         // Compile using node
                         compilerResult = batchCompilerProjectTestCase(moduleKind);
                     });
diff --git a/src/services/services.ts b/src/services/services.ts
index 13a2aa5802b..3d7a73c9139 100644
--- a/src/services/services.ts
+++ b/src/services/services.ts
@@ -174,7 +174,7 @@ namespace ts {
     let jsDocCompletionEntries: CompletionEntry[];
 
     function createNode(kind: SyntaxKind, pos: number, end: number, flags: NodeFlags, parent?: Node): NodeObject {
-        let node = <NodeObject> new (getNodeConstructor(kind))(pos, end);
+        let node = new NodeObject(kind, pos, end);
         node.flags = flags;
         node.parent = parent;
         return node;
@@ -188,6 +188,14 @@ namespace ts {
         public parent: Node;
         private _children: Node[];
 
+        constructor(kind: SyntaxKind, pos: number, end: number) {
+            this.kind = kind;
+            this.pos = pos;
+            this.end = end;
+            this.flags = NodeFlags.None;
+            this.parent = undefined;
+        }
+
         public getSourceFile(): SourceFile {
             return getSourceFileOfNode(this);
         }
@@ -806,6 +814,10 @@ namespace ts {
         public imports: LiteralExpression[];
         private namedDeclarations: Map<Declaration[]>;
 
+        constructor(kind: SyntaxKind, pos: number, end: number) {
+            super(kind, pos, end)
+        }
+        
         public update(newText: string, textChangeRange: TextChangeRange): SourceFile {
             return updateSourceFile(this, newText, textChangeRange);
         }
@@ -8058,18 +8070,8 @@ namespace ts {
 
     function initializeServices() {
         objectAllocator = {
-            getNodeConstructor: kind => {
-                function Node(pos: number, end: number) {
-                    this.pos = pos;
-                    this.end = end;
-                    this.flags = NodeFlags.None;
-                    this.parent = undefined;
-                }
-                let proto = kind === SyntaxKind.SourceFile ? new SourceFileObject() : new NodeObject();
-                proto.kind = kind;
-                Node.prototype = proto;
-                return <any>Node;
-            },
+            getNodeConstructor: () => NodeObject,
+            getSourceFileConstructor: () => SourceFileObject,
             getSymbolConstructor: () => SymbolObject,
             getTypeConstructor: () => TypeObject,
             getSignatureConstructor: () => SignatureObject,
diff --git a/tests/baselines/reference/fuzzy.errors.txt b/tests/baselines/reference/fuzzy.errors.txt
index 72ac4c816f9..0aa8207ff98 100644
--- a/tests/baselines/reference/fuzzy.errors.txt
+++ b/tests/baselines/reference/fuzzy.errors.txt
@@ -4,6 +4,7 @@ tests/cases/compiler/fuzzy.ts(21,20): error TS2322: Type '{ anything: number; on
   Types of property 'oneI' are incompatible.
     Type 'this' is not assignable to type 'I'.
       Type 'C' is not assignable to type 'I'.
+        Property 'alsoWorks' is missing in type 'C'.
 tests/cases/compiler/fuzzy.ts(25,20): error TS2352: Neither type '{ oneI: this; }' nor type 'R' is assignable to the other.
   Property 'anything' is missing in type '{ oneI: this; }'.
 
@@ -38,6 +39,7 @@ tests/cases/compiler/fuzzy.ts(25,20): error TS2352: Neither type '{ oneI: this;
 !!! error TS2322:   Types of property 'oneI' are incompatible.
 !!! error TS2322:     Type 'this' is not assignable to type 'I'.
 !!! error TS2322:       Type 'C' is not assignable to type 'I'.
+!!! error TS2322:         Property 'alsoWorks' is missing in type 'C'.
             }
     
             worksToo():R {
diff --git a/tests/baselines/reference/getEmitOutputMapRoots.baseline b/tests/baselines/reference/getEmitOutputMapRoots.baseline
index b4a4ace4d42..66130347d2d 100644
--- a/tests/baselines/reference/getEmitOutputMapRoots.baseline
+++ b/tests/baselines/reference/getEmitOutputMapRoots.baseline
@@ -1,6 +1,6 @@
 EmitSkipped: false
 FileName : declSingleFile.js.map
-{"version":3,"file":"declSingleFile.js","sourceRoot":"","sources":["../tests/cases/fourslash/inputFile.ts"],"names":["M","M.constructor"],"mappings":"AAAA,IAAI,CAAC,GAAG,GAAG,CAAC;AACZ,IAAI,GAAG,GAAG,aAAa,CAAC;AACxB;IAAAA;IAGAC,CAACA;IAADD,QAACA;AAADA,CAACA,AAHD,IAGC"}FileName : declSingleFile.js
+{"version":3,"file":"declSingleFile.js","sourceRoot":"","sources":["../inputFile.ts"],"names":["M","M.constructor"],"mappings":"AAAA,IAAI,CAAC,GAAG,GAAG,CAAC;AACZ,IAAI,GAAG,GAAG,aAAa,CAAC;AACxB;IAAAA;IAGAC,CAACA;IAADD,QAACA;AAADA,CAACA,AAHD,IAGC"}FileName : declSingleFile.js
 var x = 109;
 var foo = "hello world";
 var M = (function () {
@@ -8,4 +8,4 @@ var M = (function () {
     }
     return M;
 })();
-//# sourceMappingURL=mapRootDir/declSingleFile.js.map
+//# sourceMappingURL=tests/cases/fourslash/mapRootDir/declSingleFile.js.map
diff --git a/tests/baselines/reference/isolatedModulesOut.js b/tests/baselines/reference/isolatedModulesOut.js
index ca5eb2b7579..44f319e1031 100644
--- a/tests/baselines/reference/isolatedModulesOut.js
+++ b/tests/baselines/reference/isolatedModulesOut.js
@@ -6,7 +6,5 @@ export var x;
 //// [file2.ts]
 var y;
 
-//// [file1.js]
-export var x;
 //// [all.js]
 var y;
diff --git a/tests/baselines/reference/narrowTypeByInstanceof.types b/tests/baselines/reference/narrowTypeByInstanceof.types
index e6a3466b88f..8bc13d12ca1 100644
--- a/tests/baselines/reference/narrowTypeByInstanceof.types
+++ b/tests/baselines/reference/narrowTypeByInstanceof.types
@@ -63,7 +63,7 @@ if (elementA instanceof FileMatch && elementB instanceof FileMatch) {
 } else if (elementA instanceof Match && elementB instanceof Match) {
 >elementA instanceof Match && elementB instanceof Match : boolean
 >elementA instanceof Match : boolean
->elementA : FileMatch | Match
+>elementA : Match | FileMatch
 >Match : typeof Match
 >elementB instanceof Match : boolean
 >elementB : FileMatch | Match
diff --git a/tests/baselines/reference/out-flag2.errors.txt b/tests/baselines/reference/out-flag2.errors.txt
new file mode 100644
index 00000000000..ea6fed45bd0
--- /dev/null
+++ b/tests/baselines/reference/out-flag2.errors.txt
@@ -0,0 +1,10 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== tests/cases/compiler/a.ts (0 errors) ====
+    
+    class A { }
+    
+==== tests/cases/compiler/b.ts (0 errors) ====
+    class B { }
\ No newline at end of file
diff --git a/tests/baselines/reference/out-flag2.symbols b/tests/baselines/reference/out-flag2.symbols
deleted file mode 100644
index 1bca057c580..00000000000
--- a/tests/baselines/reference/out-flag2.symbols
+++ /dev/null
@@ -1,9 +0,0 @@
-=== tests/cases/compiler/a.ts ===
-
-class A { }
->A : Symbol(A, Decl(a.ts, 0, 0))
-
-=== tests/cases/compiler/b.ts ===
-class B { }
->B : Symbol(B, Decl(b.ts, 0, 0))
-
diff --git a/tests/baselines/reference/out-flag2.types b/tests/baselines/reference/out-flag2.types
deleted file mode 100644
index 5a13642f99f..00000000000
--- a/tests/baselines/reference/out-flag2.types
+++ /dev/null
@@ -1,9 +0,0 @@
-=== tests/cases/compiler/a.ts ===
-
-class A { }
->A : A
-
-=== tests/cases/compiler/b.ts ===
-class B { }
->B : B
-
diff --git a/tests/baselines/reference/out-flag3.errors.txt b/tests/baselines/reference/out-flag3.errors.txt
index 6b7dda7c962..c01cef151f3 100644
--- a/tests/baselines/reference/out-flag3.errors.txt
+++ b/tests/baselines/reference/out-flag3.errors.txt
@@ -1,7 +1,9 @@
 error TS5053: Option 'out' cannot be specified with option 'outFile'.
+error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
 
 
 !!! error TS5053: Option 'out' cannot be specified with option 'outFile'.
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
 ==== tests/cases/compiler/a.ts (0 errors) ====
     
     // --out and --outFile error
diff --git a/tests/baselines/reference/outModuleConcatAmd.js b/tests/baselines/reference/outModuleConcatAmd.js
new file mode 100644
index 00000000000..a1c874abb7c
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatAmd.js
@@ -0,0 +1,46 @@
+//// [tests/cases/compiler/outModuleConcatAmd.ts] ////
+
+//// [a.ts]
+
+export class A { }
+
+//// [b.ts]
+import {A} from "./ref/a";
+export class B extends A { }
+
+//// [all.js]
+var __extends = (this && this.__extends) || function (d, b) {
+    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+    function __() { this.constructor = d; }
+    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+};
+define("tests/cases/compiler/ref/a", ["require", "exports"], function (require, exports) {
+    var A = (function () {
+        function A() {
+        }
+        return A;
+    })();
+    exports.A = A;
+});
+define("tests/cases/compiler/b", ["require", "exports", "tests/cases/compiler/ref/a"], function (require, exports, a_1) {
+    var B = (function (_super) {
+        __extends(B, _super);
+        function B() {
+            _super.apply(this, arguments);
+        }
+        return B;
+    })(a_1.A);
+    exports.B = B;
+});
+//# sourceMappingURL=all.js.map
+
+//// [all.d.ts]
+declare module "tests/cases/compiler/ref/a" {
+    export class A {
+    }
+}
+declare module "tests/cases/compiler/b" {
+    import { A } from "tests/cases/compiler/ref/a";
+    export class B extends A {
+    }
+}
diff --git a/tests/baselines/reference/outModuleConcatAmd.js.map b/tests/baselines/reference/outModuleConcatAmd.js.map
new file mode 100644
index 00000000000..44cd5ce9955
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatAmd.js.map
@@ -0,0 +1,2 @@
+//// [all.js.map]
+{"version":3,"file":"all.js","sourceRoot":"","sources":["tests/cases/compiler/ref/a.ts","tests/cases/compiler/b.ts"],"names":["A","A.constructor","B","B.constructor"],"mappings":";;;;;;IACA;QAAAA;QAAiBC,CAACA;QAADD,QAACA;IAADA,CAACA,AAAlB,IAAkB;IAAL,SAAC,IAAI,CAAA;;;ICAlB;QAAuBE,qBAACA;QAAxBA;YAAuBC,8BAACA;QAAGA,CAACA;QAADD,QAACA;IAADA,CAACA,AAA5B,EAAuB,KAAC,EAAI;IAAf,SAAC,IAAc,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatAmd.sourcemap.txt b/tests/baselines/reference/outModuleConcatAmd.sourcemap.txt
new file mode 100644
index 00000000000..eec3a6014aa
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatAmd.sourcemap.txt
@@ -0,0 +1,164 @@
+===================================================================
+JsFile: all.js
+mapUrl: all.js.map
+sourceRoot: 
+sources: tests/cases/compiler/ref/a.ts,tests/cases/compiler/b.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/ref/a.ts
+-------------------------------------------------------------------
+>>>var __extends = (this && this.__extends) || function (d, b) {
+>>>    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+>>>    function __() { this.constructor = d; }
+>>>    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+>>>};
+>>>define("tests/cases/compiler/ref/a", ["require", "exports"], function (require, exports) {
+>>>    var A = (function () {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(7, 5) Source(2, 1) + SourceIndex(0)
+---
+>>>        function A() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(8, 9) Source(2, 1) + SourceIndex(0) name (A)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^->
+1->export class A { 
+2 >        }
+1->Emitted(9, 9) Source(2, 18) + SourceIndex(0) name (A.constructor)
+2 >Emitted(9, 10) Source(2, 19) + SourceIndex(0) name (A.constructor)
+---
+>>>        return A;
+1->^^^^^^^^
+2 >        ^^^^^^^^
+1->
+2 >        }
+1->Emitted(10, 9) Source(2, 18) + SourceIndex(0) name (A)
+2 >Emitted(10, 17) Source(2, 19) + SourceIndex(0) name (A)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class A { }
+1 >Emitted(11, 5) Source(2, 18) + SourceIndex(0) name (A)
+2 >Emitted(11, 6) Source(2, 19) + SourceIndex(0) name (A)
+3 >Emitted(11, 6) Source(2, 1) + SourceIndex(0)
+4 >Emitted(11, 10) Source(2, 19) + SourceIndex(0)
+---
+>>>    exports.A = A;
+1->^^^^
+2 >    ^^^^^^^^^
+3 >             ^^^^
+4 >                 ^
+1->
+2 >    A
+3 >              { }
+4 >                 
+1->Emitted(12, 5) Source(2, 14) + SourceIndex(0)
+2 >Emitted(12, 14) Source(2, 15) + SourceIndex(0)
+3 >Emitted(12, 18) Source(2, 19) + SourceIndex(0)
+4 >Emitted(12, 19) Source(2, 19) + SourceIndex(0)
+---
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/b.ts
+-------------------------------------------------------------------
+>>>});
+>>>define("tests/cases/compiler/b", ["require", "exports", "tests/cases/compiler/ref/a"], function (require, exports, a_1) {
+>>>    var B = (function (_super) {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >import {A} from "./ref/a";
+  >
+1 >Emitted(15, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        __extends(B, _super);
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^^^^^^^^^^
+1->export class B extends 
+2 >        A
+1->Emitted(16, 9) Source(2, 24) + SourceIndex(1) name (B)
+2 >Emitted(16, 30) Source(2, 25) + SourceIndex(1) name (B)
+---
+>>>        function B() {
+1 >^^^^^^^^
+2 >        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+1 >Emitted(17, 9) Source(2, 1) + SourceIndex(1) name (B)
+---
+>>>            _super.apply(this, arguments);
+1->^^^^^^^^^^^^
+2 >            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1->export class B extends 
+2 >            A
+1->Emitted(18, 13) Source(2, 24) + SourceIndex(1) name (B.constructor)
+2 >Emitted(18, 43) Source(2, 25) + SourceIndex(1) name (B.constructor)
+---
+>>>        }
+1 >^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^->
+1 > { 
+2 >        }
+1 >Emitted(19, 9) Source(2, 28) + SourceIndex(1) name (B.constructor)
+2 >Emitted(19, 10) Source(2, 29) + SourceIndex(1) name (B.constructor)
+---
+>>>        return B;
+1->^^^^^^^^
+2 >        ^^^^^^^^
+1->
+2 >        }
+1->Emitted(20, 9) Source(2, 28) + SourceIndex(1) name (B)
+2 >Emitted(20, 17) Source(2, 29) + SourceIndex(1) name (B)
+---
+>>>    })(a_1.A);
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^
+5 >       ^^^^^
+6 >            ^^
+7 >              ^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class B extends 
+5 >       A
+6 >             { }
+1 >Emitted(21, 5) Source(2, 28) + SourceIndex(1) name (B)
+2 >Emitted(21, 6) Source(2, 29) + SourceIndex(1) name (B)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 8) Source(2, 24) + SourceIndex(1)
+5 >Emitted(21, 13) Source(2, 25) + SourceIndex(1)
+6 >Emitted(21, 15) Source(2, 29) + SourceIndex(1)
+---
+>>>    exports.B = B;
+1->^^^^
+2 >    ^^^^^^^^^
+3 >             ^^^^
+4 >                 ^
+1->
+2 >    B
+3 >              extends A { }
+4 >                 
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 14) Source(2, 15) + SourceIndex(1)
+3 >Emitted(22, 18) Source(2, 29) + SourceIndex(1)
+4 >Emitted(22, 19) Source(2, 29) + SourceIndex(1)
+---
+>>>});
+>>>//# sourceMappingURL=all.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatAmd.symbols b/tests/baselines/reference/outModuleConcatAmd.symbols
new file mode 100644
index 00000000000..349de40815a
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatAmd.symbols
@@ -0,0 +1,13 @@
+=== tests/cases/compiler/ref/a.ts ===
+
+export class A { }
+>A : Symbol(A, Decl(a.ts, 0, 0))
+
+=== tests/cases/compiler/b.ts ===
+import {A} from "./ref/a";
+>A : Symbol(A, Decl(b.ts, 0, 8))
+
+export class B extends A { }
+>B : Symbol(B, Decl(b.ts, 0, 26))
+>A : Symbol(A, Decl(b.ts, 0, 8))
+
diff --git a/tests/baselines/reference/outModuleConcatAmd.types b/tests/baselines/reference/outModuleConcatAmd.types
new file mode 100644
index 00000000000..6e0d9398853
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatAmd.types
@@ -0,0 +1,13 @@
+=== tests/cases/compiler/ref/a.ts ===
+
+export class A { }
+>A : A
+
+=== tests/cases/compiler/b.ts ===
+import {A} from "./ref/a";
+>A : typeof A
+
+export class B extends A { }
+>B : B
+>A : A
+
diff --git a/tests/baselines/reference/outModuleConcatCommonjs.errors.txt b/tests/baselines/reference/outModuleConcatCommonjs.errors.txt
new file mode 100644
index 00000000000..d1a2adbc93f
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatCommonjs.errors.txt
@@ -0,0 +1,13 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== tests/cases/compiler/ref/a.ts (0 errors) ====
+    
+    // This should be an error
+    
+    export class A { }
+    
+==== tests/cases/compiler/b.ts (0 errors) ====
+    import {A} from "./ref/a";
+    export class B extends A { }
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatCommonjs.js b/tests/baselines/reference/outModuleConcatCommonjs.js
new file mode 100644
index 00000000000..c859d6c63ef
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatCommonjs.js
@@ -0,0 +1,31 @@
+//// [tests/cases/compiler/outModuleConcatCommonjs.ts] ////
+
+//// [a.ts]
+
+// This should be an error
+
+export class A { }
+
+//// [b.ts]
+import {A} from "./ref/a";
+export class B extends A { }
+
+//// [all.js]
+var __extends = (this && this.__extends) || function (d, b) {
+    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+    function __() { this.constructor = d; }
+    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+};
+// This should be an error
+//# sourceMappingURL=all.js.map
+
+//// [all.d.ts]
+declare module "tests/cases/compiler/ref/a" {
+    export class A {
+    }
+}
+declare module "tests/cases/compiler/b" {
+    import { A } from "tests/cases/compiler/ref/a";
+    export class B extends A {
+    }
+}
diff --git a/tests/baselines/reference/outModuleConcatCommonjs.js.map b/tests/baselines/reference/outModuleConcatCommonjs.js.map
new file mode 100644
index 00000000000..09646467406
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatCommonjs.js.map
@@ -0,0 +1,2 @@
+//// [all.js.map]
+{"version":3,"file":"all.js","sourceRoot":"","sources":["tests/cases/compiler/ref/a.ts","tests/cases/compiler/b.ts"],"names":[],"mappings":";;;;;AACA,0BAA0B"}
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatCommonjs.sourcemap.txt b/tests/baselines/reference/outModuleConcatCommonjs.sourcemap.txt
new file mode 100644
index 00000000000..698328649e2
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatCommonjs.sourcemap.txt
@@ -0,0 +1,26 @@
+===================================================================
+JsFile: all.js
+mapUrl: all.js.map
+sourceRoot: 
+sources: tests/cases/compiler/ref/a.ts,tests/cases/compiler/b.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/ref/a.ts
+-------------------------------------------------------------------
+>>>var __extends = (this && this.__extends) || function (d, b) {
+>>>    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+>>>    function __() { this.constructor = d; }
+>>>    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+>>>};
+>>>// This should be an error
+1 >
+2 >^^^^^^^^^^^^^^^^^^^^^^^^^^
+3 >                          ^^^^->
+1 >
+  >
+2 >// This should be an error
+1 >Emitted(6, 1) Source(2, 1) + SourceIndex(0)
+2 >Emitted(6, 27) Source(2, 27) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=all.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatES6.errors.txt b/tests/baselines/reference/outModuleConcatES6.errors.txt
new file mode 100644
index 00000000000..d1a2adbc93f
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatES6.errors.txt
@@ -0,0 +1,13 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== tests/cases/compiler/ref/a.ts (0 errors) ====
+    
+    // This should be an error
+    
+    export class A { }
+    
+==== tests/cases/compiler/b.ts (0 errors) ====
+    import {A} from "./ref/a";
+    export class B extends A { }
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatES6.js b/tests/baselines/reference/outModuleConcatES6.js
new file mode 100644
index 00000000000..037d52eb410
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatES6.js
@@ -0,0 +1,26 @@
+//// [tests/cases/compiler/outModuleConcatES6.ts] ////
+
+//// [a.ts]
+
+// This should be an error
+
+export class A { }
+
+//// [b.ts]
+import {A} from "./ref/a";
+export class B extends A { }
+
+//// [all.js]
+// This should be an error
+//# sourceMappingURL=all.js.map
+
+//// [all.d.ts]
+declare module "tests/cases/compiler/ref/a" {
+    export class A {
+    }
+}
+declare module "tests/cases/compiler/b" {
+    import { A } from "tests/cases/compiler/ref/a";
+    export class B extends A {
+    }
+}
diff --git a/tests/baselines/reference/outModuleConcatES6.js.map b/tests/baselines/reference/outModuleConcatES6.js.map
new file mode 100644
index 00000000000..bd3e6f58731
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatES6.js.map
@@ -0,0 +1,2 @@
+//// [all.js.map]
+{"version":3,"file":"all.js","sourceRoot":"","sources":["tests/cases/compiler/ref/a.ts","tests/cases/compiler/b.ts"],"names":[],"mappings":"AACA,0BAA0B"}
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatES6.sourcemap.txt b/tests/baselines/reference/outModuleConcatES6.sourcemap.txt
new file mode 100644
index 00000000000..78b6e98ac15
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatES6.sourcemap.txt
@@ -0,0 +1,21 @@
+===================================================================
+JsFile: all.js
+mapUrl: all.js.map
+sourceRoot: 
+sources: tests/cases/compiler/ref/a.ts,tests/cases/compiler/b.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/ref/a.ts
+-------------------------------------------------------------------
+>>>// This should be an error
+1 >
+2 >^^^^^^^^^^^^^^^^^^^^^^^^^^
+3 >                          ^^^^->
+1 >
+  >
+2 >// This should be an error
+1 >Emitted(1, 1) Source(2, 1) + SourceIndex(0)
+2 >Emitted(1, 27) Source(2, 27) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=all.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatSystem.js b/tests/baselines/reference/outModuleConcatSystem.js
new file mode 100644
index 00000000000..1f8bdbd8070
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatSystem.js
@@ -0,0 +1,62 @@
+//// [tests/cases/compiler/outModuleConcatSystem.ts] ////
+
+//// [a.ts]
+
+export class A { }
+
+//// [b.ts]
+import {A} from "./ref/a";
+export class B extends A { }
+
+//// [all.js]
+var __extends = (this && this.__extends) || function (d, b) {
+    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+    function __() { this.constructor = d; }
+    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+};
+System.register("tests/cases/compiler/ref/a", [], function(exports_1) {
+    var A;
+    return {
+        setters:[],
+        execute: function() {
+            A = (function () {
+                function A() {
+                }
+                return A;
+            })();
+            exports_1("A", A);
+        }
+    }
+});
+System.register("tests/cases/compiler/b", ["tests/cases/compiler/ref/a"], function(exports_2) {
+    var a_1;
+    var B;
+    return {
+        setters:[
+            function (a_1_1) {
+                a_1 = a_1_1;
+            }],
+        execute: function() {
+            B = (function (_super) {
+                __extends(B, _super);
+                function B() {
+                    _super.apply(this, arguments);
+                }
+                return B;
+            })(a_1.A);
+            exports_2("B", B);
+        }
+    }
+});
+//# sourceMappingURL=all.js.map
+
+//// [all.d.ts]
+declare module "tests/cases/compiler/ref/a" {
+    export class A {
+    }
+}
+declare module "tests/cases/compiler/b" {
+    import { A } from "tests/cases/compiler/ref/a";
+    export class B extends A {
+    }
+}
diff --git a/tests/baselines/reference/outModuleConcatSystem.js.map b/tests/baselines/reference/outModuleConcatSystem.js.map
new file mode 100644
index 00000000000..77ff05f84fb
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatSystem.js.map
@@ -0,0 +1,2 @@
+//// [all.js.map]
+{"version":3,"file":"all.js","sourceRoot":"","sources":["tests/cases/compiler/ref/a.ts","tests/cases/compiler/b.ts"],"names":["A","A.constructor","B","B.constructor"],"mappings":";;;;;;;;;;YACA;gBAAAA;gBAAiBC,CAACA;gBAADD,QAACA;YAADA,CAACA,AAAlB,IAAkB;YAAlB,iBAAkB,CAAA;;;;;;;;;;;;;YCAlB;gBAAuBE,qBAACA;gBAAxBA;oBAAuBC,8BAACA;gBAAGA,CAACA;gBAADD,QAACA;YAADA,CAACA,AAA5B,EAAuB,KAAC,EAAI;YAA5B,iBAA4B,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatSystem.sourcemap.txt b/tests/baselines/reference/outModuleConcatSystem.sourcemap.txt
new file mode 100644
index 00000000000..489487772db
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatSystem.sourcemap.txt
@@ -0,0 +1,174 @@
+===================================================================
+JsFile: all.js
+mapUrl: all.js.map
+sourceRoot: 
+sources: tests/cases/compiler/ref/a.ts,tests/cases/compiler/b.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/ref/a.ts
+-------------------------------------------------------------------
+>>>var __extends = (this && this.__extends) || function (d, b) {
+>>>    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+>>>    function __() { this.constructor = d; }
+>>>    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+>>>};
+>>>System.register("tests/cases/compiler/ref/a", [], function(exports_1) {
+>>>    var A;
+>>>    return {
+>>>        setters:[],
+>>>        execute: function() {
+>>>            A = (function () {
+1 >^^^^^^^^^^^^
+2 >            ^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(11, 13) Source(2, 1) + SourceIndex(0)
+---
+>>>                function A() {
+1->^^^^^^^^^^^^^^^^
+2 >                ^^->
+1->
+1->Emitted(12, 17) Source(2, 1) + SourceIndex(0) name (A)
+---
+>>>                }
+1->^^^^^^^^^^^^^^^^
+2 >                ^
+3 >                 ^^^^^^^^^->
+1->export class A { 
+2 >                }
+1->Emitted(13, 17) Source(2, 18) + SourceIndex(0) name (A.constructor)
+2 >Emitted(13, 18) Source(2, 19) + SourceIndex(0) name (A.constructor)
+---
+>>>                return A;
+1->^^^^^^^^^^^^^^^^
+2 >                ^^^^^^^^
+1->
+2 >                }
+1->Emitted(14, 17) Source(2, 18) + SourceIndex(0) name (A)
+2 >Emitted(14, 25) Source(2, 19) + SourceIndex(0) name (A)
+---
+>>>            })();
+1 >^^^^^^^^^^^^
+2 >            ^
+3 >             
+4 >             ^^^^
+5 >                 ^^^^^^^^^^^^^^->
+1 >
+2 >            }
+3 >             
+4 >             export class A { }
+1 >Emitted(15, 13) Source(2, 18) + SourceIndex(0) name (A)
+2 >Emitted(15, 14) Source(2, 19) + SourceIndex(0) name (A)
+3 >Emitted(15, 14) Source(2, 1) + SourceIndex(0)
+4 >Emitted(15, 18) Source(2, 19) + SourceIndex(0)
+---
+>>>            exports_1("A", A);
+1->^^^^^^^^^^^^
+2 >            ^^^^^^^^^^^^^^^^^
+3 >                             ^
+1->
+2 >            export class A { }
+3 >                             
+1->Emitted(16, 13) Source(2, 1) + SourceIndex(0)
+2 >Emitted(16, 30) Source(2, 19) + SourceIndex(0)
+3 >Emitted(16, 31) Source(2, 19) + SourceIndex(0)
+---
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/b.ts
+-------------------------------------------------------------------
+>>>        }
+>>>    }
+>>>});
+>>>System.register("tests/cases/compiler/b", ["tests/cases/compiler/ref/a"], function(exports_2) {
+>>>    var a_1;
+>>>    var B;
+>>>    return {
+>>>        setters:[
+>>>            function (a_1_1) {
+>>>                a_1 = a_1_1;
+>>>            }],
+>>>        execute: function() {
+>>>            B = (function (_super) {
+1 >^^^^^^^^^^^^
+2 >            ^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >import {A} from "./ref/a";
+  >
+1 >Emitted(29, 13) Source(2, 1) + SourceIndex(1)
+---
+>>>                __extends(B, _super);
+1->^^^^^^^^^^^^^^^^
+2 >                ^^^^^^^^^^^^^^^^^^^^^
+1->export class B extends 
+2 >                A
+1->Emitted(30, 17) Source(2, 24) + SourceIndex(1) name (B)
+2 >Emitted(30, 38) Source(2, 25) + SourceIndex(1) name (B)
+---
+>>>                function B() {
+1 >^^^^^^^^^^^^^^^^
+2 >                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+1 >Emitted(31, 17) Source(2, 1) + SourceIndex(1) name (B)
+---
+>>>                    _super.apply(this, arguments);
+1->^^^^^^^^^^^^^^^^^^^^
+2 >                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1->export class B extends 
+2 >                    A
+1->Emitted(32, 21) Source(2, 24) + SourceIndex(1) name (B.constructor)
+2 >Emitted(32, 51) Source(2, 25) + SourceIndex(1) name (B.constructor)
+---
+>>>                }
+1 >^^^^^^^^^^^^^^^^
+2 >                ^
+3 >                 ^^^^^^^^^->
+1 > { 
+2 >                }
+1 >Emitted(33, 17) Source(2, 28) + SourceIndex(1) name (B.constructor)
+2 >Emitted(33, 18) Source(2, 29) + SourceIndex(1) name (B.constructor)
+---
+>>>                return B;
+1->^^^^^^^^^^^^^^^^
+2 >                ^^^^^^^^
+1->
+2 >                }
+1->Emitted(34, 17) Source(2, 28) + SourceIndex(1) name (B)
+2 >Emitted(34, 25) Source(2, 29) + SourceIndex(1) name (B)
+---
+>>>            })(a_1.A);
+1 >^^^^^^^^^^^^
+2 >            ^
+3 >             
+4 >             ^^
+5 >               ^^^^^
+6 >                    ^^
+7 >                      ^^^^^^^^^->
+1 >
+2 >            }
+3 >             
+4 >             export class B extends 
+5 >               A
+6 >                     { }
+1 >Emitted(35, 13) Source(2, 28) + SourceIndex(1) name (B)
+2 >Emitted(35, 14) Source(2, 29) + SourceIndex(1) name (B)
+3 >Emitted(35, 14) Source(2, 1) + SourceIndex(1)
+4 >Emitted(35, 16) Source(2, 24) + SourceIndex(1)
+5 >Emitted(35, 21) Source(2, 25) + SourceIndex(1)
+6 >Emitted(35, 23) Source(2, 29) + SourceIndex(1)
+---
+>>>            exports_2("B", B);
+1->^^^^^^^^^^^^
+2 >            ^^^^^^^^^^^^^^^^^
+3 >                             ^
+1->
+2 >            export class B extends A { }
+3 >                             
+1->Emitted(36, 13) Source(2, 1) + SourceIndex(1)
+2 >Emitted(36, 30) Source(2, 29) + SourceIndex(1)
+3 >Emitted(36, 31) Source(2, 29) + SourceIndex(1)
+---
+>>>        }
+>>>    }
+>>>});
+>>>//# sourceMappingURL=all.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatSystem.symbols b/tests/baselines/reference/outModuleConcatSystem.symbols
new file mode 100644
index 00000000000..349de40815a
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatSystem.symbols
@@ -0,0 +1,13 @@
+=== tests/cases/compiler/ref/a.ts ===
+
+export class A { }
+>A : Symbol(A, Decl(a.ts, 0, 0))
+
+=== tests/cases/compiler/b.ts ===
+import {A} from "./ref/a";
+>A : Symbol(A, Decl(b.ts, 0, 8))
+
+export class B extends A { }
+>B : Symbol(B, Decl(b.ts, 0, 26))
+>A : Symbol(A, Decl(b.ts, 0, 8))
+
diff --git a/tests/baselines/reference/outModuleConcatSystem.types b/tests/baselines/reference/outModuleConcatSystem.types
new file mode 100644
index 00000000000..6e0d9398853
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatSystem.types
@@ -0,0 +1,13 @@
+=== tests/cases/compiler/ref/a.ts ===
+
+export class A { }
+>A : A
+
+=== tests/cases/compiler/b.ts ===
+import {A} from "./ref/a";
+>A : typeof A
+
+export class B extends A { }
+>B : B
+>A : A
+
diff --git a/tests/baselines/reference/outModuleConcatUmd.errors.txt b/tests/baselines/reference/outModuleConcatUmd.errors.txt
new file mode 100644
index 00000000000..8695199c7eb
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatUmd.errors.txt
@@ -0,0 +1,13 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== tests/cases/compiler/ref/a.ts (0 errors) ====
+    
+    // This should error
+    
+    export class A { }
+    
+==== tests/cases/compiler/b.ts (0 errors) ====
+    import {A} from "./ref/a";
+    export class B extends A { }
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatUmd.js b/tests/baselines/reference/outModuleConcatUmd.js
new file mode 100644
index 00000000000..c4aad41c6ed
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatUmd.js
@@ -0,0 +1,31 @@
+//// [tests/cases/compiler/outModuleConcatUmd.ts] ////
+
+//// [a.ts]
+
+// This should error
+
+export class A { }
+
+//// [b.ts]
+import {A} from "./ref/a";
+export class B extends A { }
+
+//// [all.js]
+var __extends = (this && this.__extends) || function (d, b) {
+    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+    function __() { this.constructor = d; }
+    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+};
+// This should error
+//# sourceMappingURL=all.js.map
+
+//// [all.d.ts]
+declare module "tests/cases/compiler/ref/a" {
+    export class A {
+    }
+}
+declare module "tests/cases/compiler/b" {
+    import { A } from "tests/cases/compiler/ref/a";
+    export class B extends A {
+    }
+}
diff --git a/tests/baselines/reference/outModuleConcatUmd.js.map b/tests/baselines/reference/outModuleConcatUmd.js.map
new file mode 100644
index 00000000000..7a9fcd77bdf
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatUmd.js.map
@@ -0,0 +1,2 @@
+//// [all.js.map]
+{"version":3,"file":"all.js","sourceRoot":"","sources":["tests/cases/compiler/ref/a.ts","tests/cases/compiler/b.ts"],"names":[],"mappings":";;;;;AACA,oBAAoB"}
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleConcatUmd.sourcemap.txt b/tests/baselines/reference/outModuleConcatUmd.sourcemap.txt
new file mode 100644
index 00000000000..d2fbe17fe65
--- /dev/null
+++ b/tests/baselines/reference/outModuleConcatUmd.sourcemap.txt
@@ -0,0 +1,26 @@
+===================================================================
+JsFile: all.js
+mapUrl: all.js.map
+sourceRoot: 
+sources: tests/cases/compiler/ref/a.ts,tests/cases/compiler/b.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/ref/a.ts
+-------------------------------------------------------------------
+>>>var __extends = (this && this.__extends) || function (d, b) {
+>>>    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+>>>    function __() { this.constructor = d; }
+>>>    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+>>>};
+>>>// This should error
+1 >
+2 >^^^^^^^^^^^^^^^^^^^^
+3 >                    ^^^^^^^^^^->
+1 >
+  >
+2 >// This should error
+1 >Emitted(6, 1) Source(2, 1) + SourceIndex(0)
+2 >Emitted(6, 21) Source(2, 21) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=all.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleTripleSlashRefs.js b/tests/baselines/reference/outModuleTripleSlashRefs.js
new file mode 100644
index 00000000000..ae4ac43b5c9
--- /dev/null
+++ b/tests/baselines/reference/outModuleTripleSlashRefs.js
@@ -0,0 +1,81 @@
+//// [tests/cases/compiler/outModuleTripleSlashRefs.ts] ////
+
+//// [a.ts]
+
+/// <reference path="./b.ts" />
+export class A {
+	member: typeof GlobalFoo;
+}
+
+//// [b.ts]
+/// <reference path="./c.d.ts" />
+class Foo {
+	member: Bar;
+}
+declare var GlobalFoo: Foo;
+
+//// [c.d.ts]
+/// <reference path="./d.d.ts" />
+declare class Bar {
+	member: Baz;
+}
+
+//// [d.d.ts]
+declare class Baz {
+	member: number;
+}
+
+//// [b.ts]
+import {A} from "./ref/a";
+export class B extends A { }
+
+
+//// [all.js]
+var __extends = (this && this.__extends) || function (d, b) {
+    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+    function __() { this.constructor = d; }
+    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+};
+/// <reference path="./c.d.ts" />
+var Foo = (function () {
+    function Foo() {
+    }
+    return Foo;
+})();
+define("tests/cases/compiler/ref/a", ["require", "exports"], function (require, exports) {
+    /// <reference path="./b.ts" />
+    var A = (function () {
+        function A() {
+        }
+        return A;
+    })();
+    exports.A = A;
+});
+define("tests/cases/compiler/b", ["require", "exports", "tests/cases/compiler/ref/a"], function (require, exports, a_1) {
+    var B = (function (_super) {
+        __extends(B, _super);
+        function B() {
+            _super.apply(this, arguments);
+        }
+        return B;
+    })(a_1.A);
+    exports.B = B;
+});
+//# sourceMappingURL=all.js.map
+
+//// [all.d.ts]
+/// <reference path="tests/cases/compiler/ref/c.d.ts" />
+declare class Foo {
+    member: Bar;
+}
+declare var GlobalFoo: Foo;
+declare module "tests/cases/compiler/ref/a" {
+    export class A {
+        member: typeof GlobalFoo;
+    }
+}
+declare module "tests/cases/compiler/b" {
+    import { A } from "tests/cases/compiler/ref/a";
+    export class B extends A {
+    }
+}
diff --git a/tests/baselines/reference/outModuleTripleSlashRefs.js.map b/tests/baselines/reference/outModuleTripleSlashRefs.js.map
new file mode 100644
index 00000000000..711163a76e8
--- /dev/null
+++ b/tests/baselines/reference/outModuleTripleSlashRefs.js.map
@@ -0,0 +1,2 @@
+//// [all.js.map]
+{"version":3,"file":"all.js","sourceRoot":"","sources":["tests/cases/compiler/ref/b.ts","tests/cases/compiler/ref/a.ts","tests/cases/compiler/b.ts"],"names":["Foo","Foo.constructor","A","A.constructor","B","B.constructor"],"mappings":";;;;;AAAA,iCAAiC;AACjC;IAAAA;IAEAC,CAACA;IAADD,UAACA;AAADA,CAACA,AAFD,IAEC;;ICFD,+BAA+B;IAC/B;QAAAE;QAEAC,CAACA;QAADD,QAACA;IAADA,CAACA,AAFD,IAEC;IAFY,SAAC,IAEb,CAAA;;;ICHD;QAAuBE,qBAACA;QAAxBA;YAAuBC,8BAACA;QAAGA,CAACA;QAADD,QAACA;IAADA,CAACA,AAA5B,EAAuB,KAAC,EAAI;IAAf,SAAC,IAAc,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleTripleSlashRefs.sourcemap.txt b/tests/baselines/reference/outModuleTripleSlashRefs.sourcemap.txt
new file mode 100644
index 00000000000..c95eb22cb10
--- /dev/null
+++ b/tests/baselines/reference/outModuleTripleSlashRefs.sourcemap.txt
@@ -0,0 +1,240 @@
+===================================================================
+JsFile: all.js
+mapUrl: all.js.map
+sourceRoot: 
+sources: tests/cases/compiler/ref/b.ts,tests/cases/compiler/ref/a.ts,tests/cases/compiler/b.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/ref/b.ts
+-------------------------------------------------------------------
+>>>var __extends = (this && this.__extends) || function (d, b) {
+>>>    for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
+>>>    function __() { this.constructor = d; }
+>>>    d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+>>>};
+>>>/// <reference path="./c.d.ts" />
+1 >
+2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1 >
+2 >/// <reference path="./c.d.ts" />
+1 >Emitted(6, 1) Source(1, 1) + SourceIndex(0)
+2 >Emitted(6, 34) Source(1, 34) + SourceIndex(0)
+---
+>>>var Foo = (function () {
+1 >
+2 >^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(7, 1) Source(2, 1) + SourceIndex(0)
+---
+>>>    function Foo() {
+1->^^^^
+2 >    ^^->
+1->
+1->Emitted(8, 5) Source(2, 1) + SourceIndex(0) name (Foo)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^->
+1->class Foo {
+  >	member: Bar;
+  >
+2 >    }
+1->Emitted(9, 5) Source(4, 1) + SourceIndex(0) name (Foo.constructor)
+2 >Emitted(9, 6) Source(4, 2) + SourceIndex(0) name (Foo.constructor)
+---
+>>>    return Foo;
+1->^^^^
+2 >    ^^^^^^^^^^
+1->
+2 >    }
+1->Emitted(10, 5) Source(4, 1) + SourceIndex(0) name (Foo)
+2 >Emitted(10, 15) Source(4, 2) + SourceIndex(0) name (Foo)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class Foo {
+  > 	member: Bar;
+  > }
+1 >Emitted(11, 1) Source(4, 1) + SourceIndex(0) name (Foo)
+2 >Emitted(11, 2) Source(4, 2) + SourceIndex(0) name (Foo)
+3 >Emitted(11, 2) Source(2, 1) + SourceIndex(0)
+4 >Emitted(11, 6) Source(4, 2) + SourceIndex(0)
+---
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/ref/a.ts
+-------------------------------------------------------------------
+>>>define("tests/cases/compiler/ref/a", ["require", "exports"], function (require, exports) {
+>>>    /// <reference path="./b.ts" />
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1->
+  >
+2 >    /// <reference path="./b.ts" />
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+2 >Emitted(13, 36) Source(2, 32) + SourceIndex(1)
+---
+>>>    var A = (function () {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(14, 5) Source(3, 1) + SourceIndex(1)
+---
+>>>        function A() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(15, 9) Source(3, 1) + SourceIndex(1) name (A)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^->
+1->export class A {
+  >	member: typeof GlobalFoo;
+  >
+2 >        }
+1->Emitted(16, 9) Source(5, 1) + SourceIndex(1) name (A.constructor)
+2 >Emitted(16, 10) Source(5, 2) + SourceIndex(1) name (A.constructor)
+---
+>>>        return A;
+1->^^^^^^^^
+2 >        ^^^^^^^^
+1->
+2 >        }
+1->Emitted(17, 9) Source(5, 1) + SourceIndex(1) name (A)
+2 >Emitted(17, 17) Source(5, 2) + SourceIndex(1) name (A)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class A {
+  >     	member: typeof GlobalFoo;
+  >     }
+1 >Emitted(18, 5) Source(5, 1) + SourceIndex(1) name (A)
+2 >Emitted(18, 6) Source(5, 2) + SourceIndex(1) name (A)
+3 >Emitted(18, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(18, 10) Source(5, 2) + SourceIndex(1)
+---
+>>>    exports.A = A;
+1->^^^^
+2 >    ^^^^^^^^^
+3 >             ^^^^
+4 >                 ^
+1->
+2 >    A
+3 >              {
+  >             	member: typeof GlobalFoo;
+  >             }
+4 >                 
+1->Emitted(19, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(19, 14) Source(3, 15) + SourceIndex(1)
+3 >Emitted(19, 18) Source(5, 2) + SourceIndex(1)
+4 >Emitted(19, 19) Source(5, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:all.js
+sourceFile:tests/cases/compiler/b.ts
+-------------------------------------------------------------------
+>>>});
+>>>define("tests/cases/compiler/b", ["require", "exports", "tests/cases/compiler/ref/a"], function (require, exports, a_1) {
+>>>    var B = (function (_super) {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >import {A} from "./ref/a";
+  >
+1 >Emitted(22, 5) Source(2, 1) + SourceIndex(2)
+---
+>>>        __extends(B, _super);
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^^^^^^^^^^
+1->export class B extends 
+2 >        A
+1->Emitted(23, 9) Source(2, 24) + SourceIndex(2) name (B)
+2 >Emitted(23, 30) Source(2, 25) + SourceIndex(2) name (B)
+---
+>>>        function B() {
+1 >^^^^^^^^
+2 >        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+1 >Emitted(24, 9) Source(2, 1) + SourceIndex(2) name (B)
+---
+>>>            _super.apply(this, arguments);
+1->^^^^^^^^^^^^
+2 >            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1->export class B extends 
+2 >            A
+1->Emitted(25, 13) Source(2, 24) + SourceIndex(2) name (B.constructor)
+2 >Emitted(25, 43) Source(2, 25) + SourceIndex(2) name (B.constructor)
+---
+>>>        }
+1 >^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^->
+1 > { 
+2 >        }
+1 >Emitted(26, 9) Source(2, 28) + SourceIndex(2) name (B.constructor)
+2 >Emitted(26, 10) Source(2, 29) + SourceIndex(2) name (B.constructor)
+---
+>>>        return B;
+1->^^^^^^^^
+2 >        ^^^^^^^^
+1->
+2 >        }
+1->Emitted(27, 9) Source(2, 28) + SourceIndex(2) name (B)
+2 >Emitted(27, 17) Source(2, 29) + SourceIndex(2) name (B)
+---
+>>>    })(a_1.A);
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^
+5 >       ^^^^^
+6 >            ^^
+7 >              ^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class B extends 
+5 >       A
+6 >             { }
+1 >Emitted(28, 5) Source(2, 28) + SourceIndex(2) name (B)
+2 >Emitted(28, 6) Source(2, 29) + SourceIndex(2) name (B)
+3 >Emitted(28, 6) Source(2, 1) + SourceIndex(2)
+4 >Emitted(28, 8) Source(2, 24) + SourceIndex(2)
+5 >Emitted(28, 13) Source(2, 25) + SourceIndex(2)
+6 >Emitted(28, 15) Source(2, 29) + SourceIndex(2)
+---
+>>>    exports.B = B;
+1->^^^^
+2 >    ^^^^^^^^^
+3 >             ^^^^
+4 >                 ^
+1->
+2 >    B
+3 >              extends A { }
+4 >                 
+1->Emitted(29, 5) Source(2, 14) + SourceIndex(2)
+2 >Emitted(29, 14) Source(2, 15) + SourceIndex(2)
+3 >Emitted(29, 18) Source(2, 29) + SourceIndex(2)
+4 >Emitted(29, 19) Source(2, 29) + SourceIndex(2)
+---
+>>>});
+>>>//# sourceMappingURL=all.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/outModuleTripleSlashRefs.symbols b/tests/baselines/reference/outModuleTripleSlashRefs.symbols
new file mode 100644
index 00000000000..f8d550aedb6
--- /dev/null
+++ b/tests/baselines/reference/outModuleTripleSlashRefs.symbols
@@ -0,0 +1,50 @@
+=== tests/cases/compiler/ref/a.ts ===
+
+/// <reference path="./b.ts" />
+export class A {
+>A : Symbol(A, Decl(a.ts, 0, 0))
+
+	member: typeof GlobalFoo;
+>member : Symbol(member, Decl(a.ts, 2, 16))
+>GlobalFoo : Symbol(GlobalFoo, Decl(b.ts, 4, 11))
+}
+
+=== tests/cases/compiler/ref/b.ts ===
+/// <reference path="./c.d.ts" />
+class Foo {
+>Foo : Symbol(Foo, Decl(b.ts, 0, 0))
+
+	member: Bar;
+>member : Symbol(member, Decl(b.ts, 1, 11))
+>Bar : Symbol(Bar, Decl(c.d.ts, 0, 0))
+}
+declare var GlobalFoo: Foo;
+>GlobalFoo : Symbol(GlobalFoo, Decl(b.ts, 4, 11))
+>Foo : Symbol(Foo, Decl(b.ts, 0, 0))
+
+=== tests/cases/compiler/ref/c.d.ts ===
+/// <reference path="./d.d.ts" />
+declare class Bar {
+>Bar : Symbol(Bar, Decl(c.d.ts, 0, 0))
+
+	member: Baz;
+>member : Symbol(member, Decl(c.d.ts, 1, 19))
+>Baz : Symbol(Baz, Decl(d.d.ts, 0, 0))
+}
+
+=== tests/cases/compiler/ref/d.d.ts ===
+declare class Baz {
+>Baz : Symbol(Baz, Decl(d.d.ts, 0, 0))
+
+	member: number;
+>member : Symbol(member, Decl(d.d.ts, 0, 19))
+}
+
+=== tests/cases/compiler/b.ts ===
+import {A} from "./ref/a";
+>A : Symbol(A, Decl(b.ts, 0, 8))
+
+export class B extends A { }
+>B : Symbol(B, Decl(b.ts, 0, 26))
+>A : Symbol(A, Decl(b.ts, 0, 8))
+
diff --git a/tests/baselines/reference/outModuleTripleSlashRefs.types b/tests/baselines/reference/outModuleTripleSlashRefs.types
new file mode 100644
index 00000000000..917704cce5a
--- /dev/null
+++ b/tests/baselines/reference/outModuleTripleSlashRefs.types
@@ -0,0 +1,50 @@
+=== tests/cases/compiler/ref/a.ts ===
+
+/// <reference path="./b.ts" />
+export class A {
+>A : A
+
+	member: typeof GlobalFoo;
+>member : Foo
+>GlobalFoo : Foo
+}
+
+=== tests/cases/compiler/ref/b.ts ===
+/// <reference path="./c.d.ts" />
+class Foo {
+>Foo : Foo
+
+	member: Bar;
+>member : Bar
+>Bar : Bar
+}
+declare var GlobalFoo: Foo;
+>GlobalFoo : Foo
+>Foo : Foo
+
+=== tests/cases/compiler/ref/c.d.ts ===
+/// <reference path="./d.d.ts" />
+declare class Bar {
+>Bar : Bar
+
+	member: Baz;
+>member : Baz
+>Baz : Baz
+}
+
+=== tests/cases/compiler/ref/d.d.ts ===
+declare class Baz {
+>Baz : Baz
+
+	member: number;
+>member : number
+}
+
+=== tests/cases/compiler/b.ts ===
+import {A} from "./ref/a";
+>A : typeof A
+
+export class B extends A { }
+>B : B
+>A : A
+
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index 7ef36232b8d..af837fd2031 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
index a1d591a0497..94371fe696d 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
index ee020b0ff80..2f0cd8e1230 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
index 133c266cc9e..94348f987ce 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: /tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map
-sourceRoot: 
-sources: ../../ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:../../ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map===================================================================
 JsFile: test.js
 mapUrl: /tests/cases/projects/outputdir_mixed_subfolder/mapFiles/test.js.map
 sourceRoot: 
-sources: ../ref/m1.ts,../test.ts
+sources: ../ref/m1.ts,../ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -306,7 +134,7 @@ sourceFile:../ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:../ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
+sourceFile:../ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
 sourceFile:../test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:../test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:../test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:../test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:../test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:../test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:../test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index 9dad0db002a..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
deleted file mode 100644
index 0e907c1a2ca..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
index a1d591a0497..a580c050d07 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
index ee020b0ff80..2f0cd8e1230 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
index 0b573b627cf..3f16355ad76 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: /tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map
-sourceRoot: 
-sources: ../../ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:../../ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map===================================================================
 JsFile: test.js
 mapUrl: /tests/cases/projects/outputdir_mixed_subfolder/mapFiles/test.js.map
 sourceRoot: 
-sources: ../ref/m1.ts,../test.ts
+sources: ../ref/m1.ts,../ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -322,8 +151,8 @@ sourceFile:../test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:../test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:../test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:../test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:../test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:../test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:../test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index 3eaebd5c136..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
deleted file mode 100644
index cbb2dc36492..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index fc53d59d7cb..de704afeedb 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
index 4f87045fd25..22aaecafe2d 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../ref/m1.ts","../ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index ed7bcd289e7..24fb56c1fd2 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -18,9 +18,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index a9e2e3f0e3c..c0dbdb42cdf 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: /tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map
-sourceRoot: 
-sources: ../../ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:../../ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: /tests/cases/projects/outputdir_mixed_subfolder/mapFiles/outAndOutDirFile.js.map
 sourceRoot: 
-sources: ../ref/m1.ts,../test.ts
+sources: ../ref/m1.ts,../ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -306,7 +134,7 @@ sourceFile:../ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:../ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
+sourceFile:../ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/outAndOutDirFile.js
 sourceFile:../test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:../test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:../test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:../test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:../test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:../test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:../test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index 9dad0db002a..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 0e907c1a2ca..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
index 4f87045fd25..2eab0f87324 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../ref/m1.ts","../ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index ed7bcd289e7..24fb56c1fd2 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -18,9 +18,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index c4c267ec395..963b3f3bb22 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: /tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map
-sourceRoot: 
-sources: ../../ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:../../ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: /tests/cases/projects/outputdir_mixed_subfolder/mapFiles/outAndOutDirFile.js.map
 sourceRoot: 
-sources: ../ref/m1.ts,../test.ts
+sources: ../ref/m1.ts,../ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -322,8 +151,8 @@ sourceFile:../test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:../test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:../test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:../test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:../test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:../test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:../test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index 3eaebd5c136..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_mixed_subfolder/mapFiles/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index cbb2dc36492..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index 18e06e5bc50..25cd156c4ab 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,45 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
 //# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..c532c3846d9 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../../outputdir_module_multifolder_ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICNU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
deleted file mode 100644
index b02c7fdd8c2..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../../outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
deleted file mode 100644
index 8fe95a1506f..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder_ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
index 6432d5ae91e..4869993ca92 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
@@ -17,15 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
index da94013dea3..4462b142d98 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/ref/m1.js.map
+JsFile: test.js
+mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/test.js.map
 sourceRoot: 
-sources: ../../../ref/m1.ts
+sources: ../ref/m1.ts,../../outputdir_module_multifolder_ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:../../../ref/m1.ts
+emittedFile:bin/test.js
+sourceFile:../ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:../../../ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
+sourceFile:../../outputdir_module_multifolder_ref/m2.ts
+-------------------------------------------------------------------
 >>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/ref/m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder_ref/m2.js.map
-sourceRoot: 
-sources: ../../../outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
 >>>    exports.m2_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -193,24 +187,24 @@ sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
 3 >                  = 
 4 >                    10
 5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
+1 >Emitted(16, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(16, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(16, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(16, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(16, 24) Source(1, 23) + SourceIndex(1)
 ---
 >>>    var m2_c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(2, 1) + SourceIndex(1)
 ---
 >>>        function m2_c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
+1->Emitted(18, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -220,16 +214,16 @@ sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
   >    public m2_c1_p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
+1->Emitted(19, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(19, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
 ---
 >>>        return m2_c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
+1->Emitted(20, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(20, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
 ---
 >>>    })();
 1 >^^^^
@@ -243,10 +237,10 @@ sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
 4 >     export class m2_c1 {
   >         public m2_c1_p1: number;
   >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(21, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_c1 = m2_c1;
 1->^^^^
@@ -260,10 +254,10 @@ sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
   >                     public m2_c1_p1: number;
   >                 }
 4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(22, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(22, 27) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_instance1 = new m2_c1();
 1->^^^^
@@ -282,20 +276,20 @@ sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
 5 >                               m2_c1
 6 >                                    ()
 7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
+1->Emitted(23, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(23, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(23, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(23, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(23, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(23, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(23, 40) Source(6, 39) + SourceIndex(1)
 ---
 >>>    function m2_f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(7, 1) + SourceIndex(1)
 ---
 >>>        return exports.m2_instance1;
 1->^^^^^^^^
@@ -309,11 +303,11 @@ sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
 3 >               
 4 >               m2_instance1
 5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
+1->Emitted(25, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(25, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(25, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(25, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(25, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
 ---
 >>>    }
 1 >^^^^
@@ -322,8 +316,8 @@ sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
+1 >Emitted(26, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(26, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
 ---
 >>>    exports.m2_f1 = m2_f1;
 1->^^^^
@@ -336,23 +330,17 @@ sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
   >                     return m2_instance1;
   >                 }
 4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(27, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(27, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(27, 27) Source(9, 2) + SourceIndex(1)
 ---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
+sourceFile:../test.ts
+-------------------------------------------------------------------
 >>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder_ref/m2.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/test.js.map
-sourceRoot: 
-sources: ../../test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:../../test.ts
--------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+>>>define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -367,24 +355,24 @@ sourceFile:../../test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(3, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(3, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(3, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(3, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(3, 20) + SourceIndex(0)
+1 >Emitted(30, 5) Source(3, 12) + SourceIndex(2)
+2 >Emitted(30, 15) Source(3, 14) + SourceIndex(2)
+3 >Emitted(30, 18) Source(3, 17) + SourceIndex(2)
+4 >Emitted(30, 20) Source(3, 19) + SourceIndex(2)
+5 >Emitted(30, 21) Source(3, 20) + SourceIndex(2)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(4, 1) + SourceIndex(0)
+1->Emitted(31, 5) Source(4, 1) + SourceIndex(2)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(4, 1) + SourceIndex(0) name (c1)
+1->Emitted(32, 9) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -394,16 +382,16 @@ sourceFile:../../test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(6, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(33, 9) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(33, 10) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(6, 2) + SourceIndex(0) name (c1)
+1->Emitted(34, 9) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(34, 18) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -417,10 +405,10 @@ sourceFile:../../test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(4, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(6, 2) + SourceIndex(0)
+1 >Emitted(35, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(35, 6) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(35, 6) Source(4, 1) + SourceIndex(2)
+4 >Emitted(35, 10) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -434,10 +422,10 @@ sourceFile:../../test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(4, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(4, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(6, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(6, 2) + SourceIndex(0)
+1->Emitted(36, 5) Source(4, 14) + SourceIndex(2)
+2 >Emitted(36, 15) Source(4, 16) + SourceIndex(2)
+3 >Emitted(36, 20) Source(6, 2) + SourceIndex(2)
+4 >Emitted(36, 21) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -456,20 +444,20 @@ sourceFile:../../test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(8, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(8, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(8, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(8, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(8, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(8, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(8, 33) + SourceIndex(0)
+1->Emitted(37, 5) Source(8, 12) + SourceIndex(2)
+2 >Emitted(37, 22) Source(8, 21) + SourceIndex(2)
+3 >Emitted(37, 25) Source(8, 24) + SourceIndex(2)
+4 >Emitted(37, 29) Source(8, 28) + SourceIndex(2)
+5 >Emitted(37, 31) Source(8, 30) + SourceIndex(2)
+6 >Emitted(37, 33) Source(8, 32) + SourceIndex(2)
+7 >Emitted(37, 34) Source(8, 33) + SourceIndex(2)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(9, 1) + SourceIndex(0)
+1 >Emitted(38, 5) Source(9, 1) + SourceIndex(2)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -483,11 +471,11 @@ sourceFile:../../test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(10, 22) + SourceIndex(0) name (f1)
+1->Emitted(39, 9) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(39, 15) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(39, 16) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(39, 33) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(39, 34) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -496,8 +484,8 @@ sourceFile:../../test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(11, 2) + SourceIndex(0) name (f1)
+1 >Emitted(40, 5) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(40, 6) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -511,10 +499,10 @@ sourceFile:../../test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(9, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(9, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(11, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(11, 2) + SourceIndex(0)
+1->Emitted(41, 5) Source(9, 17) + SourceIndex(2)
+2 >Emitted(41, 15) Source(9, 19) + SourceIndex(2)
+3 >Emitted(41, 20) Source(11, 2) + SourceIndex(2)
+4 >Emitted(41, 21) Source(11, 2) + SourceIndex(2)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -534,13 +522,13 @@ sourceFile:../../test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(13, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(13, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(13, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(13, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(13, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(13, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(13, 26) + SourceIndex(0)
+1->Emitted(42, 5) Source(13, 12) + SourceIndex(2)
+2 >Emitted(42, 15) Source(13, 14) + SourceIndex(2)
+3 >Emitted(42, 18) Source(13, 17) + SourceIndex(2)
+4 >Emitted(42, 20) Source(13, 19) + SourceIndex(2)
+5 >Emitted(42, 21) Source(13, 20) + SourceIndex(2)
+6 >Emitted(42, 26) Source(13, 25) + SourceIndex(2)
+7 >Emitted(42, 27) Source(13, 26) + SourceIndex(2)
 ---
 >>>    exports.a3 = m2.m2_c1;
 1->^^^^
@@ -558,19 +546,13 @@ sourceFile:../../test.ts
 5 >                   .
 6 >                    m2_c1
 7 >                         ;
-1->Emitted(15, 5) Source(14, 12) + SourceIndex(0)
-2 >Emitted(15, 15) Source(14, 14) + SourceIndex(0)
-3 >Emitted(15, 18) Source(14, 17) + SourceIndex(0)
-4 >Emitted(15, 20) Source(14, 19) + SourceIndex(0)
-5 >Emitted(15, 21) Source(14, 20) + SourceIndex(0)
-6 >Emitted(15, 26) Source(14, 25) + SourceIndex(0)
-7 >Emitted(15, 27) Source(14, 26) + SourceIndex(0)
+1->Emitted(43, 5) Source(14, 12) + SourceIndex(2)
+2 >Emitted(43, 15) Source(14, 14) + SourceIndex(2)
+3 >Emitted(43, 18) Source(14, 17) + SourceIndex(2)
+4 >Emitted(43, 20) Source(14, 19) + SourceIndex(2)
+5 >Emitted(43, 21) Source(14, 20) + SourceIndex(2)
+6 >Emitted(43, 26) Source(14, 25) + SourceIndex(2)
+7 >Emitted(43, 27) Source(14, 26) + SourceIndex(2)
 ---
 >>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/test.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index 52b5e682660..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 652d934d602..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../../../ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index a2a29b4dcfc..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index be0b3a580f5..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../../test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IAEW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..2974abdc1cc 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../../outputdir_module_multifolder_ref/m2.ts","../test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
deleted file mode 100644
index f9d0dd89e9c..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../../outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js
deleted file mode 100644
index 589c5838a2c..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder_ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
index 6432d5ae91e..4869993ca92 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
@@ -17,15 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
index f348cfad93c..5b0497285e2 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,620 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/ref/m1.js.map
-sourceRoot: 
-sources: ../../../ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:../../../ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/ref/m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder_ref/m2.js.map
-sourceRoot: 
-sources: ../../../outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:../../../outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder_ref/m2.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/test.js.map
-sourceRoot: 
-sources: ../../test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:../../test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-8 >                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>var m2 = require("../outputdir_module_multifolder_ref/m2");
-1->
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-6 >                                                         ^
-7 >                                                          ^
-1->
-  >
-2 >import 
-3 >    m2
-4 >       = require(
-5 >                 "../outputdir_module_multifolder_ref/m2"
-6 >                                                         )
-7 >                                                          ;
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
-2 >Emitted(2, 5) Source(2, 8) + SourceIndex(0)
-3 >Emitted(2, 7) Source(2, 10) + SourceIndex(0)
-4 >Emitted(2, 18) Source(2, 21) + SourceIndex(0)
-5 >Emitted(2, 58) Source(2, 61) + SourceIndex(0)
-6 >Emitted(2, 59) Source(2, 62) + SourceIndex(0)
-7 >Emitted(2, 60) Source(2, 63) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(3, 1) Source(3, 12) + SourceIndex(0)
-2 >Emitted(3, 11) Source(3, 14) + SourceIndex(0)
-3 >Emitted(3, 14) Source(3, 17) + SourceIndex(0)
-4 >Emitted(3, 16) Source(3, 19) + SourceIndex(0)
-5 >Emitted(3, 17) Source(3, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(4, 1) Source(4, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(6, 5) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(6, 6) Source(6, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 14) Source(6, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(8, 1) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(8, 2) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(8, 2) Source(4, 1) + SourceIndex(0)
-4 >Emitted(8, 6) Source(6, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(9, 1) Source(4, 14) + SourceIndex(0)
-2 >Emitted(9, 11) Source(4, 16) + SourceIndex(0)
-3 >Emitted(9, 16) Source(6, 2) + SourceIndex(0)
-4 >Emitted(9, 17) Source(6, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(10, 1) Source(8, 12) + SourceIndex(0)
-2 >Emitted(10, 18) Source(8, 21) + SourceIndex(0)
-3 >Emitted(10, 21) Source(8, 24) + SourceIndex(0)
-4 >Emitted(10, 25) Source(8, 28) + SourceIndex(0)
-5 >Emitted(10, 27) Source(8, 30) + SourceIndex(0)
-6 >Emitted(10, 29) Source(8, 32) + SourceIndex(0)
-7 >Emitted(10, 30) Source(8, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(12, 5) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(12, 11) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(12, 12) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(12, 29) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(12, 30) Source(10, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(13, 1) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(13, 2) Source(11, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(14, 1) Source(9, 17) + SourceIndex(0)
-2 >Emitted(14, 11) Source(9, 19) + SourceIndex(0)
-3 >Emitted(14, 16) Source(11, 2) + SourceIndex(0)
-4 >Emitted(14, 17) Source(11, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(15, 1) Source(13, 12) + SourceIndex(0)
-2 >Emitted(15, 11) Source(13, 14) + SourceIndex(0)
-3 >Emitted(15, 14) Source(13, 17) + SourceIndex(0)
-4 >Emitted(15, 16) Source(13, 19) + SourceIndex(0)
-5 >Emitted(15, 17) Source(13, 20) + SourceIndex(0)
-6 >Emitted(15, 22) Source(13, 25) + SourceIndex(0)
-7 >Emitted(15, 23) Source(13, 26) + SourceIndex(0)
----
->>>exports.a3 = m2.m2_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >export var 
-2 >a3
-3 >           = 
-4 >             m2
-5 >               .
-6 >                m2_c1
-7 >                     ;
-1->Emitted(16, 1) Source(14, 12) + SourceIndex(0)
-2 >Emitted(16, 11) Source(14, 14) + SourceIndex(0)
-3 >Emitted(16, 14) Source(14, 17) + SourceIndex(0)
-4 >Emitted(16, 16) Source(14, 19) + SourceIndex(0)
-5 >Emitted(16, 17) Source(14, 20) + SourceIndex(0)
-6 >Emitted(16, 22) Source(14, 25) + SourceIndex(0)
-7 >Emitted(16, 23) Source(14, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/test.js.map===================================================================
 JsFile: test.js
 mapUrl: /tests/cases/projects/outputdir_module_multifolder/mapFiles/test.js.map
 sourceRoot: 
-sources: 
+sources: ../ref/m1.ts,../../outputdir_module_multifolder_ref/m2.ts,../test.ts
 ===================================================================
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index b0e6a265bc9..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 15bddd32fe5..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../../../ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 16422a234c5..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_multifolder/mapFiles/outputdir_module_multifolder/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index eae921435ac..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../../test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AAC9B,IAAO,EAAE,WAAW,wCAAwC,CAAC,CAAC;AACnD,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;AACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
index f6e3eb542f4..d3d9bd9dc85 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..6377a26395e 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index 86c0ba41238..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js.map
deleted file mode 100644
index 7f5576a8a9c..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.json
index f703a63b71f..742acdc7a25 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
index 759b9dab302..d8ab3db1266 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: /tests/cases/projects/outputdir_module_simple/mapFiles/m1.js.map
+JsFile: test.js
+mapUrl: /tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
 sourceRoot: 
-sources: ../m1.ts
+sources: ../m1.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:m1.js
+emittedFile:bin/test.js
 sourceFile:../m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:../m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
-sourceRoot: 
-sources: ../test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:../test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:../test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:../test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:../test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:../test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:../test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:../test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:../test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:../test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 6e24571a3f2..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 80d6bbf450b..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..f491a9ec373 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../m1.ts","../test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index c8a4f5c91a4..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js.map
deleted file mode 100644
index ce271e4a3cd..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.json
index f703a63b71f..742acdc7a25 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
index 75228e5ea64..1eef0eba6f2 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/mapRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: /tests/cases/projects/outputdir_module_simple/mapFiles/m1.js.map
-sourceRoot: 
-sources: ../m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:../m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/m1.js.map===================================================================
 JsFile: test.js
 mapUrl: /tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
 sourceRoot: 
-sources: ../test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:../test.ts
--------------------------------------------------------------------
->>>var m1 = require("m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^
-6 >                     ^
-7 >                      ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "m1"
-6 >                     )
-7 >                      ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 22) Source(1, 25) + SourceIndex(0)
-6 >Emitted(1, 23) Source(1, 26) + SourceIndex(0)
-7 >Emitted(1, 24) Source(1, 27) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
-sourceRoot: 
-sources: 
+sources: ../m1.ts,../test.ts
 ===================================================================
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index 080dcf6e818..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_simple/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index de9ec1f9859..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,IAAI,CAAC,CAAC;AACf,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index 7ff280253f1..176c3f78407 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..f77c1351b15 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
index d8f4cc74008..21d6e50f28a 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 18b397608e4..d63cf86d236 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: /tests/cases/projects/outputdir_module_subfolder/mapFiles/ref/m1.js.map
+JsFile: test.js
+mapUrl: /tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
 sourceRoot: 
-sources: ../../ref/m1.ts
+sources: ../ref/m1.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:../../ref/m1.ts
+emittedFile:bin/test.js
+sourceFile:../ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:../../ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/ref/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
-sourceRoot: 
-sources: ../test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:../test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:../test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:../test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:../test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:../test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:../test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:../test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:../test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:../test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index e819d557c40..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 88e67e19b36..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../../ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 3b2cd1a24c4..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 80d6bbf450b..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..bfdacf69428 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
index d8f4cc74008..21d6e50f28a 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 97c6b8a85e4..20f2ab47188 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: /tests/cases/projects/outputdir_module_subfolder/mapFiles/ref/m1.js.map
-sourceRoot: 
-sources: ../../ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:../../ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/ref/m1.js.map===================================================================
 JsFile: test.js
 mapUrl: /tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
 sourceRoot: 
-sources: ../test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:../test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map===================================================================
-JsFile: test.js
-mapUrl: /tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
-sourceRoot: 
-sources: 
+sources: ../ref/m1.ts,../test.ts
 ===================================================================
 >>>//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index a420241c901..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 420650feeac..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../../ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index f6319258d8f..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=/tests/cases/projects/outputdir_module_subfolder/mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 15d4e3e1c9b..00000000000
--- a/tests/baselines/reference/project/mapRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AACnB,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/node/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/node/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/node/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/node/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/node/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/node/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSingleFileSpecifyOutputFile/node/mapRootAbsolutePathSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSingleFileSpecifyOutputFile/node/mapRootAbsolutePathSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSingleFileSpecifyOutputFile/node/mapRootAbsolutePathSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/node/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/node/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/node/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index c4c79e0454b..bd14cd07502 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
index b63911a2bc8..ca8dd0934b5 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_mixed_subfolder/ref/m1.ts","../outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_mixed_subfolder/ref/m1.ts","../outputdir_mixed_subfolder/ref/m2.ts","../outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.json
index 8e87f61b8df..f3b0bdd119e 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
index f1cc6df9de8..cfd0952c941 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: ../../mapFiles/ref/m2.js.map
-sourceRoot: 
-sources: ../../outputdir_mixed_subfolder/ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:../../outputdir_mixed_subfolder/ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=../../mapFiles/ref/m2.js.map===================================================================
 JsFile: test.js
 mapUrl: ../../mapFiles/test.js.map
 sourceRoot: 
-sources: ../outputdir_mixed_subfolder/ref/m1.ts,../outputdir_mixed_subfolder/test.ts
+sources: ../outputdir_mixed_subfolder/ref/m1.ts,../outputdir_mixed_subfolder/ref/m2.ts,../outputdir_mixed_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -306,7 +134,7 @@ sourceFile:../outputdir_mixed_subfolder/ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:../outputdir_mixed_subfolder/ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
+sourceFile:../outputdir_mixed_subfolder/ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
 sourceFile:../outputdir_mixed_subfolder/test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index 4f0b35f21c7..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=../../mapFiles/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
deleted file mode 100644
index 81bb9202e5a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../outputdir_mixed_subfolder/ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
index b63911a2bc8..02be1ec09fb 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_mixed_subfolder/ref/m1.ts","../outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_mixed_subfolder/ref/m1.ts","../outputdir_mixed_subfolder/ref/m2.ts","../outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.json
index 8e87f61b8df..f3b0bdd119e 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
index 0a373a20359..931a09b3ae6 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: ../../mapFiles/ref/m2.js.map
-sourceRoot: 
-sources: ../../outputdir_mixed_subfolder/ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:../../outputdir_mixed_subfolder/ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=../../mapFiles/ref/m2.js.map===================================================================
 JsFile: test.js
 mapUrl: ../../mapFiles/test.js.map
 sourceRoot: 
-sources: ../outputdir_mixed_subfolder/ref/m1.ts,../outputdir_mixed_subfolder/test.ts
+sources: ../outputdir_mixed_subfolder/ref/m1.ts,../outputdir_mixed_subfolder/ref/m2.ts,../outputdir_mixed_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -322,8 +151,8 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index f13773b3384..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=../../mapFiles/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
deleted file mode 100644
index 98da596cfa4..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../outputdir_mixed_subfolder/ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index c0138423cae..59405bccb9c 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
index 630508cb9f8..794d2a58176 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../outputdir_mixed_subfolder/ref/m1.ts","../outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../outputdir_mixed_subfolder/ref/m1.ts","../outputdir_mixed_subfolder/ref/m2.ts","../outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 4ed441e2552..0d6c009961b 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index fd08e128cfe..cb14a553f05 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: ../../../../mapFiles/ref/m2.js.map
-sourceRoot: 
-sources: ../../outputdir_mixed_subfolder/ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:../../outputdir_mixed_subfolder/ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=../../../../mapFiles/ref/m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: ../../mapFiles/outAndOutDirFile.js.map
 sourceRoot: 
-sources: ../outputdir_mixed_subfolder/ref/m1.ts,../outputdir_mixed_subfolder/test.ts
+sources: ../outputdir_mixed_subfolder/ref/m1.ts,../outputdir_mixed_subfolder/ref/m2.ts,../outputdir_mixed_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -306,7 +134,7 @@ sourceFile:../outputdir_mixed_subfolder/ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:../outputdir_mixed_subfolder/ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
+sourceFile:../outputdir_mixed_subfolder/ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/outAndOutDirFile.js
 sourceFile:../outputdir_mixed_subfolder/test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=../../mapFiles/outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index e4c8f7b3610..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=../../../../mapFiles/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 81bb9202e5a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../outputdir_mixed_subfolder/ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
index 630508cb9f8..43710b5f061 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../outputdir_mixed_subfolder/ref/m1.ts","../outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../outputdir_mixed_subfolder/ref/m1.ts","../outputdir_mixed_subfolder/ref/m2.ts","../outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 4ed441e2552..0d6c009961b 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index eb9ad2993b2..eddbc79711c 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: ../../../../mapFiles/ref/m2.js.map
-sourceRoot: 
-sources: ../../outputdir_mixed_subfolder/ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:../../outputdir_mixed_subfolder/ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=../../../../mapFiles/ref/m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: ../../mapFiles/outAndOutDirFile.js.map
 sourceRoot: 
-sources: ../outputdir_mixed_subfolder/ref/m1.ts,../outputdir_mixed_subfolder/test.ts
+sources: ../outputdir_mixed_subfolder/ref/m1.ts,../outputdir_mixed_subfolder/ref/m2.ts,../outputdir_mixed_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -322,8 +151,8 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:../outputdir_mixed_subfolder/test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=../../mapFiles/outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index d78261fe225..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=../../../../mapFiles/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 98da596cfa4..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../outputdir_mixed_subfolder/ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index f359cef4be2..8b109433561 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,45 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
 //# sourceMappingURL=../../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..a7235c6c2b3 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../projects/outputdir_module_multifolder/ref/m1.ts","../projects/outputdir_module_multifolder_ref/m2.ts","../projects/outputdir_module_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICNU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
deleted file mode 100644
index 9745ad1a4ab..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../projects/outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
deleted file mode 100644
index ad9b3f68611..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=../../mapFiles/outputdir_module_multifolder_ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/mapRootRelativePathModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/mapRootRelativePathModuleMultifolderSpecifyOutputFile.json
index f3c86f22eb7..283c0703f90 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/mapRootRelativePathModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/mapRootRelativePathModuleMultifolderSpecifyOutputFile.json
@@ -16,15 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/mapRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/mapRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
index c2eacec3bdc..47e1835365a 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/mapRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/mapRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: ../../../mapFiles/outputdir_module_multifolder/ref/m1.js.map
+JsFile: test.js
+mapUrl: ../../../mapFiles/test.js.map
 sourceRoot: 
-sources: ../../../projects/outputdir_module_multifolder/ref/m1.ts
+sources: ../projects/outputdir_module_multifolder/ref/m1.ts,../projects/outputdir_module_multifolder_ref/m2.ts,../projects/outputdir_module_multifolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:../../../projects/outputdir_module_multifolder/ref/m1.ts
+emittedFile:bin/test.js
+sourceFile:../projects/outputdir_module_multifolder/ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:../../../projects/outputdir_module_multifolder/ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
+sourceFile:../projects/outputdir_module_multifolder_ref/m2.ts
+-------------------------------------------------------------------
 >>>});
->>>//# sourceMappingURL=../../../mapFiles/outputdir_module_multifolder/ref/m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: ../../mapFiles/outputdir_module_multifolder_ref/m2.js.map
-sourceRoot: 
-sources: ../../projects/outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
 >>>    exports.m2_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -193,24 +187,24 @@ sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
 3 >                  = 
 4 >                    10
 5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
+1 >Emitted(16, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(16, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(16, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(16, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(16, 24) Source(1, 23) + SourceIndex(1)
 ---
 >>>    var m2_c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(2, 1) + SourceIndex(1)
 ---
 >>>        function m2_c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
+1->Emitted(18, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -220,16 +214,16 @@ sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
   >    public m2_c1_p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
+1->Emitted(19, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(19, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
 ---
 >>>        return m2_c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
+1->Emitted(20, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(20, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
 ---
 >>>    })();
 1 >^^^^
@@ -243,10 +237,10 @@ sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
 4 >     export class m2_c1 {
   >         public m2_c1_p1: number;
   >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(21, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_c1 = m2_c1;
 1->^^^^
@@ -260,10 +254,10 @@ sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
   >                     public m2_c1_p1: number;
   >                 }
 4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(22, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(22, 27) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_instance1 = new m2_c1();
 1->^^^^
@@ -282,20 +276,20 @@ sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
 5 >                               m2_c1
 6 >                                    ()
 7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
+1->Emitted(23, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(23, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(23, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(23, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(23, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(23, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(23, 40) Source(6, 39) + SourceIndex(1)
 ---
 >>>    function m2_f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(7, 1) + SourceIndex(1)
 ---
 >>>        return exports.m2_instance1;
 1->^^^^^^^^
@@ -309,11 +303,11 @@ sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
 3 >               
 4 >               m2_instance1
 5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
+1->Emitted(25, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(25, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(25, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(25, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(25, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
 ---
 >>>    }
 1 >^^^^
@@ -322,8 +316,8 @@ sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
+1 >Emitted(26, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(26, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
 ---
 >>>    exports.m2_f1 = m2_f1;
 1->^^^^
@@ -336,23 +330,17 @@ sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
   >                     return m2_instance1;
   >                 }
 4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(27, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(27, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(27, 27) Source(9, 2) + SourceIndex(1)
 ---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
+sourceFile:../projects/outputdir_module_multifolder/test.ts
+-------------------------------------------------------------------
 >>>});
->>>//# sourceMappingURL=../../mapFiles/outputdir_module_multifolder_ref/m2.js.map===================================================================
-JsFile: test.js
-mapUrl: ../../mapFiles/outputdir_module_multifolder/test.js.map
-sourceRoot: 
-sources: ../../projects/outputdir_module_multifolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:../../projects/outputdir_module_multifolder/test.ts
--------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+>>>define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -367,24 +355,24 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(3, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(3, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(3, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(3, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(3, 20) + SourceIndex(0)
+1 >Emitted(30, 5) Source(3, 12) + SourceIndex(2)
+2 >Emitted(30, 15) Source(3, 14) + SourceIndex(2)
+3 >Emitted(30, 18) Source(3, 17) + SourceIndex(2)
+4 >Emitted(30, 20) Source(3, 19) + SourceIndex(2)
+5 >Emitted(30, 21) Source(3, 20) + SourceIndex(2)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(4, 1) + SourceIndex(0)
+1->Emitted(31, 5) Source(4, 1) + SourceIndex(2)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(4, 1) + SourceIndex(0) name (c1)
+1->Emitted(32, 9) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -394,16 +382,16 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(6, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(33, 9) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(33, 10) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(6, 2) + SourceIndex(0) name (c1)
+1->Emitted(34, 9) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(34, 18) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -417,10 +405,10 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(4, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(6, 2) + SourceIndex(0)
+1 >Emitted(35, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(35, 6) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(35, 6) Source(4, 1) + SourceIndex(2)
+4 >Emitted(35, 10) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -434,10 +422,10 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(4, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(4, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(6, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(6, 2) + SourceIndex(0)
+1->Emitted(36, 5) Source(4, 14) + SourceIndex(2)
+2 >Emitted(36, 15) Source(4, 16) + SourceIndex(2)
+3 >Emitted(36, 20) Source(6, 2) + SourceIndex(2)
+4 >Emitted(36, 21) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -456,20 +444,20 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(8, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(8, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(8, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(8, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(8, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(8, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(8, 33) + SourceIndex(0)
+1->Emitted(37, 5) Source(8, 12) + SourceIndex(2)
+2 >Emitted(37, 22) Source(8, 21) + SourceIndex(2)
+3 >Emitted(37, 25) Source(8, 24) + SourceIndex(2)
+4 >Emitted(37, 29) Source(8, 28) + SourceIndex(2)
+5 >Emitted(37, 31) Source(8, 30) + SourceIndex(2)
+6 >Emitted(37, 33) Source(8, 32) + SourceIndex(2)
+7 >Emitted(37, 34) Source(8, 33) + SourceIndex(2)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(9, 1) + SourceIndex(0)
+1 >Emitted(38, 5) Source(9, 1) + SourceIndex(2)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -483,11 +471,11 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(10, 22) + SourceIndex(0) name (f1)
+1->Emitted(39, 9) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(39, 15) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(39, 16) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(39, 33) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(39, 34) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -496,8 +484,8 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(11, 2) + SourceIndex(0) name (f1)
+1 >Emitted(40, 5) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(40, 6) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -511,10 +499,10 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(9, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(9, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(11, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(11, 2) + SourceIndex(0)
+1->Emitted(41, 5) Source(9, 17) + SourceIndex(2)
+2 >Emitted(41, 15) Source(9, 19) + SourceIndex(2)
+3 >Emitted(41, 20) Source(11, 2) + SourceIndex(2)
+4 >Emitted(41, 21) Source(11, 2) + SourceIndex(2)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -534,13 +522,13 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(13, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(13, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(13, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(13, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(13, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(13, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(13, 26) + SourceIndex(0)
+1->Emitted(42, 5) Source(13, 12) + SourceIndex(2)
+2 >Emitted(42, 15) Source(13, 14) + SourceIndex(2)
+3 >Emitted(42, 18) Source(13, 17) + SourceIndex(2)
+4 >Emitted(42, 20) Source(13, 19) + SourceIndex(2)
+5 >Emitted(42, 21) Source(13, 20) + SourceIndex(2)
+6 >Emitted(42, 26) Source(13, 25) + SourceIndex(2)
+7 >Emitted(42, 27) Source(13, 26) + SourceIndex(2)
 ---
 >>>    exports.a3 = m2.m2_c1;
 1->^^^^
@@ -558,19 +546,13 @@ sourceFile:../../projects/outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m2_c1
 7 >                         ;
-1->Emitted(15, 5) Source(14, 12) + SourceIndex(0)
-2 >Emitted(15, 15) Source(14, 14) + SourceIndex(0)
-3 >Emitted(15, 18) Source(14, 17) + SourceIndex(0)
-4 >Emitted(15, 20) Source(14, 19) + SourceIndex(0)
-5 >Emitted(15, 21) Source(14, 20) + SourceIndex(0)
-6 >Emitted(15, 26) Source(14, 25) + SourceIndex(0)
-7 >Emitted(15, 27) Source(14, 26) + SourceIndex(0)
+1->Emitted(43, 5) Source(14, 12) + SourceIndex(2)
+2 >Emitted(43, 15) Source(14, 14) + SourceIndex(2)
+3 >Emitted(43, 18) Source(14, 17) + SourceIndex(2)
+4 >Emitted(43, 20) Source(14, 19) + SourceIndex(2)
+5 >Emitted(43, 21) Source(14, 20) + SourceIndex(2)
+6 >Emitted(43, 26) Source(14, 25) + SourceIndex(2)
+7 >Emitted(43, 27) Source(14, 26) + SourceIndex(2)
 ---
 >>>});
->>>//# sourceMappingURL=../../mapFiles/outputdir_module_multifolder/test.js.map===================================================================
-JsFile: test.js
-mapUrl: ../../../mapFiles/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=../../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index 09fbf68994d..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=../../../mapFiles/outputdir_module_multifolder/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index e7200adafdb..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../../../projects/outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 90dee0800c7..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
-//# sourceMappingURL=../../mapFiles/outputdir_module_multifolder/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index f2b1ea70110..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../../projects/outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IAEW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..ca280b23052 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../projects/outputdir_module_multifolder/ref/m1.ts","../projects/outputdir_module_multifolder_ref/m2.ts","../projects/outputdir_module_multifolder/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
deleted file mode 100644
index c2ac2bc2710..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../projects/outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js
deleted file mode 100644
index 573ce2ac6c5..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=../../mapFiles/outputdir_module_multifolder_ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.json
index f3c86f22eb7..283c0703f90 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.json
@@ -16,15 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
index 1d6a282976d..ce08ef2c878 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/mapRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,620 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: ../../../mapFiles/outputdir_module_multifolder/ref/m1.js.map
-sourceRoot: 
-sources: ../../../projects/outputdir_module_multifolder/ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:../../../projects/outputdir_module_multifolder/ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=../../../mapFiles/outputdir_module_multifolder/ref/m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: ../../mapFiles/outputdir_module_multifolder_ref/m2.js.map
-sourceRoot: 
-sources: ../../projects/outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:../../projects/outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=../../mapFiles/outputdir_module_multifolder_ref/m2.js.map===================================================================
-JsFile: test.js
-mapUrl: ../../mapFiles/outputdir_module_multifolder/test.js.map
-sourceRoot: 
-sources: ../../projects/outputdir_module_multifolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:../../projects/outputdir_module_multifolder/test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-8 >                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>var m2 = require("../outputdir_module_multifolder_ref/m2");
-1->
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-6 >                                                         ^
-7 >                                                          ^
-1->
-  >
-2 >import 
-3 >    m2
-4 >       = require(
-5 >                 "../outputdir_module_multifolder_ref/m2"
-6 >                                                         )
-7 >                                                          ;
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
-2 >Emitted(2, 5) Source(2, 8) + SourceIndex(0)
-3 >Emitted(2, 7) Source(2, 10) + SourceIndex(0)
-4 >Emitted(2, 18) Source(2, 21) + SourceIndex(0)
-5 >Emitted(2, 58) Source(2, 61) + SourceIndex(0)
-6 >Emitted(2, 59) Source(2, 62) + SourceIndex(0)
-7 >Emitted(2, 60) Source(2, 63) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(3, 1) Source(3, 12) + SourceIndex(0)
-2 >Emitted(3, 11) Source(3, 14) + SourceIndex(0)
-3 >Emitted(3, 14) Source(3, 17) + SourceIndex(0)
-4 >Emitted(3, 16) Source(3, 19) + SourceIndex(0)
-5 >Emitted(3, 17) Source(3, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(4, 1) Source(4, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(6, 5) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(6, 6) Source(6, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 14) Source(6, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(8, 1) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(8, 2) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(8, 2) Source(4, 1) + SourceIndex(0)
-4 >Emitted(8, 6) Source(6, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(9, 1) Source(4, 14) + SourceIndex(0)
-2 >Emitted(9, 11) Source(4, 16) + SourceIndex(0)
-3 >Emitted(9, 16) Source(6, 2) + SourceIndex(0)
-4 >Emitted(9, 17) Source(6, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(10, 1) Source(8, 12) + SourceIndex(0)
-2 >Emitted(10, 18) Source(8, 21) + SourceIndex(0)
-3 >Emitted(10, 21) Source(8, 24) + SourceIndex(0)
-4 >Emitted(10, 25) Source(8, 28) + SourceIndex(0)
-5 >Emitted(10, 27) Source(8, 30) + SourceIndex(0)
-6 >Emitted(10, 29) Source(8, 32) + SourceIndex(0)
-7 >Emitted(10, 30) Source(8, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(12, 5) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(12, 11) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(12, 12) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(12, 29) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(12, 30) Source(10, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(13, 1) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(13, 2) Source(11, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(14, 1) Source(9, 17) + SourceIndex(0)
-2 >Emitted(14, 11) Source(9, 19) + SourceIndex(0)
-3 >Emitted(14, 16) Source(11, 2) + SourceIndex(0)
-4 >Emitted(14, 17) Source(11, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(15, 1) Source(13, 12) + SourceIndex(0)
-2 >Emitted(15, 11) Source(13, 14) + SourceIndex(0)
-3 >Emitted(15, 14) Source(13, 17) + SourceIndex(0)
-4 >Emitted(15, 16) Source(13, 19) + SourceIndex(0)
-5 >Emitted(15, 17) Source(13, 20) + SourceIndex(0)
-6 >Emitted(15, 22) Source(13, 25) + SourceIndex(0)
-7 >Emitted(15, 23) Source(13, 26) + SourceIndex(0)
----
->>>exports.a3 = m2.m2_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >export var 
-2 >a3
-3 >           = 
-4 >             m2
-5 >               .
-6 >                m2_c1
-7 >                     ;
-1->Emitted(16, 1) Source(14, 12) + SourceIndex(0)
-2 >Emitted(16, 11) Source(14, 14) + SourceIndex(0)
-3 >Emitted(16, 14) Source(14, 17) + SourceIndex(0)
-4 >Emitted(16, 16) Source(14, 19) + SourceIndex(0)
-5 >Emitted(16, 17) Source(14, 20) + SourceIndex(0)
-6 >Emitted(16, 22) Source(14, 25) + SourceIndex(0)
-7 >Emitted(16, 23) Source(14, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=../../mapFiles/outputdir_module_multifolder/test.js.map===================================================================
 JsFile: test.js
 mapUrl: ../../../mapFiles/test.js.map
 sourceRoot: 
-sources: 
+sources: ../projects/outputdir_module_multifolder/ref/m1.ts,../projects/outputdir_module_multifolder_ref/m2.ts,../projects/outputdir_module_multifolder/test.ts
 ===================================================================
 >>>//# sourceMappingURL=../../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 87f1f3a51b7..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=../../../mapFiles/outputdir_module_multifolder/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 074ab743af3..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../../../projects/outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 6e2fb8d7851..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
-//# sourceMappingURL=../../mapFiles/outputdir_module_multifolder/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 85da8e39421..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../../projects/outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AAC9B,IAAO,EAAE,WAAW,wCAAwC,CAAC,CAAC;AACnD,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;AACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
index 58e831a041d..8ff2bbdb75b 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..b94a5ff18e5 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_module_simple/m1.ts","../outputdir_module_simple/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index 1fe3446e4bc..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=../mapFiles/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js.map
deleted file mode 100644
index e2625035edb..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../outputdir_module_simple/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/mapRootRelativePathModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/mapRootRelativePathModuleSimpleSpecifyOutputFile.json
index fe0b8045a5c..b4efe9ebb39 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/mapRootRelativePathModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/mapRootRelativePathModuleSimpleSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/mapRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/mapRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
index 410dc94963f..8099c2f176a 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/mapRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/mapRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: ../mapFiles/m1.js.map
+JsFile: test.js
+mapUrl: ../../mapFiles/test.js.map
 sourceRoot: 
-sources: ../outputdir_module_simple/m1.ts
+sources: ../outputdir_module_simple/m1.ts,../outputdir_module_simple/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:m1.js
+emittedFile:bin/test.js
 sourceFile:../outputdir_module_simple/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:../outputdir_module_simple/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=../mapFiles/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: ../mapFiles/test.js.map
-sourceRoot: 
-sources: ../outputdir_module_simple/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:../outputdir_module_simple/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:../outputdir_module_simple/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:../outputdir_module_simple/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:../outputdir_module_simple/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:../outputdir_module_simple/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:../outputdir_module_simple/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:../outputdir_module_simple/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:../outputdir_module_simple/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:../outputdir_module_simple/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:../outputdir_module_simple/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=../mapFiles/test.js.map===================================================================
-JsFile: test.js
-mapUrl: ../../mapFiles/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 14471b6e983..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 5ce16293424..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_module_simple/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..847236565f8 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_module_simple/m1.ts","../outputdir_module_simple/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index 73a399fe253..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=../mapFiles/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js.map
deleted file mode 100644
index 0950101384d..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../outputdir_module_simple/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.json
index fe0b8045a5c..b4efe9ebb39 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
index 0af20dc5ef9..4c009331988 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/mapRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: ../mapFiles/m1.js.map
-sourceRoot: 
-sources: ../outputdir_module_simple/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:../outputdir_module_simple/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=../mapFiles/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: ../mapFiles/test.js.map
-sourceRoot: 
-sources: ../outputdir_module_simple/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:../outputdir_module_simple/test.ts
--------------------------------------------------------------------
->>>var m1 = require("m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^
-6 >                     ^
-7 >                      ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "m1"
-6 >                     )
-7 >                      ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 22) Source(1, 25) + SourceIndex(0)
-6 >Emitted(1, 23) Source(1, 26) + SourceIndex(0)
-7 >Emitted(1, 24) Source(1, 27) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=../mapFiles/test.js.map===================================================================
 JsFile: test.js
 mapUrl: ../../mapFiles/test.js.map
 sourceRoot: 
-sources: 
+sources: ../outputdir_module_simple/m1.ts,../outputdir_module_simple/test.ts
 ===================================================================
 >>>//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index 1a2a4fc5e6a..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index c0654a8e141..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_module_simple/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,IAAI,CAAC,CAAC;AACf,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index 58e831a041d..ccc0a7b503b 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..ae6d9b42221 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_module_subfolder/ref/m1.ts","../outputdir_module_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/mapRootRelativePathModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/mapRootRelativePathModuleSubfolderSpecifyOutputFile.json
index a87c7d36d8e..51ad7ddf1b2 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/mapRootRelativePathModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/mapRootRelativePathModuleSubfolderSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/mapRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/mapRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
index fe747e98d9c..e666ef224a3 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/mapRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/mapRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: ../../mapFiles/ref/m1.js.map
+JsFile: test.js
+mapUrl: ../../mapFiles/test.js.map
 sourceRoot: 
-sources: ../../outputdir_module_subfolder/ref/m1.ts
+sources: ../outputdir_module_subfolder/ref/m1.ts,../outputdir_module_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:../../outputdir_module_subfolder/ref/m1.ts
+emittedFile:bin/test.js
+sourceFile:../outputdir_module_subfolder/ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:../../outputdir_module_subfolder/ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=../../mapFiles/ref/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: ../mapFiles/test.js.map
-sourceRoot: 
-sources: ../outputdir_module_subfolder/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:../outputdir_module_subfolder/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:../outputdir_module_subfolder/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:../outputdir_module_subfolder/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:../outputdir_module_subfolder/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:../outputdir_module_subfolder/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:../outputdir_module_subfolder/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:../outputdir_module_subfolder/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:../outputdir_module_subfolder/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:../outputdir_module_subfolder/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:../outputdir_module_subfolder/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=../mapFiles/test.js.map===================================================================
-JsFile: test.js
-mapUrl: ../../mapFiles/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index 3e8406858e2..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=../../mapFiles/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 66acf4aace7..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../../outputdir_module_subfolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 84b62ed0fc7..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 6139e8293b0..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_module_subfolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..b8c7cced3ae 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_module_subfolder/ref/m1.ts","../outputdir_module_subfolder/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.json
index a87c7d36d8e..51ad7ddf1b2 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 8f609cc28d9..a57632c4e07 100644
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/mapRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: ../../mapFiles/ref/m1.js.map
-sourceRoot: 
-sources: ../../outputdir_module_subfolder/ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:../../outputdir_module_subfolder/ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=../../mapFiles/ref/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: ../mapFiles/test.js.map
-sourceRoot: 
-sources: ../outputdir_module_subfolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:../outputdir_module_subfolder/test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=../mapFiles/test.js.map===================================================================
 JsFile: test.js
 mapUrl: ../../mapFiles/test.js.map
 sourceRoot: 
-sources: 
+sources: ../outputdir_module_subfolder/ref/m1.ts,../outputdir_module_subfolder/test.ts
 ===================================================================
 >>>//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 2dbac1edb8e..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=../../mapFiles/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 7e9c3643b99..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["../../outputdir_module_subfolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index c6dd0639fb7..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 64b21aa3115..00000000000
--- a/tests/baselines/reference/project/mapRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_module_subfolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AACnB,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/bin/test.js
index 8fafee438e6..acd2d113c02 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -30,4 +30,4 @@ var instance1 = new c1();
 function f1() {
     return instance1;
 }
-//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
+//# sourceMappingURL=../../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/bin/test.js.map
index 03cefb2f8d3..fc3b27ea65c 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_multifolder/ref/m1.ts","../outputdir_multifolder_ref/m2.ts","../outputdir_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAC;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,0DAA0D;AAC1D,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../projects/outputdir_multifolder/ref/m1.ts","../projects/outputdir_multifolder_ref/m2.ts","../projects/outputdir_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAC;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,0DAA0D;AAC1D,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/mapRootRelativePathMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/mapRootRelativePathMultifolderSpecifyOutputFile.sourcemap.txt
index d173bd36fb2..534e9184f7b 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/mapRootRelativePathMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/mapRootRelativePathMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,12 +1,12 @@
 ===================================================================
 JsFile: test.js
-mapUrl: ../../mapFiles/test.js.map
+mapUrl: ../../../mapFiles/test.js.map
 sourceRoot: 
-sources: ../outputdir_multifolder/ref/m1.ts,../outputdir_multifolder_ref/m2.ts,../outputdir_multifolder/test.ts
+sources: ../projects/outputdir_multifolder/ref/m1.ts,../projects/outputdir_multifolder_ref/m2.ts,../projects/outputdir_multifolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
-sourceFile:../outputdir_multifolder/ref/m1.ts
+sourceFile:../projects/outputdir_multifolder/ref/m1.ts
 -------------------------------------------------------------------
 >>>var m1_a1 = 10;
 1 >
@@ -143,7 +143,7 @@ sourceFile:../outputdir_multifolder/ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
-sourceFile:../outputdir_multifolder_ref/m2.ts
+sourceFile:../projects/outputdir_multifolder_ref/m2.ts
 -------------------------------------------------------------------
 >>>var m2_a1 = 10;
 1->
@@ -280,7 +280,7 @@ sourceFile:../outputdir_multifolder_ref/m2.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
-sourceFile:../outputdir_multifolder/test.ts
+sourceFile:../projects/outputdir_multifolder/test.ts
 -------------------------------------------------------------------
 >>>/// <reference path='ref/m1.ts'/>
 1->
@@ -427,11 +427,11 @@ sourceFile:../outputdir_multifolder/test.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
 1 >Emitted(32, 1) Source(11, 1) + SourceIndex(2) name (f1)
 2 >Emitted(32, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
->>>//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
+>>>//# sourceMappingURL=../../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/bin/test.js b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/bin/test.js
index 8fafee438e6..acd2d113c02 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/bin/test.js
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/bin/test.js
@@ -30,4 +30,4 @@ var instance1 = new c1();
 function f1() {
     return instance1;
 }
-//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
+//# sourceMappingURL=../../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/bin/test.js.map
index 03cefb2f8d3..fc3b27ea65c 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../outputdir_multifolder/ref/m1.ts","../outputdir_multifolder_ref/m2.ts","../outputdir_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAC;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,0DAA0D;AAC1D,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../projects/outputdir_multifolder/ref/m1.ts","../projects/outputdir_multifolder_ref/m2.ts","../projects/outputdir_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAC;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,0DAA0D;AAC1D,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.sourcemap.txt
index d173bd36fb2..534e9184f7b 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,12 +1,12 @@
 ===================================================================
 JsFile: test.js
-mapUrl: ../../mapFiles/test.js.map
+mapUrl: ../../../mapFiles/test.js.map
 sourceRoot: 
-sources: ../outputdir_multifolder/ref/m1.ts,../outputdir_multifolder_ref/m2.ts,../outputdir_multifolder/test.ts
+sources: ../projects/outputdir_multifolder/ref/m1.ts,../projects/outputdir_multifolder_ref/m2.ts,../projects/outputdir_multifolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
-sourceFile:../outputdir_multifolder/ref/m1.ts
+sourceFile:../projects/outputdir_multifolder/ref/m1.ts
 -------------------------------------------------------------------
 >>>var m1_a1 = 10;
 1 >
@@ -143,7 +143,7 @@ sourceFile:../outputdir_multifolder/ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
-sourceFile:../outputdir_multifolder_ref/m2.ts
+sourceFile:../projects/outputdir_multifolder_ref/m2.ts
 -------------------------------------------------------------------
 >>>var m2_a1 = 10;
 1->
@@ -280,7 +280,7 @@ sourceFile:../outputdir_multifolder_ref/m2.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
-sourceFile:../outputdir_multifolder/test.ts
+sourceFile:../projects/outputdir_multifolder/test.ts
 -------------------------------------------------------------------
 >>>/// <reference path='ref/m1.ts'/>
 1->
@@ -427,11 +427,11 @@ sourceFile:../outputdir_multifolder/test.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
 1 >Emitted(32, 1) Source(11, 1) + SourceIndex(2) name (f1)
 2 >Emitted(32, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
->>>//# sourceMappingURL=../../mapFiles/test.js.map
\ No newline at end of file
+>>>//# sourceMappingURL=../../../mapFiles/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/node/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/node/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/node/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSingleFileSpecifyOutputFile/node/mapRootRelativePathSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSingleFileSpecifyOutputFile/node/mapRootRelativePathSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSingleFileSpecifyOutputFile/node/mapRootRelativePathSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/node/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/node/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/node/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index af0071d7e46..6fbac81a12d 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
index df57785d945..c6996bb53b9 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.json
index f987aa49ffe..b65b2477c8e 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
index 0c806666ef0..0fa723ff01b 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/ref/m2.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
+sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -306,7 +134,7 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
+sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
 sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index aa404804b45..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
deleted file mode 100644
index c2157bc3b1b..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
index df57785d945..0b202d40b8c 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.json
index f987aa49ffe..b65b2477c8e 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
index aede30c6f73..bfe9f5dff6a 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/ref/m2.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
+sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -322,8 +151,8 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index a39f0f50e5f..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
deleted file mode 100644
index 0230aad40a5..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index 2ebe138ffda..8c16871c4a7 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
index e7042dca90a..d78e3b4607a 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 2bb23cdc610..9b7785a024b 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index 5637274312d..6746d0609b6 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/ref/m2.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: http://www.typescriptlang.org/outAndOutDirFile.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
+sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -306,7 +134,7 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
+sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/outAndOutDirFile.js
 sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=http://www.typescriptlang.org/outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index aa404804b45..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index c2157bc3b1b..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
index e7042dca90a..363ef3c21bf 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts","file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 2bb23cdc610..9b7785a024b 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index fa3d5513061..14ca884e9f7 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/ref/m2.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: http://www.typescriptlang.org/outAndOutDirFile.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
+sources: file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts,file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -322,8 +151,8 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:file:///tests/cases/projects/outputdir_mixed_subfolder/test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=http://www.typescriptlang.org/outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index a39f0f50e5f..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 0230aad40a5..00000000000
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_mixed_subfolder/ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index 52f1b822100..0734d350e11 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,45 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
 //# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..211bf71cbed 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts","file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts","file:///tests/cases/projects/outputdir_module_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICNU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
deleted file mode 100644
index 66c8fa96a0b..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
deleted file mode 100644
index e926e95f3c3..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlModuleMultifolderSpecifyOutputFile.json
index e061982b32f..2ff88c9696f 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlModuleMultifolderSpecifyOutputFile.json
@@ -16,15 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
index 1fce6af3084..5805c876be8 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map
+JsFile: test.js
+mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts
+sources: file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts,file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts,file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:diskFile1.js
+emittedFile:bin/test.js
 sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>});
+>>>define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
 >>>    exports.m2_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -193,24 +187,24 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
 3 >                  = 
 4 >                    10
 5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
+1 >Emitted(16, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(16, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(16, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(16, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(16, 24) Source(1, 23) + SourceIndex(1)
 ---
 >>>    var m2_c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(2, 1) + SourceIndex(1)
 ---
 >>>        function m2_c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
+1->Emitted(18, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -220,16 +214,16 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
   >    public m2_c1_p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
+1->Emitted(19, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(19, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
 ---
 >>>        return m2_c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
+1->Emitted(20, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(20, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
 ---
 >>>    })();
 1 >^^^^
@@ -243,10 +237,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
 4 >     export class m2_c1 {
   >         public m2_c1_p1: number;
   >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(21, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_c1 = m2_c1;
 1->^^^^
@@ -260,10 +254,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
   >                     public m2_c1_p1: number;
   >                 }
 4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(22, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(22, 27) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_instance1 = new m2_c1();
 1->^^^^
@@ -282,20 +276,20 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
 5 >                               m2_c1
 6 >                                    ()
 7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
+1->Emitted(23, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(23, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(23, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(23, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(23, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(23, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(23, 40) Source(6, 39) + SourceIndex(1)
 ---
 >>>    function m2_f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(7, 1) + SourceIndex(1)
 ---
 >>>        return exports.m2_instance1;
 1->^^^^^^^^
@@ -309,11 +303,11 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
 3 >               
 4 >               m2_instance1
 5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
+1->Emitted(25, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(25, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(25, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(25, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(25, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
 ---
 >>>    }
 1 >^^^^
@@ -322,8 +316,8 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
+1 >Emitted(26, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(26, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
 ---
 >>>    exports.m2_f1 = m2_f1;
 1->^^^^
@@ -336,23 +330,17 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
   >                     return m2_instance1;
   >                 }
 4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(27, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(27, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(27, 27) Source(9, 2) + SourceIndex(1)
 ---
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_multifolder/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -367,24 +355,24 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(3, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(3, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(3, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(3, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(3, 20) + SourceIndex(0)
+1 >Emitted(30, 5) Source(3, 12) + SourceIndex(2)
+2 >Emitted(30, 15) Source(3, 14) + SourceIndex(2)
+3 >Emitted(30, 18) Source(3, 17) + SourceIndex(2)
+4 >Emitted(30, 20) Source(3, 19) + SourceIndex(2)
+5 >Emitted(30, 21) Source(3, 20) + SourceIndex(2)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(4, 1) + SourceIndex(0)
+1->Emitted(31, 5) Source(4, 1) + SourceIndex(2)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(4, 1) + SourceIndex(0) name (c1)
+1->Emitted(32, 9) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -394,16 +382,16 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(6, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(33, 9) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(33, 10) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(6, 2) + SourceIndex(0) name (c1)
+1->Emitted(34, 9) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(34, 18) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -417,10 +405,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(4, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(6, 2) + SourceIndex(0)
+1 >Emitted(35, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(35, 6) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(35, 6) Source(4, 1) + SourceIndex(2)
+4 >Emitted(35, 10) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -434,10 +422,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(4, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(4, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(6, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(6, 2) + SourceIndex(0)
+1->Emitted(36, 5) Source(4, 14) + SourceIndex(2)
+2 >Emitted(36, 15) Source(4, 16) + SourceIndex(2)
+3 >Emitted(36, 20) Source(6, 2) + SourceIndex(2)
+4 >Emitted(36, 21) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -456,20 +444,20 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(8, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(8, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(8, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(8, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(8, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(8, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(8, 33) + SourceIndex(0)
+1->Emitted(37, 5) Source(8, 12) + SourceIndex(2)
+2 >Emitted(37, 22) Source(8, 21) + SourceIndex(2)
+3 >Emitted(37, 25) Source(8, 24) + SourceIndex(2)
+4 >Emitted(37, 29) Source(8, 28) + SourceIndex(2)
+5 >Emitted(37, 31) Source(8, 30) + SourceIndex(2)
+6 >Emitted(37, 33) Source(8, 32) + SourceIndex(2)
+7 >Emitted(37, 34) Source(8, 33) + SourceIndex(2)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(9, 1) + SourceIndex(0)
+1 >Emitted(38, 5) Source(9, 1) + SourceIndex(2)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -483,11 +471,11 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(10, 22) + SourceIndex(0) name (f1)
+1->Emitted(39, 9) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(39, 15) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(39, 16) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(39, 33) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(39, 34) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -496,8 +484,8 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(11, 2) + SourceIndex(0) name (f1)
+1 >Emitted(40, 5) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(40, 6) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -511,10 +499,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(9, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(9, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(11, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(11, 2) + SourceIndex(0)
+1->Emitted(41, 5) Source(9, 17) + SourceIndex(2)
+2 >Emitted(41, 15) Source(9, 19) + SourceIndex(2)
+3 >Emitted(41, 20) Source(11, 2) + SourceIndex(2)
+4 >Emitted(41, 21) Source(11, 2) + SourceIndex(2)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -534,13 +522,13 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(13, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(13, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(13, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(13, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(13, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(13, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(13, 26) + SourceIndex(0)
+1->Emitted(42, 5) Source(13, 12) + SourceIndex(2)
+2 >Emitted(42, 15) Source(13, 14) + SourceIndex(2)
+3 >Emitted(42, 18) Source(13, 17) + SourceIndex(2)
+4 >Emitted(42, 20) Source(13, 19) + SourceIndex(2)
+5 >Emitted(42, 21) Source(13, 20) + SourceIndex(2)
+6 >Emitted(42, 26) Source(13, 25) + SourceIndex(2)
+7 >Emitted(42, 27) Source(13, 26) + SourceIndex(2)
 ---
 >>>    exports.a3 = m2.m2_c1;
 1->^^^^
@@ -558,19 +546,13 @@ sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m2_c1
 7 >                         ;
-1->Emitted(15, 5) Source(14, 12) + SourceIndex(0)
-2 >Emitted(15, 15) Source(14, 14) + SourceIndex(0)
-3 >Emitted(15, 18) Source(14, 17) + SourceIndex(0)
-4 >Emitted(15, 20) Source(14, 19) + SourceIndex(0)
-5 >Emitted(15, 21) Source(14, 20) + SourceIndex(0)
-6 >Emitted(15, 26) Source(14, 25) + SourceIndex(0)
-7 >Emitted(15, 27) Source(14, 26) + SourceIndex(0)
+1->Emitted(43, 5) Source(14, 12) + SourceIndex(2)
+2 >Emitted(43, 15) Source(14, 14) + SourceIndex(2)
+3 >Emitted(43, 18) Source(14, 17) + SourceIndex(2)
+4 >Emitted(43, 20) Source(14, 19) + SourceIndex(2)
+5 >Emitted(43, 21) Source(14, 20) + SourceIndex(2)
+6 >Emitted(43, 26) Source(14, 25) + SourceIndex(2)
+7 >Emitted(43, 27) Source(14, 26) + SourceIndex(2)
 ---
 >>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index e8004c87aad..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 37bc8039271..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 01ad8f96e78..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 4e7e9721b83..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IAEW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..1c42486b782 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts","file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts","file:///tests/cases/projects/outputdir_module_multifolder/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
deleted file mode 100644
index ec29dfcad18..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js
deleted file mode 100644
index 721fdf3827f..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.json
index e061982b32f..2ff88c9696f 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.json
@@ -16,15 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
index aaf57c9d055..e66e92ff5cf 100644
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,620 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_multifolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:file:///tests/cases/projects/outputdir_module_multifolder/test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-8 >                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>var m2 = require("../outputdir_module_multifolder_ref/m2");
-1->
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-6 >                                                         ^
-7 >                                                          ^
-1->
-  >
-2 >import 
-3 >    m2
-4 >       = require(
-5 >                 "../outputdir_module_multifolder_ref/m2"
-6 >                                                         )
-7 >                                                          ;
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
-2 >Emitted(2, 5) Source(2, 8) + SourceIndex(0)
-3 >Emitted(2, 7) Source(2, 10) + SourceIndex(0)
-4 >Emitted(2, 18) Source(2, 21) + SourceIndex(0)
-5 >Emitted(2, 58) Source(2, 61) + SourceIndex(0)
-6 >Emitted(2, 59) Source(2, 62) + SourceIndex(0)
-7 >Emitted(2, 60) Source(2, 63) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(3, 1) Source(3, 12) + SourceIndex(0)
-2 >Emitted(3, 11) Source(3, 14) + SourceIndex(0)
-3 >Emitted(3, 14) Source(3, 17) + SourceIndex(0)
-4 >Emitted(3, 16) Source(3, 19) + SourceIndex(0)
-5 >Emitted(3, 17) Source(3, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(4, 1) Source(4, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(6, 5) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(6, 6) Source(6, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 14) Source(6, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(8, 1) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(8, 2) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(8, 2) Source(4, 1) + SourceIndex(0)
-4 >Emitted(8, 6) Source(6, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(9, 1) Source(4, 14) + SourceIndex(0)
-2 >Emitted(9, 11) Source(4, 16) + SourceIndex(0)
-3 >Emitted(9, 16) Source(6, 2) + SourceIndex(0)
-4 >Emitted(9, 17) Source(6, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(10, 1) Source(8, 12) + SourceIndex(0)
-2 >Emitted(10, 18) Source(8, 21) + SourceIndex(0)
-3 >Emitted(10, 21) Source(8, 24) + SourceIndex(0)
-4 >Emitted(10, 25) Source(8, 28) + SourceIndex(0)
-5 >Emitted(10, 27) Source(8, 30) + SourceIndex(0)
-6 >Emitted(10, 29) Source(8, 32) + SourceIndex(0)
-7 >Emitted(10, 30) Source(8, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(12, 5) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(12, 11) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(12, 12) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(12, 29) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(12, 30) Source(10, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(13, 1) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(13, 2) Source(11, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(14, 1) Source(9, 17) + SourceIndex(0)
-2 >Emitted(14, 11) Source(9, 19) + SourceIndex(0)
-3 >Emitted(14, 16) Source(11, 2) + SourceIndex(0)
-4 >Emitted(14, 17) Source(11, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(15, 1) Source(13, 12) + SourceIndex(0)
-2 >Emitted(15, 11) Source(13, 14) + SourceIndex(0)
-3 >Emitted(15, 14) Source(13, 17) + SourceIndex(0)
-4 >Emitted(15, 16) Source(13, 19) + SourceIndex(0)
-5 >Emitted(15, 17) Source(13, 20) + SourceIndex(0)
-6 >Emitted(15, 22) Source(13, 25) + SourceIndex(0)
-7 >Emitted(15, 23) Source(13, 26) + SourceIndex(0)
----
->>>exports.a3 = m2.m2_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >export var 
-2 >a3
-3 >           = 
-4 >             m2
-5 >               .
-6 >                m2_c1
-7 >                     ;
-1->Emitted(16, 1) Source(14, 12) + SourceIndex(0)
-2 >Emitted(16, 11) Source(14, 14) + SourceIndex(0)
-3 >Emitted(16, 14) Source(14, 17) + SourceIndex(0)
-4 >Emitted(16, 16) Source(14, 19) + SourceIndex(0)
-5 >Emitted(16, 17) Source(14, 20) + SourceIndex(0)
-6 >Emitted(16, 22) Source(14, 25) + SourceIndex(0)
-7 >Emitted(16, 23) Source(14, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: 
-sources: 
+sources: file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts,file:///tests/cases/projects/outputdir_module_multifolder_ref/m2.ts,file:///tests/cases/projects/outputdir_module_multifolder/test.ts
 ===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 7b14808a067..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index c88465aaec4..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index b9191db7d5f..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 6a18d277c10..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AAC9B,IAAO,EAAE,WAAW,wCAAwC,CAAC,CAAC;AACnD,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;AACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
index 52f1b822100..77db9e80a53 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..445268f27c1 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_simple/m1.ts","file:///tests/cases/projects/outputdir_module_simple/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index 1a4d200cdcb..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map
deleted file mode 100644
index d2270dfd2ce..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_simple/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlModuleSimpleSpecifyOutputFile.json
index e636ce61f7e..1dbc9780b95 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlModuleSimpleSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
index 7c3fae48716..36bfe394d39 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/m1.js.map
+JsFile: test.js
+mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_simple/m1.ts
+sources: file:///tests/cases/projects/outputdir_module_simple/m1.ts,file:///tests/cases/projects/outputdir_module_simple/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:m1.js
+emittedFile:bin/test.js
 sourceFile:file:///tests/cases/projects/outputdir_module_simple/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_simple/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index d752d7f8395..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index de9d99184d2..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_simple/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..a7424e92122 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_simple/m1.ts","file:///tests/cases/projects/outputdir_module_simple/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index 02ca4ab81c7..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map
deleted file mode 100644
index bc2e2667bcd..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_simple/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.json
index e636ce61f7e..1dbc9780b95 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
index 804e4408446..ef808a08b3f 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/m1.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_simple/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:file:///tests/cases/projects/outputdir_module_simple/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/m1.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_simple/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:file:///tests/cases/projects/outputdir_module_simple/test.ts
--------------------------------------------------------------------
->>>var m1 = require("m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^
-6 >                     ^
-7 >                      ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "m1"
-6 >                     )
-7 >                      ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 22) Source(1, 25) + SourceIndex(0)
-6 >Emitted(1, 23) Source(1, 26) + SourceIndex(0)
-7 >Emitted(1, 24) Source(1, 27) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: 
-sources: 
+sources: file:///tests/cases/projects/outputdir_module_simple/m1.ts,file:///tests/cases/projects/outputdir_module_simple/test.ts
 ===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index 1d5a32f0ad5..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index b9c164bb732..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSimpleSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_simple/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,IAAI,CAAC,CAAC;AACf,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index 52f1b822100..10c38a74411 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..439677f8aba 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_module_subfolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlModuleSubfolderSpecifyOutputFile.json
index 05da8c15292..b33bd42f045 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlModuleSubfolderSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 894bcf6cef4..617b90f7c81 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/ref/m1.js.map
+JsFile: test.js
+mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts
+sources: file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_subfolder/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index 73309eabe30..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index ec8a7690d47..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 270604ea7cb..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 35691a873b8..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_subfolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..44276925bda 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts","file:///tests/cases/projects/outputdir_module_subfolder/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.json
index 05da8c15292..b33bd42f045 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 9a7f754c534..16bcb98e00c 100644
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/ref/m1.js.map
-sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m1.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: 
-sources: file:///tests/cases/projects/outputdir_module_subfolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:file:///tests/cases/projects/outputdir_module_subfolder/test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: 
-sources: 
+sources: file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts,file:///tests/cases/projects/outputdir_module_subfolder/test.ts
 ===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 8f31dc2aaa2..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 95de442e92d..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_subfolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 9bb4ed0180a..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index fee2f4cb129..00000000000
--- a/tests/baselines/reference/project/maprootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["file:///tests/cases/projects/outputdir_module_subfolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AACnB,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/node/maprootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/node/maprootUrlMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/node/maprootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/node/maprootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/node/maprootUrlSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/node/maprootUrlSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSingleFileSpecifyOutputFile/node/maprootUrlSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlSingleFileSpecifyOutputFile/node/maprootUrlSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSingleFileSpecifyOutputFile/node/maprootUrlSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/node/maprootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/node/maprootUrlSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/node/maprootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index af0071d7e46..6fbac81a12d 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
index 7a70d18105c..37bb9be8a95 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.json
index c36f3ade5e0..2de7a33388a 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
index 49c44cde80e..1a75ab0b601 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/ref/m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -306,7 +134,7 @@ sourceFile:ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
+sourceFile:ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index aa404804b45..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
deleted file mode 100644
index 04f168a6289..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
index 7a70d18105c..a6626039aa2 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.json
index c36f3ade5e0..2de7a33388a 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
index d54d4d6245e..d1ab16ddf2b 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/ref/m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -322,8 +151,8 @@ sourceFile:test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index a39f0f50e5f..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
deleted file mode 100644
index 0ce68e169af..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index 2ebe138ffda..8c16871c4a7 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
index 53e31e30260..f3058d9f878 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 4741b9cf9e1..8d29a569320 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -18,9 +18,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index 7793026dd6e..2a4bc95cbc2 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/ref/m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: http://www.typescriptlang.org/outAndOutDirFile.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -306,7 +134,7 @@ sourceFile:ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
+sourceFile:ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/outAndOutDirFile.js
 sourceFile:test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=http://www.typescriptlang.org/outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index aa404804b45..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 04f168a6289..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
index 53e31e30260..ba9f4ee590c 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 4741b9cf9e1..8d29a569320 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -18,9 +18,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index a6deca12207..da3d501acb7 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/ref/m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: http://www.typescriptlang.org/outAndOutDirFile.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -322,8 +151,8 @@ sourceFile:test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=http://www.typescriptlang.org/outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index a39f0f50e5f..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 0ce68e169af..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index 52f1b822100..0734d350e11 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,45 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
 //# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
index d3e851981ec..85e465474d3 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/ref/m1.ts","outputdir_module_multifolder_ref/m2.ts","outputdir_module_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICNU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
deleted file mode 100644
index 3b00d82ab66..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
deleted file mode 100644
index e926e95f3c3..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.json
index 3ecf4bc4cc4..ae51d051ff0 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.json
@@ -17,15 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
index deb74d2ae36..20a97890399 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map
+JsFile: test.js
+mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder/ref/m1.ts
+sources: outputdir_module_multifolder/ref/m1.ts,outputdir_module_multifolder_ref/m2.ts,outputdir_module_multifolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder/ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:outputdir_module_multifolder/ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder_ref/m2.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:diskFile1.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder_ref/m2.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>});
+>>>define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
 >>>    exports.m2_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -193,24 +187,24 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 3 >                  = 
 4 >                    10
 5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
+1 >Emitted(16, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(16, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(16, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(16, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(16, 24) Source(1, 23) + SourceIndex(1)
 ---
 >>>    var m2_c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(2, 1) + SourceIndex(1)
 ---
 >>>        function m2_c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
+1->Emitted(18, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -220,16 +214,16 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >    public m2_c1_p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
+1->Emitted(19, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(19, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
 ---
 >>>        return m2_c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
+1->Emitted(20, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(20, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
 ---
 >>>    })();
 1 >^^^^
@@ -243,10 +237,10 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 4 >     export class m2_c1 {
   >         public m2_c1_p1: number;
   >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(21, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_c1 = m2_c1;
 1->^^^^
@@ -260,10 +254,10 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >                     public m2_c1_p1: number;
   >                 }
 4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(22, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(22, 27) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_instance1 = new m2_c1();
 1->^^^^
@@ -282,20 +276,20 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 5 >                               m2_c1
 6 >                                    ()
 7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
+1->Emitted(23, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(23, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(23, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(23, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(23, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(23, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(23, 40) Source(6, 39) + SourceIndex(1)
 ---
 >>>    function m2_f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(7, 1) + SourceIndex(1)
 ---
 >>>        return exports.m2_instance1;
 1->^^^^^^^^
@@ -309,11 +303,11 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 3 >               
 4 >               m2_instance1
 5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
+1->Emitted(25, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(25, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(25, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(25, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(25, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
 ---
 >>>    }
 1 >^^^^
@@ -322,8 +316,8 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
+1 >Emitted(26, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(26, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
 ---
 >>>    exports.m2_f1 = m2_f1;
 1->^^^^
@@ -336,23 +330,17 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >                     return m2_instance1;
   >                 }
 4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(27, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(27, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(27, 27) Source(9, 2) + SourceIndex(1)
 ---
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -367,24 +355,24 @@ sourceFile:outputdir_module_multifolder/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(3, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(3, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(3, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(3, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(3, 20) + SourceIndex(0)
+1 >Emitted(30, 5) Source(3, 12) + SourceIndex(2)
+2 >Emitted(30, 15) Source(3, 14) + SourceIndex(2)
+3 >Emitted(30, 18) Source(3, 17) + SourceIndex(2)
+4 >Emitted(30, 20) Source(3, 19) + SourceIndex(2)
+5 >Emitted(30, 21) Source(3, 20) + SourceIndex(2)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(4, 1) + SourceIndex(0)
+1->Emitted(31, 5) Source(4, 1) + SourceIndex(2)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(4, 1) + SourceIndex(0) name (c1)
+1->Emitted(32, 9) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -394,16 +382,16 @@ sourceFile:outputdir_module_multifolder/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(6, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(33, 9) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(33, 10) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(6, 2) + SourceIndex(0) name (c1)
+1->Emitted(34, 9) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(34, 18) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -417,10 +405,10 @@ sourceFile:outputdir_module_multifolder/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(4, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(6, 2) + SourceIndex(0)
+1 >Emitted(35, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(35, 6) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(35, 6) Source(4, 1) + SourceIndex(2)
+4 >Emitted(35, 10) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -434,10 +422,10 @@ sourceFile:outputdir_module_multifolder/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(4, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(4, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(6, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(6, 2) + SourceIndex(0)
+1->Emitted(36, 5) Source(4, 14) + SourceIndex(2)
+2 >Emitted(36, 15) Source(4, 16) + SourceIndex(2)
+3 >Emitted(36, 20) Source(6, 2) + SourceIndex(2)
+4 >Emitted(36, 21) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -456,20 +444,20 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(8, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(8, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(8, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(8, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(8, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(8, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(8, 33) + SourceIndex(0)
+1->Emitted(37, 5) Source(8, 12) + SourceIndex(2)
+2 >Emitted(37, 22) Source(8, 21) + SourceIndex(2)
+3 >Emitted(37, 25) Source(8, 24) + SourceIndex(2)
+4 >Emitted(37, 29) Source(8, 28) + SourceIndex(2)
+5 >Emitted(37, 31) Source(8, 30) + SourceIndex(2)
+6 >Emitted(37, 33) Source(8, 32) + SourceIndex(2)
+7 >Emitted(37, 34) Source(8, 33) + SourceIndex(2)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(9, 1) + SourceIndex(0)
+1 >Emitted(38, 5) Source(9, 1) + SourceIndex(2)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -483,11 +471,11 @@ sourceFile:outputdir_module_multifolder/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(10, 22) + SourceIndex(0) name (f1)
+1->Emitted(39, 9) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(39, 15) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(39, 16) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(39, 33) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(39, 34) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -496,8 +484,8 @@ sourceFile:outputdir_module_multifolder/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(11, 2) + SourceIndex(0) name (f1)
+1 >Emitted(40, 5) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(40, 6) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -511,10 +499,10 @@ sourceFile:outputdir_module_multifolder/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(9, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(9, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(11, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(11, 2) + SourceIndex(0)
+1->Emitted(41, 5) Source(9, 17) + SourceIndex(2)
+2 >Emitted(41, 15) Source(9, 19) + SourceIndex(2)
+3 >Emitted(41, 20) Source(11, 2) + SourceIndex(2)
+4 >Emitted(41, 21) Source(11, 2) + SourceIndex(2)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -534,13 +522,13 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(13, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(13, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(13, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(13, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(13, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(13, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(13, 26) + SourceIndex(0)
+1->Emitted(42, 5) Source(13, 12) + SourceIndex(2)
+2 >Emitted(42, 15) Source(13, 14) + SourceIndex(2)
+3 >Emitted(42, 18) Source(13, 17) + SourceIndex(2)
+4 >Emitted(42, 20) Source(13, 19) + SourceIndex(2)
+5 >Emitted(42, 21) Source(13, 20) + SourceIndex(2)
+6 >Emitted(42, 26) Source(13, 25) + SourceIndex(2)
+7 >Emitted(42, 27) Source(13, 26) + SourceIndex(2)
 ---
 >>>    exports.a3 = m2.m2_c1;
 1->^^^^
@@ -558,19 +546,13 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m2_c1
 7 >                         ;
-1->Emitted(15, 5) Source(14, 12) + SourceIndex(0)
-2 >Emitted(15, 15) Source(14, 14) + SourceIndex(0)
-3 >Emitted(15, 18) Source(14, 17) + SourceIndex(0)
-4 >Emitted(15, 20) Source(14, 19) + SourceIndex(0)
-5 >Emitted(15, 21) Source(14, 20) + SourceIndex(0)
-6 >Emitted(15, 26) Source(14, 25) + SourceIndex(0)
-7 >Emitted(15, 27) Source(14, 26) + SourceIndex(0)
+1->Emitted(43, 5) Source(14, 12) + SourceIndex(2)
+2 >Emitted(43, 15) Source(14, 14) + SourceIndex(2)
+3 >Emitted(43, 18) Source(14, 17) + SourceIndex(2)
+4 >Emitted(43, 20) Source(14, 19) + SourceIndex(2)
+5 >Emitted(43, 21) Source(14, 20) + SourceIndex(2)
+6 >Emitted(43, 26) Source(14, 25) + SourceIndex(2)
+7 >Emitted(43, 27) Source(14, 26) + SourceIndex(2)
 ---
 >>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index e8004c87aad..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 8c257bd1111..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 01ad8f96e78..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 8612cd0d108..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IAEW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
index d3e851981ec..f84040526ba 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/ref/m1.ts","outputdir_module_multifolder_ref/m2.ts","outputdir_module_multifolder/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
deleted file mode 100644
index 058e405b606..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js
deleted file mode 100644
index 721fdf3827f..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.json
index 3ecf4bc4cc4..ae51d051ff0 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.json
@@ -17,15 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
index 5f476cfb8ed..909ae1c3750 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,620 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder/ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:outputdir_module_multifolder/ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder_ref/m2.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:outputdir_module_multifolder/test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-8 >                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>var m2 = require("../outputdir_module_multifolder_ref/m2");
-1->
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-6 >                                                         ^
-7 >                                                          ^
-1->
-  >
-2 >import 
-3 >    m2
-4 >       = require(
-5 >                 "../outputdir_module_multifolder_ref/m2"
-6 >                                                         )
-7 >                                                          ;
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
-2 >Emitted(2, 5) Source(2, 8) + SourceIndex(0)
-3 >Emitted(2, 7) Source(2, 10) + SourceIndex(0)
-4 >Emitted(2, 18) Source(2, 21) + SourceIndex(0)
-5 >Emitted(2, 58) Source(2, 61) + SourceIndex(0)
-6 >Emitted(2, 59) Source(2, 62) + SourceIndex(0)
-7 >Emitted(2, 60) Source(2, 63) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(3, 1) Source(3, 12) + SourceIndex(0)
-2 >Emitted(3, 11) Source(3, 14) + SourceIndex(0)
-3 >Emitted(3, 14) Source(3, 17) + SourceIndex(0)
-4 >Emitted(3, 16) Source(3, 19) + SourceIndex(0)
-5 >Emitted(3, 17) Source(3, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(4, 1) Source(4, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(6, 5) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(6, 6) Source(6, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 14) Source(6, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(8, 1) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(8, 2) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(8, 2) Source(4, 1) + SourceIndex(0)
-4 >Emitted(8, 6) Source(6, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(9, 1) Source(4, 14) + SourceIndex(0)
-2 >Emitted(9, 11) Source(4, 16) + SourceIndex(0)
-3 >Emitted(9, 16) Source(6, 2) + SourceIndex(0)
-4 >Emitted(9, 17) Source(6, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(10, 1) Source(8, 12) + SourceIndex(0)
-2 >Emitted(10, 18) Source(8, 21) + SourceIndex(0)
-3 >Emitted(10, 21) Source(8, 24) + SourceIndex(0)
-4 >Emitted(10, 25) Source(8, 28) + SourceIndex(0)
-5 >Emitted(10, 27) Source(8, 30) + SourceIndex(0)
-6 >Emitted(10, 29) Source(8, 32) + SourceIndex(0)
-7 >Emitted(10, 30) Source(8, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(12, 5) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(12, 11) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(12, 12) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(12, 29) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(12, 30) Source(10, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(13, 1) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(13, 2) Source(11, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(14, 1) Source(9, 17) + SourceIndex(0)
-2 >Emitted(14, 11) Source(9, 19) + SourceIndex(0)
-3 >Emitted(14, 16) Source(11, 2) + SourceIndex(0)
-4 >Emitted(14, 17) Source(11, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(15, 1) Source(13, 12) + SourceIndex(0)
-2 >Emitted(15, 11) Source(13, 14) + SourceIndex(0)
-3 >Emitted(15, 14) Source(13, 17) + SourceIndex(0)
-4 >Emitted(15, 16) Source(13, 19) + SourceIndex(0)
-5 >Emitted(15, 17) Source(13, 20) + SourceIndex(0)
-6 >Emitted(15, 22) Source(13, 25) + SourceIndex(0)
-7 >Emitted(15, 23) Source(13, 26) + SourceIndex(0)
----
->>>exports.a3 = m2.m2_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >export var 
-2 >a3
-3 >           = 
-4 >             m2
-5 >               .
-6 >                m2_c1
-7 >                     ;
-1->Emitted(16, 1) Source(14, 12) + SourceIndex(0)
-2 >Emitted(16, 11) Source(14, 14) + SourceIndex(0)
-3 >Emitted(16, 14) Source(14, 17) + SourceIndex(0)
-4 >Emitted(16, 16) Source(14, 19) + SourceIndex(0)
-5 >Emitted(16, 17) Source(14, 20) + SourceIndex(0)
-6 >Emitted(16, 22) Source(14, 25) + SourceIndex(0)
-7 >Emitted(16, 23) Source(14, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: 
+sources: outputdir_module_multifolder/ref/m1.ts,outputdir_module_multifolder_ref/m2.ts,outputdir_module_multifolder/test.ts
 ===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 7b14808a067..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index e7f54a4a2e1..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index b9191db7d5f..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
-//# sourceMappingURL=http://www.typescriptlang.org/outputdir_module_multifolder/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 4ac74c2fcdb..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AAC9B,IAAO,EAAE,WAAW,wCAAwC,CAAC,CAAC;AACnD,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;AACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
index 52f1b822100..77db9e80a53 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
index d3e851981ec..2ace469f902 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index 1a4d200cdcb..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map
deleted file mode 100644
index 6751f2f82cd..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.json
index 2cfc9aebda2..d8ff0027520 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
index 8b526ff5859..bd33dbb5ec7 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/m1.js.map
+JsFile: test.js
+mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: m1.ts
+sources: m1.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:m1.js
+emittedFile:bin/test.js
 sourceFile:m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index d752d7f8395..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index a57b57d2b17..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
index d3e851981ec..3b75f2878c9 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["m1.ts","test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index 02ca4ab81c7..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map
deleted file mode 100644
index ca45773f423..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.json
index 2cfc9aebda2..d8ff0027520 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
index ff984bf74ee..d9df59725a9 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/m1.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/m1.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^
-6 >                     ^
-7 >                      ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "m1"
-6 >                     )
-7 >                      ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 22) Source(1, 25) + SourceIndex(0)
-6 >Emitted(1, 23) Source(1, 26) + SourceIndex(0)
-7 >Emitted(1, 24) Source(1, 27) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
+sources: m1.ts,test.ts
 ===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index 1d5a32f0ad5..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 41d3e11e995..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,IAAI,CAAC,CAAC;AACf,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index 52f1b822100..10c38a74411 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
index d3e851981ec..29e01bc0bc6 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.json
index cfa0ec5cb81..cd7c4867bc3 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 67e50350919..557f15f4e2a 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/ref/m1.js.map
+JsFile: test.js
+mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts
+sources: ref/m1.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m1.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index 73309eabe30..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 6c5413f630e..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 270604ea7cb..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index a57b57d2b17..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
index d3e851981ec..4409af8d0a7 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.json
index cfa0ec5cb81..cd7c4867bc3 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
index c5bce1a19d5..3a403373a8f 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: http://www.typescriptlang.org/ref/m1.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/ref/m1.js.map===================================================================
 JsFile: test.js
 mapUrl: http://www.typescriptlang.org/test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map===================================================================
-JsFile: test.js
-mapUrl: http://www.typescriptlang.org/test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
+sources: ref/m1.ts,test.ts
 ===================================================================
 >>>//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 8f31dc2aaa2..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=http://www.typescriptlang.org/ref/m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 35e7e9a48dd..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 9bb4ed0180a..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=http://www.typescriptlang.org/test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index d0638b6c34c..00000000000
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AACnB,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSingleFileSpecifyOutputFile/node/maprootUrlsourcerootUrlSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSingleFileSpecifyOutputFile/node/maprootUrlsourcerootUrlSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSingleFileSpecifyOutputFile/node/maprootUrlsourcerootUrlSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index ad3b4896eec..40bdaa24fc9 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/outMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/outMixedSubfolderSpecifyOutputFile.json
index 975fcf59ca9..1b96d09cd3a 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/outMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/outMixedSubfolderSpecifyOutputFile.json
@@ -14,8 +14,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js",
         "bin/test.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index 2c61fd1d935..00000000000
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,14 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.json
index 975fcf59ca9..1b96d09cd3a 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.json
@@ -14,8 +14,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js",
         "bin/test.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index b7c7f5d8139..00000000000
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,12 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index ad3b4896eec..40bdaa24fc9 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 2b0a20e739a..f2ea5b95015 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -15,8 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index 2c61fd1d935..00000000000
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,14 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 2b0a20e739a..f2ea5b95015 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -15,8 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index b7c7f5d8139..00000000000
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,12 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index e69de29bb2d..0814424ca39 100644
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -0,0 +1,44 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/diskFile0.js b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/diskFile0.js
deleted file mode 100644
index 2c61fd1d935..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/diskFile0.js
+++ /dev/null
@@ -1,14 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/diskFile1.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/diskFile1.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/diskFile1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/outModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/outModuleMultifolderSpecifyOutputFile.json
index 66eced5cc01..ef27e5d6f40 100644
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/outModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/outModuleMultifolderSpecifyOutputFile.json
@@ -14,12 +14,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js",
-        "test.d.ts",
         "bin/test.js",
         "bin/test.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index c2a6326846e..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,14 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index f83ccabfd35..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/diskFile0.js b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/diskFile0.js
deleted file mode 100644
index b7c7f5d8139..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/diskFile0.js
+++ /dev/null
@@ -1,12 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/diskFile1.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/diskFile1.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/diskFile1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/outModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/outModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/outModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/outModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/outModuleMultifolderSpecifyOutputFile.json
index 66eced5cc01..ef27e5d6f40 100644
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/outModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/outModuleMultifolderSpecifyOutputFile.json
@@ -14,12 +14,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js",
-        "test.d.ts",
         "bin/test.js",
         "bin/test.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 37f4ec486b2..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,12 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index d1c1b22a85b..00000000000
--- a/tests/baselines/reference/project/outModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/bin/test.js
index e69de29bb2d..d07eebbd726 100644
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -0,0 +1,29 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index c2a6326846e..00000000000
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,14 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/outModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/outModuleSimpleSpecifyOutputFile.json
index 166aaa982e7..11bd042a34c 100644
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/outModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/outModuleSimpleSpecifyOutputFile.json
@@ -13,10 +13,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js",
-        "m1.d.ts",
-        "test.js",
-        "test.d.ts",
         "bin/test.js",
         "bin/test.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index b6c62f75f3c..00000000000
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index 37f4ec486b2..00000000000
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,12 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/outModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/outModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/outModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/outModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/outModuleSimpleSpecifyOutputFile.json
index 166aaa982e7..11bd042a34c 100644
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/outModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/outModuleSimpleSpecifyOutputFile.json
@@ -13,10 +13,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js",
-        "m1.d.ts",
-        "test.js",
-        "test.d.ts",
         "bin/test.js",
         "bin/test.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index d016c5ff00a..00000000000
--- a/tests/baselines/reference/project/outModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,14 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index e69de29bb2d..a1bb15d7b35 100644
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -0,0 +1,29 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/outModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/outModuleSubfolderSpecifyOutputFile.json
index f11b95edde9..d37850e3f0b 100644
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/outModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/outModuleSubfolderSpecifyOutputFile.json
@@ -13,10 +13,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js",
-        "test.d.ts",
         "bin/test.js",
         "bin/test.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index c2a6326846e..00000000000
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,14 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index ef183a5773c..00000000000
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/outModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/outModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/outModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/outModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/outModuleSubfolderSpecifyOutputFile.json
index f11b95edde9..d37850e3f0b 100644
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/outModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/outModuleSubfolderSpecifyOutputFile.json
@@ -13,10 +13,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js",
-        "test.d.ts",
         "bin/test.js",
         "bin/test.d.ts"
     ]
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 37f4ec486b2..00000000000
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,12 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 548a35e714c..00000000000
--- a/tests/baselines/reference/project/outModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,14 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
diff --git a/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/node/outMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/node/outMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/node/outMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleSpecifyOutputFile/node/outSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outSimpleSpecifyOutputFile/node/outSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/outSimpleSpecifyOutputFile/node/outSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSingleFileSpecifyOutputFile/node/outSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outSingleFileSpecifyOutputFile/node/outSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/outSingleFileSpecifyOutputFile/node/outSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/node/outSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/node/outSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/node/outSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/prologueEmit/amd/out.js b/tests/baselines/reference/project/prologueEmit/amd/out.js
index fb0ca5dfac0..42313b7ce64 100644
--- a/tests/baselines/reference/project/prologueEmit/amd/out.js
+++ b/tests/baselines/reference/project/prologueEmit/amd/out.js
@@ -1,11 +1,11 @@
-var _this = this;
-// Add a lambda to ensure global 'this' capture is triggered
-(function () { return _this.window; });
 var __extends = (this && this.__extends) || function (d, b) {
     for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
     function __() { this.constructor = d; }
     d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
 };
+var _this = this;
+// Add a lambda to ensure global 'this' capture is triggered
+(function () { return _this.window; });
 // class inheritance to ensure __extends is emitted
 var m;
 (function (m) {
diff --git a/tests/baselines/reference/project/prologueEmit/node/out.js b/tests/baselines/reference/project/prologueEmit/node/out.js
index fb0ca5dfac0..42313b7ce64 100644
--- a/tests/baselines/reference/project/prologueEmit/node/out.js
+++ b/tests/baselines/reference/project/prologueEmit/node/out.js
@@ -1,11 +1,11 @@
-var _this = this;
-// Add a lambda to ensure global 'this' capture is triggered
-(function () { return _this.window; });
 var __extends = (this && this.__extends) || function (d, b) {
     for (var p in b) if (b.hasOwnProperty(p)) d[p] = b[p];
     function __() { this.constructor = d; }
     d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
 };
+var _this = this;
+// Add a lambda to ensure global 'this' capture is triggered
+(function () { return _this.window; });
 // class inheritance to ensure __extends is emitted
 var m;
 (function (m) {
diff --git a/tests/baselines/reference/project/prologueEmit/node/prologueEmit.errors.txt b/tests/baselines/reference/project/prologueEmit/node/prologueEmit.errors.txt
new file mode 100644
index 00000000000..ef77af7372e
--- /dev/null
+++ b/tests/baselines/reference/project/prologueEmit/node/prologueEmit.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== globalThisCapture.ts (0 errors) ====
+    // Add a lambda to ensure global 'this' capture is triggered
+    (()=>this.window);
+    
+==== __extends.ts (0 errors) ====
+    // class inheritance to ensure __extends is emitted
+    module m {
+        export class base {}
+        export class child extends base {}
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt
index dfbdd679685..cde83785831 100644
--- a/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt
@@ -2,11 +2,11 @@ error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/Fo
 
 
 !!! error TS6059: File 'fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
-==== FolderA/FolderB/FolderC/fileC.ts (0 errors) ====
+==== fileC.ts (0 errors) ====
     class C {
     }
     
-==== FolderA/FolderB/fileB.ts (0 errors) ====
+==== fileB.ts (0 errors) ====
     /// <reference path='FolderC/fileC.ts'/>
     class B {
         public c: C;
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt
index dfbdd679685..cde83785831 100644
--- a/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt
@@ -2,11 +2,11 @@ error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/Fo
 
 
 !!! error TS6059: File 'fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
-==== FolderA/FolderB/FolderC/fileC.ts (0 errors) ====
+==== fileC.ts (0 errors) ====
     class C {
     }
     
-==== FolderA/FolderB/fileB.ts (0 errors) ====
+==== fileB.ts (0 errors) ====
     /// <reference path='FolderC/fileC.ts'/>
     class B {
         public c: C;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index 5af28cf8560..13e9de8f87f 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
index 65bbb0e67c2..3aa34b0f833 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
deleted file mode 100644
index 381b239c573..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
index 09c6092f164..1772111176c 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
index bbad2c102f9..7ede7f02c36 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: /tests/cases/projects/outputdir_mixed_subfolder/src/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: /tests/cases/projects/outputdir_mixed_subfolder/src/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -306,7 +134,7 @@ sourceFile:ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
+sourceFile:ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
index 65bbb0e67c2..cf4a14ae9e9 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
deleted file mode 100644
index 2963737a5a0..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
index 09c6092f164..1772111176c 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
index c409dc99f14..7330eac1399 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: /tests/cases/projects/outputdir_mixed_subfolder/src/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: /tests/cases/projects/outputdir_mixed_subfolder/src/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -322,8 +151,8 @@ sourceFile:test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index 1750a5975ae..81bb710c580 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
index 820efe6d9d1..454bdf3acb0 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 381b239c573..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 6fb17fa06b8..8d7c349b481 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -18,9 +18,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index 8536097d111..b686585c977 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: /tests/cases/projects/outputdir_mixed_subfolder/src/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: outAndOutDirFile.js.map
 sourceRoot: /tests/cases/projects/outputdir_mixed_subfolder/src/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -306,7 +134,7 @@ sourceFile:ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
+sourceFile:ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/outAndOutDirFile.js
 sourceFile:test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
index 820efe6d9d1..f7d00d1aff9 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 2963737a5a0..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"/tests/cases/projects/outputdir_mixed_subfolder/src/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 6fb17fa06b8..8d7c349b481 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -18,9 +18,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index 47e9f1da73a..71a33c01806 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: /tests/cases/projects/outputdir_mixed_subfolder/src/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: outAndOutDirFile.js.map
 sourceRoot: /tests/cases/projects/outputdir_mixed_subfolder/src/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -322,8 +151,8 @@ sourceFile:test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..994e21ca032 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,45 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
index e53f2e0a755..0fd0b2def0c 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":["outputdir_module_multifolder/ref/m1.ts","outputdir_module_multifolder_ref/m2.ts","outputdir_module_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICNU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
deleted file mode 100644
index c4c57a82e12..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":["outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 71e1da5d3cc..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":["outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
index b3e80123c04..722a6fbd4da 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
@@ -17,15 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
index e1bca270ba0..8c710d9c4da 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: /tests/cases/projects/outputdir_module_multifolder/src/
-sources: outputdir_module_multifolder/ref/m1.ts
+sources: outputdir_module_multifolder/ref/m1.ts,outputdir_module_multifolder_ref/m2.ts,outputdir_module_multifolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder/ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:outputdir_module_multifolder/ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_multifolder/src/
-sources: outputdir_module_multifolder_ref/m2.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:diskFile1.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder_ref/m2.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>});
+>>>define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
 >>>    exports.m2_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -193,24 +187,24 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 3 >                  = 
 4 >                    10
 5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
+1 >Emitted(16, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(16, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(16, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(16, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(16, 24) Source(1, 23) + SourceIndex(1)
 ---
 >>>    var m2_c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(2, 1) + SourceIndex(1)
 ---
 >>>        function m2_c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
+1->Emitted(18, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -220,16 +214,16 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >    public m2_c1_p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
+1->Emitted(19, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(19, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
 ---
 >>>        return m2_c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
+1->Emitted(20, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(20, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
 ---
 >>>    })();
 1 >^^^^
@@ -243,10 +237,10 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 4 >     export class m2_c1 {
   >         public m2_c1_p1: number;
   >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(21, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_c1 = m2_c1;
 1->^^^^
@@ -260,10 +254,10 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >                     public m2_c1_p1: number;
   >                 }
 4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(22, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(22, 27) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_instance1 = new m2_c1();
 1->^^^^
@@ -282,20 +276,20 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 5 >                               m2_c1
 6 >                                    ()
 7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
+1->Emitted(23, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(23, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(23, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(23, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(23, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(23, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(23, 40) Source(6, 39) + SourceIndex(1)
 ---
 >>>    function m2_f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(7, 1) + SourceIndex(1)
 ---
 >>>        return exports.m2_instance1;
 1->^^^^^^^^
@@ -309,11 +303,11 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 3 >               
 4 >               m2_instance1
 5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
+1->Emitted(25, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(25, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(25, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(25, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(25, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
 ---
 >>>    }
 1 >^^^^
@@ -322,8 +316,8 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
+1 >Emitted(26, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(26, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
 ---
 >>>    exports.m2_f1 = m2_f1;
 1->^^^^
@@ -336,23 +330,17 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >                     return m2_instance1;
   >                 }
 4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(27, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(27, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(27, 27) Source(9, 2) + SourceIndex(1)
 ---
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_multifolder/src/
-sources: outputdir_module_multifolder/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -367,24 +355,24 @@ sourceFile:outputdir_module_multifolder/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(3, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(3, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(3, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(3, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(3, 20) + SourceIndex(0)
+1 >Emitted(30, 5) Source(3, 12) + SourceIndex(2)
+2 >Emitted(30, 15) Source(3, 14) + SourceIndex(2)
+3 >Emitted(30, 18) Source(3, 17) + SourceIndex(2)
+4 >Emitted(30, 20) Source(3, 19) + SourceIndex(2)
+5 >Emitted(30, 21) Source(3, 20) + SourceIndex(2)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(4, 1) + SourceIndex(0)
+1->Emitted(31, 5) Source(4, 1) + SourceIndex(2)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(4, 1) + SourceIndex(0) name (c1)
+1->Emitted(32, 9) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -394,16 +382,16 @@ sourceFile:outputdir_module_multifolder/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(6, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(33, 9) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(33, 10) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(6, 2) + SourceIndex(0) name (c1)
+1->Emitted(34, 9) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(34, 18) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -417,10 +405,10 @@ sourceFile:outputdir_module_multifolder/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(4, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(6, 2) + SourceIndex(0)
+1 >Emitted(35, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(35, 6) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(35, 6) Source(4, 1) + SourceIndex(2)
+4 >Emitted(35, 10) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -434,10 +422,10 @@ sourceFile:outputdir_module_multifolder/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(4, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(4, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(6, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(6, 2) + SourceIndex(0)
+1->Emitted(36, 5) Source(4, 14) + SourceIndex(2)
+2 >Emitted(36, 15) Source(4, 16) + SourceIndex(2)
+3 >Emitted(36, 20) Source(6, 2) + SourceIndex(2)
+4 >Emitted(36, 21) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -456,20 +444,20 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(8, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(8, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(8, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(8, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(8, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(8, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(8, 33) + SourceIndex(0)
+1->Emitted(37, 5) Source(8, 12) + SourceIndex(2)
+2 >Emitted(37, 22) Source(8, 21) + SourceIndex(2)
+3 >Emitted(37, 25) Source(8, 24) + SourceIndex(2)
+4 >Emitted(37, 29) Source(8, 28) + SourceIndex(2)
+5 >Emitted(37, 31) Source(8, 30) + SourceIndex(2)
+6 >Emitted(37, 33) Source(8, 32) + SourceIndex(2)
+7 >Emitted(37, 34) Source(8, 33) + SourceIndex(2)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(9, 1) + SourceIndex(0)
+1 >Emitted(38, 5) Source(9, 1) + SourceIndex(2)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -483,11 +471,11 @@ sourceFile:outputdir_module_multifolder/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(10, 22) + SourceIndex(0) name (f1)
+1->Emitted(39, 9) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(39, 15) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(39, 16) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(39, 33) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(39, 34) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -496,8 +484,8 @@ sourceFile:outputdir_module_multifolder/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(11, 2) + SourceIndex(0) name (f1)
+1 >Emitted(40, 5) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(40, 6) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -511,10 +499,10 @@ sourceFile:outputdir_module_multifolder/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(9, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(9, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(11, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(11, 2) + SourceIndex(0)
+1->Emitted(41, 5) Source(9, 17) + SourceIndex(2)
+2 >Emitted(41, 15) Source(9, 19) + SourceIndex(2)
+3 >Emitted(41, 20) Source(11, 2) + SourceIndex(2)
+4 >Emitted(41, 21) Source(11, 2) + SourceIndex(2)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -534,13 +522,13 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(13, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(13, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(13, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(13, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(13, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(13, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(13, 26) + SourceIndex(0)
+1->Emitted(42, 5) Source(13, 12) + SourceIndex(2)
+2 >Emitted(42, 15) Source(13, 14) + SourceIndex(2)
+3 >Emitted(42, 18) Source(13, 17) + SourceIndex(2)
+4 >Emitted(42, 20) Source(13, 19) + SourceIndex(2)
+5 >Emitted(42, 21) Source(13, 20) + SourceIndex(2)
+6 >Emitted(42, 26) Source(13, 25) + SourceIndex(2)
+7 >Emitted(42, 27) Source(13, 26) + SourceIndex(2)
 ---
 >>>    exports.a3 = m2.m2_c1;
 1->^^^^
@@ -558,19 +546,13 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m2_c1
 7 >                         ;
-1->Emitted(15, 5) Source(14, 12) + SourceIndex(0)
-2 >Emitted(15, 15) Source(14, 14) + SourceIndex(0)
-3 >Emitted(15, 18) Source(14, 17) + SourceIndex(0)
-4 >Emitted(15, 20) Source(14, 19) + SourceIndex(0)
-5 >Emitted(15, 21) Source(14, 20) + SourceIndex(0)
-6 >Emitted(15, 26) Source(14, 25) + SourceIndex(0)
-7 >Emitted(15, 27) Source(14, 26) + SourceIndex(0)
+1->Emitted(43, 5) Source(14, 12) + SourceIndex(2)
+2 >Emitted(43, 15) Source(14, 14) + SourceIndex(2)
+3 >Emitted(43, 18) Source(14, 17) + SourceIndex(2)
+4 >Emitted(43, 20) Source(14, 19) + SourceIndex(2)
+5 >Emitted(43, 21) Source(14, 20) + SourceIndex(2)
+6 >Emitted(43, 26) Source(14, 25) + SourceIndex(2)
+7 >Emitted(43, 27) Source(14, 26) + SourceIndex(2)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_multifolder/src/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 5cca04a0f25..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index aeb0a1c3c5d..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":["outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IAEW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
index e53f2e0a755..027f9569ebc 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":["outputdir_module_multifolder/ref/m1.ts","outputdir_module_multifolder_ref/m2.ts","outputdir_module_multifolder/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
deleted file mode 100644
index 7e08245de72..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":["outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index de341c87ec1..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":["outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
index b3e80123c04..722a6fbd4da 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.json
@@ -17,15 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
index 63e22ab64ba..e129af6a045 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,620 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_multifolder/src/
-sources: outputdir_module_multifolder/ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:outputdir_module_multifolder/ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_multifolder/src/
-sources: outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: /tests/cases/projects/outputdir_module_multifolder/src/
-sources: outputdir_module_multifolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:outputdir_module_multifolder/test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-8 >                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>var m2 = require("../outputdir_module_multifolder_ref/m2");
-1->
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-6 >                                                         ^
-7 >                                                          ^
-1->
-  >
-2 >import 
-3 >    m2
-4 >       = require(
-5 >                 "../outputdir_module_multifolder_ref/m2"
-6 >                                                         )
-7 >                                                          ;
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
-2 >Emitted(2, 5) Source(2, 8) + SourceIndex(0)
-3 >Emitted(2, 7) Source(2, 10) + SourceIndex(0)
-4 >Emitted(2, 18) Source(2, 21) + SourceIndex(0)
-5 >Emitted(2, 58) Source(2, 61) + SourceIndex(0)
-6 >Emitted(2, 59) Source(2, 62) + SourceIndex(0)
-7 >Emitted(2, 60) Source(2, 63) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(3, 1) Source(3, 12) + SourceIndex(0)
-2 >Emitted(3, 11) Source(3, 14) + SourceIndex(0)
-3 >Emitted(3, 14) Source(3, 17) + SourceIndex(0)
-4 >Emitted(3, 16) Source(3, 19) + SourceIndex(0)
-5 >Emitted(3, 17) Source(3, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(4, 1) Source(4, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(6, 5) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(6, 6) Source(6, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 14) Source(6, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(8, 1) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(8, 2) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(8, 2) Source(4, 1) + SourceIndex(0)
-4 >Emitted(8, 6) Source(6, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(9, 1) Source(4, 14) + SourceIndex(0)
-2 >Emitted(9, 11) Source(4, 16) + SourceIndex(0)
-3 >Emitted(9, 16) Source(6, 2) + SourceIndex(0)
-4 >Emitted(9, 17) Source(6, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(10, 1) Source(8, 12) + SourceIndex(0)
-2 >Emitted(10, 18) Source(8, 21) + SourceIndex(0)
-3 >Emitted(10, 21) Source(8, 24) + SourceIndex(0)
-4 >Emitted(10, 25) Source(8, 28) + SourceIndex(0)
-5 >Emitted(10, 27) Source(8, 30) + SourceIndex(0)
-6 >Emitted(10, 29) Source(8, 32) + SourceIndex(0)
-7 >Emitted(10, 30) Source(8, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(12, 5) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(12, 11) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(12, 12) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(12, 29) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(12, 30) Source(10, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(13, 1) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(13, 2) Source(11, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(14, 1) Source(9, 17) + SourceIndex(0)
-2 >Emitted(14, 11) Source(9, 19) + SourceIndex(0)
-3 >Emitted(14, 16) Source(11, 2) + SourceIndex(0)
-4 >Emitted(14, 17) Source(11, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(15, 1) Source(13, 12) + SourceIndex(0)
-2 >Emitted(15, 11) Source(13, 14) + SourceIndex(0)
-3 >Emitted(15, 14) Source(13, 17) + SourceIndex(0)
-4 >Emitted(15, 16) Source(13, 19) + SourceIndex(0)
-5 >Emitted(15, 17) Source(13, 20) + SourceIndex(0)
-6 >Emitted(15, 22) Source(13, 25) + SourceIndex(0)
-7 >Emitted(15, 23) Source(13, 26) + SourceIndex(0)
----
->>>exports.a3 = m2.m2_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >export var 
-2 >a3
-3 >           = 
-4 >             m2
-5 >               .
-6 >                m2_c1
-7 >                     ;
-1->Emitted(16, 1) Source(14, 12) + SourceIndex(0)
-2 >Emitted(16, 11) Source(14, 14) + SourceIndex(0)
-3 >Emitted(16, 14) Source(14, 17) + SourceIndex(0)
-4 >Emitted(16, 16) Source(14, 19) + SourceIndex(0)
-5 >Emitted(16, 17) Source(14, 20) + SourceIndex(0)
-6 >Emitted(16, 22) Source(14, 25) + SourceIndex(0)
-7 >Emitted(16, 23) Source(14, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_multifolder/src/
-sources: 
+sources: outputdir_module_multifolder/ref/m1.ts,outputdir_module_multifolder_ref/m2.ts,outputdir_module_multifolder/test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 14c09e444a5..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 0b67e7ee481..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleMultifolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_multifolder/src/","sources":["outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AAC9B,IAAO,EAAE,WAAW,wCAAwC,CAAC,CAAC;AACnD,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;AACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..f385e49ecd1 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
index 42e5a82e74b..a910369c3e4 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_simple/src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_simple/src/","sources":["m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js.map
deleted file mode 100644
index 89373fc1cfa..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"/tests/cases/projects/outputdir_module_simple/src/","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.json
index e2621b2fa52..f9e2736f65a 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
index 0fc6cd6eb2a..827aa235ef2 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: /tests/cases/projects/outputdir_module_simple/src/
-sources: m1.ts
+sources: m1.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:m1.js
+emittedFile:bin/test.js
 sourceFile:m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_simple/src/
-sources: test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_simple/src/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 372f1052b89..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 945ed0583ad..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_simple/src/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
index 42e5a82e74b..487d57bd2ae 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_simple/src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_simple/src/","sources":["m1.ts","test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js.map
deleted file mode 100644
index 9bf6e024b3f..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"/tests/cases/projects/outputdir_module_simple/src/","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.json
index e2621b2fa52..f9e2736f65a 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
index 08491d50151..0a161bb4886 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_simple/src/
-sources: m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: /tests/cases/projects/outputdir_module_simple/src/
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^
-6 >                     ^
-7 >                      ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "m1"
-6 >                     )
-7 >                      ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 22) Source(1, 25) + SourceIndex(0)
-6 >Emitted(1, 23) Source(1, 26) + SourceIndex(0)
-7 >Emitted(1, 24) Source(1, 27) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_simple/src/
-sources: 
+sources: m1.ts,test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index c2e7dfa443b..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index a7792ef5242..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSimpleSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_simple/src/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,IAAI,CAAC,CAAC;AACf,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..18d212c7e69 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
index 279042a1a0f..30bac946d14 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_subfolder/src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_subfolder/src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 6f750f89857..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"/tests/cases/projects/outputdir_module_subfolder/src/","sources":["ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
index a43e0f69172..50dc5aaf60f 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 5e87f2ef555..af6c2b21fdc 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: /tests/cases/projects/outputdir_module_subfolder/src/
-sources: ref/m1.ts
+sources: ref/m1.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_subfolder/src/
-sources: test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_subfolder/src/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 6c8aeb3190b..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index f65cfa554d1..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_subfolder/src/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
index 279042a1a0f..622f2c91c95 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_subfolder/src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_subfolder/src/","sources":["ref/m1.ts","test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 19b046a427c..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"/tests/cases/projects/outputdir_module_subfolder/src/","sources":["ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
index a43e0f69172..50dc5aaf60f 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.json
@@ -16,12 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 67fc9030f41..5d837611e49 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_subfolder/src/
-sources: ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: /tests/cases/projects/outputdir_module_subfolder/src/
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: /tests/cases/projects/outputdir_module_subfolder/src/
-sources: 
+sources: ref/m1.ts,test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 46c9f29e55a..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index c63a0943976..00000000000
--- a/tests/baselines/reference/project/sourceRootAbsolutePathModuleSubfolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"/tests/cases/projects/outputdir_module_subfolder/src/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AACnB,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/node/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/node/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/node/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSingleFileSpecifyOutputFile/node/sourceRootAbsolutePathSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSingleFileSpecifyOutputFile/node/sourceRootAbsolutePathSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSingleFileSpecifyOutputFile/node/sourceRootAbsolutePathSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index 5af28cf8560..13e9de8f87f 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
index 86afcf32e25..62f932a571e 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
deleted file mode 100644
index 0927206ec1b..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"../src/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.json
index 82ef1c7d882..2dcfc8a5a2c 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
index 94b86ffdde1..d722bc8936a 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: ../src/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: ../src/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -306,7 +134,7 @@ sourceFile:ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
+sourceFile:ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
index 86afcf32e25..03976e6a8d6 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
deleted file mode 100644
index 84f18c56247..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"../src/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.json
index 82ef1c7d882..2dcfc8a5a2c 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
index 12a6fdbc6dd..b71c21b5b99 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: ../src/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: ../src/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -322,8 +151,8 @@ sourceFile:test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index 1750a5975ae..81bb710c580 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
index 13b958b1025..a9529891ffd 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"../src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"../src/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 0927206ec1b..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"../src/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index d5f4fd9c654..4247e9dadc2 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index 11e34ee5a2e..d1799c07a98 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: ../src/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: outAndOutDirFile.js.map
 sourceRoot: ../src/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -306,7 +134,7 @@ sourceFile:ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
+sourceFile:ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/outAndOutDirFile.js
 sourceFile:test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
index 13b958b1025..23957761470 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"../src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"../src/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 84f18c56247..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"../src/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index d5f4fd9c654..4247e9dadc2 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index 5b9ec51c270..2a0cc630cc0 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: ../src/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: outAndOutDirFile.js.map
 sourceRoot: ../src/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -322,8 +151,8 @@ sourceFile:test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..994e21ca032 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,45 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
index 512eba0e11a..39dcc66e06b 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["outputdir_module_multifolder/ref/m1.ts","outputdir_module_multifolder_ref/m2.ts","outputdir_module_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICNU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
deleted file mode 100644
index 414fa845b2e..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"../src/","sources":["outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 0cdc44d330d..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"../src/","sources":["outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.json
index 69a577baffd..77179246af5 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.json
@@ -16,15 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
index 9c817da60e9..43c4340ba37 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: ../src/
-sources: outputdir_module_multifolder/ref/m1.ts
+sources: outputdir_module_multifolder/ref/m1.ts,outputdir_module_multifolder_ref/m2.ts,outputdir_module_multifolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder/ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:outputdir_module_multifolder/ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: ../src/
-sources: outputdir_module_multifolder_ref/m2.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:diskFile1.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder_ref/m2.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>});
+>>>define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
 >>>    exports.m2_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -193,24 +187,24 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 3 >                  = 
 4 >                    10
 5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
+1 >Emitted(16, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(16, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(16, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(16, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(16, 24) Source(1, 23) + SourceIndex(1)
 ---
 >>>    var m2_c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(2, 1) + SourceIndex(1)
 ---
 >>>        function m2_c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
+1->Emitted(18, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -220,16 +214,16 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >    public m2_c1_p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
+1->Emitted(19, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(19, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
 ---
 >>>        return m2_c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
+1->Emitted(20, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(20, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
 ---
 >>>    })();
 1 >^^^^
@@ -243,10 +237,10 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 4 >     export class m2_c1 {
   >         public m2_c1_p1: number;
   >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(21, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_c1 = m2_c1;
 1->^^^^
@@ -260,10 +254,10 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >                     public m2_c1_p1: number;
   >                 }
 4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(22, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(22, 27) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_instance1 = new m2_c1();
 1->^^^^
@@ -282,20 +276,20 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 5 >                               m2_c1
 6 >                                    ()
 7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
+1->Emitted(23, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(23, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(23, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(23, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(23, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(23, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(23, 40) Source(6, 39) + SourceIndex(1)
 ---
 >>>    function m2_f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(7, 1) + SourceIndex(1)
 ---
 >>>        return exports.m2_instance1;
 1->^^^^^^^^
@@ -309,11 +303,11 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 3 >               
 4 >               m2_instance1
 5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
+1->Emitted(25, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(25, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(25, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(25, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(25, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
 ---
 >>>    }
 1 >^^^^
@@ -322,8 +316,8 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
+1 >Emitted(26, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(26, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
 ---
 >>>    exports.m2_f1 = m2_f1;
 1->^^^^
@@ -336,23 +330,17 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >                     return m2_instance1;
   >                 }
 4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(27, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(27, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(27, 27) Source(9, 2) + SourceIndex(1)
 ---
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: outputdir_module_multifolder/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -367,24 +355,24 @@ sourceFile:outputdir_module_multifolder/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(3, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(3, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(3, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(3, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(3, 20) + SourceIndex(0)
+1 >Emitted(30, 5) Source(3, 12) + SourceIndex(2)
+2 >Emitted(30, 15) Source(3, 14) + SourceIndex(2)
+3 >Emitted(30, 18) Source(3, 17) + SourceIndex(2)
+4 >Emitted(30, 20) Source(3, 19) + SourceIndex(2)
+5 >Emitted(30, 21) Source(3, 20) + SourceIndex(2)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(4, 1) + SourceIndex(0)
+1->Emitted(31, 5) Source(4, 1) + SourceIndex(2)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(4, 1) + SourceIndex(0) name (c1)
+1->Emitted(32, 9) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -394,16 +382,16 @@ sourceFile:outputdir_module_multifolder/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(6, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(33, 9) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(33, 10) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(6, 2) + SourceIndex(0) name (c1)
+1->Emitted(34, 9) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(34, 18) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -417,10 +405,10 @@ sourceFile:outputdir_module_multifolder/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(4, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(6, 2) + SourceIndex(0)
+1 >Emitted(35, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(35, 6) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(35, 6) Source(4, 1) + SourceIndex(2)
+4 >Emitted(35, 10) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -434,10 +422,10 @@ sourceFile:outputdir_module_multifolder/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(4, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(4, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(6, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(6, 2) + SourceIndex(0)
+1->Emitted(36, 5) Source(4, 14) + SourceIndex(2)
+2 >Emitted(36, 15) Source(4, 16) + SourceIndex(2)
+3 >Emitted(36, 20) Source(6, 2) + SourceIndex(2)
+4 >Emitted(36, 21) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -456,20 +444,20 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(8, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(8, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(8, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(8, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(8, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(8, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(8, 33) + SourceIndex(0)
+1->Emitted(37, 5) Source(8, 12) + SourceIndex(2)
+2 >Emitted(37, 22) Source(8, 21) + SourceIndex(2)
+3 >Emitted(37, 25) Source(8, 24) + SourceIndex(2)
+4 >Emitted(37, 29) Source(8, 28) + SourceIndex(2)
+5 >Emitted(37, 31) Source(8, 30) + SourceIndex(2)
+6 >Emitted(37, 33) Source(8, 32) + SourceIndex(2)
+7 >Emitted(37, 34) Source(8, 33) + SourceIndex(2)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(9, 1) + SourceIndex(0)
+1 >Emitted(38, 5) Source(9, 1) + SourceIndex(2)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -483,11 +471,11 @@ sourceFile:outputdir_module_multifolder/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(10, 22) + SourceIndex(0) name (f1)
+1->Emitted(39, 9) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(39, 15) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(39, 16) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(39, 33) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(39, 34) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -496,8 +484,8 @@ sourceFile:outputdir_module_multifolder/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(11, 2) + SourceIndex(0) name (f1)
+1 >Emitted(40, 5) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(40, 6) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -511,10 +499,10 @@ sourceFile:outputdir_module_multifolder/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(9, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(9, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(11, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(11, 2) + SourceIndex(0)
+1->Emitted(41, 5) Source(9, 17) + SourceIndex(2)
+2 >Emitted(41, 15) Source(9, 19) + SourceIndex(2)
+3 >Emitted(41, 20) Source(11, 2) + SourceIndex(2)
+4 >Emitted(41, 21) Source(11, 2) + SourceIndex(2)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -534,13 +522,13 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(13, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(13, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(13, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(13, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(13, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(13, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(13, 26) + SourceIndex(0)
+1->Emitted(42, 5) Source(13, 12) + SourceIndex(2)
+2 >Emitted(42, 15) Source(13, 14) + SourceIndex(2)
+3 >Emitted(42, 18) Source(13, 17) + SourceIndex(2)
+4 >Emitted(42, 20) Source(13, 19) + SourceIndex(2)
+5 >Emitted(42, 21) Source(13, 20) + SourceIndex(2)
+6 >Emitted(42, 26) Source(13, 25) + SourceIndex(2)
+7 >Emitted(42, 27) Source(13, 26) + SourceIndex(2)
 ---
 >>>    exports.a3 = m2.m2_c1;
 1->^^^^
@@ -558,19 +546,13 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m2_c1
 7 >                         ;
-1->Emitted(15, 5) Source(14, 12) + SourceIndex(0)
-2 >Emitted(15, 15) Source(14, 14) + SourceIndex(0)
-3 >Emitted(15, 18) Source(14, 17) + SourceIndex(0)
-4 >Emitted(15, 20) Source(14, 19) + SourceIndex(0)
-5 >Emitted(15, 21) Source(14, 20) + SourceIndex(0)
-6 >Emitted(15, 26) Source(14, 25) + SourceIndex(0)
-7 >Emitted(15, 27) Source(14, 26) + SourceIndex(0)
+1->Emitted(43, 5) Source(14, 12) + SourceIndex(2)
+2 >Emitted(43, 15) Source(14, 14) + SourceIndex(2)
+3 >Emitted(43, 18) Source(14, 17) + SourceIndex(2)
+4 >Emitted(43, 20) Source(14, 19) + SourceIndex(2)
+5 >Emitted(43, 21) Source(14, 20) + SourceIndex(2)
+6 >Emitted(43, 26) Source(14, 25) + SourceIndex(2)
+7 >Emitted(43, 27) Source(14, 26) + SourceIndex(2)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 5cca04a0f25..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 20138821cfe..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IAEW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
index 512eba0e11a..a3ab2ebecdb 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["outputdir_module_multifolder/ref/m1.ts","outputdir_module_multifolder_ref/m2.ts","outputdir_module_multifolder/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
deleted file mode 100644
index 92fd6e19cfb..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"../src/","sources":["outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 292dcb61933..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"../src/","sources":["outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.json
index 69a577baffd..77179246af5 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.json
@@ -16,15 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
index e34bffc6f61..7ef7adace73 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/sourceRootRelativePathModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,620 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: ../src/
-sources: outputdir_module_multifolder/ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:outputdir_module_multifolder/ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: ../src/
-sources: outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: ../src/
-sources: outputdir_module_multifolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:outputdir_module_multifolder/test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-8 >                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>var m2 = require("../outputdir_module_multifolder_ref/m2");
-1->
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-6 >                                                         ^
-7 >                                                          ^
-1->
-  >
-2 >import 
-3 >    m2
-4 >       = require(
-5 >                 "../outputdir_module_multifolder_ref/m2"
-6 >                                                         )
-7 >                                                          ;
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
-2 >Emitted(2, 5) Source(2, 8) + SourceIndex(0)
-3 >Emitted(2, 7) Source(2, 10) + SourceIndex(0)
-4 >Emitted(2, 18) Source(2, 21) + SourceIndex(0)
-5 >Emitted(2, 58) Source(2, 61) + SourceIndex(0)
-6 >Emitted(2, 59) Source(2, 62) + SourceIndex(0)
-7 >Emitted(2, 60) Source(2, 63) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(3, 1) Source(3, 12) + SourceIndex(0)
-2 >Emitted(3, 11) Source(3, 14) + SourceIndex(0)
-3 >Emitted(3, 14) Source(3, 17) + SourceIndex(0)
-4 >Emitted(3, 16) Source(3, 19) + SourceIndex(0)
-5 >Emitted(3, 17) Source(3, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(4, 1) Source(4, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(6, 5) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(6, 6) Source(6, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 14) Source(6, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(8, 1) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(8, 2) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(8, 2) Source(4, 1) + SourceIndex(0)
-4 >Emitted(8, 6) Source(6, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(9, 1) Source(4, 14) + SourceIndex(0)
-2 >Emitted(9, 11) Source(4, 16) + SourceIndex(0)
-3 >Emitted(9, 16) Source(6, 2) + SourceIndex(0)
-4 >Emitted(9, 17) Source(6, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(10, 1) Source(8, 12) + SourceIndex(0)
-2 >Emitted(10, 18) Source(8, 21) + SourceIndex(0)
-3 >Emitted(10, 21) Source(8, 24) + SourceIndex(0)
-4 >Emitted(10, 25) Source(8, 28) + SourceIndex(0)
-5 >Emitted(10, 27) Source(8, 30) + SourceIndex(0)
-6 >Emitted(10, 29) Source(8, 32) + SourceIndex(0)
-7 >Emitted(10, 30) Source(8, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(12, 5) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(12, 11) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(12, 12) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(12, 29) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(12, 30) Source(10, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(13, 1) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(13, 2) Source(11, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(14, 1) Source(9, 17) + SourceIndex(0)
-2 >Emitted(14, 11) Source(9, 19) + SourceIndex(0)
-3 >Emitted(14, 16) Source(11, 2) + SourceIndex(0)
-4 >Emitted(14, 17) Source(11, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(15, 1) Source(13, 12) + SourceIndex(0)
-2 >Emitted(15, 11) Source(13, 14) + SourceIndex(0)
-3 >Emitted(15, 14) Source(13, 17) + SourceIndex(0)
-4 >Emitted(15, 16) Source(13, 19) + SourceIndex(0)
-5 >Emitted(15, 17) Source(13, 20) + SourceIndex(0)
-6 >Emitted(15, 22) Source(13, 25) + SourceIndex(0)
-7 >Emitted(15, 23) Source(13, 26) + SourceIndex(0)
----
->>>exports.a3 = m2.m2_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >export var 
-2 >a3
-3 >           = 
-4 >             m2
-5 >               .
-6 >                m2_c1
-7 >                     ;
-1->Emitted(16, 1) Source(14, 12) + SourceIndex(0)
-2 >Emitted(16, 11) Source(14, 14) + SourceIndex(0)
-3 >Emitted(16, 14) Source(14, 17) + SourceIndex(0)
-4 >Emitted(16, 16) Source(14, 19) + SourceIndex(0)
-5 >Emitted(16, 17) Source(14, 20) + SourceIndex(0)
-6 >Emitted(16, 22) Source(14, 25) + SourceIndex(0)
-7 >Emitted(16, 23) Source(14, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: 
+sources: outputdir_module_multifolder/ref/m1.ts,outputdir_module_multifolder_ref/m2.ts,outputdir_module_multifolder/test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 14c09e444a5..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index a603394fc15..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleMultifolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AAC9B,IAAO,EAAE,WAAW,wCAAwC,CAAC,CAAC;AACnD,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;AACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..f385e49ecd1 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
index 512eba0e11a..262e5cdc1f3 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js.map
deleted file mode 100644
index e0af3af9b22..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"../src/","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/sourceRootRelativePathModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/sourceRootRelativePathModuleSimpleSpecifyOutputFile.json
index a4a6698d3ca..8213a1478ae 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/sourceRootRelativePathModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/sourceRootRelativePathModuleSimpleSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/sourceRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/sourceRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
index c259bb45210..fc0f367f343 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/sourceRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/sourceRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: ../src/
-sources: m1.ts
+sources: m1.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:m1.js
+emittedFile:bin/test.js
 sourceFile:m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 372f1052b89..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 22f07c17544..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
index 512eba0e11a..f55a72e7977 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["m1.ts","test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js.map
deleted file mode 100644
index 05c53f0182e..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"../src/","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.json
index a4a6698d3ca..8213a1478ae 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
index 65bea50d84f..2910ad61478 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/sourceRootRelativePathModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: ../src/
-sources: m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: ../src/
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^
-6 >                     ^
-7 >                      ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "m1"
-6 >                     )
-7 >                      ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 22) Source(1, 25) + SourceIndex(0)
-6 >Emitted(1, 23) Source(1, 26) + SourceIndex(0)
-7 >Emitted(1, 24) Source(1, 27) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: 
+sources: m1.ts,test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index c2e7dfa443b..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 1e72e2a2203..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSimpleSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,IAAI,CAAC,CAAC;AACf,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..18d212c7e69 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
index 512eba0e11a..dc294ebd160 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index aaae11bb5b5..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"../src/","sources":["ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.json
index 71896f202b2..a5966ef08b8 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 7be1fe1fb8f..83f9ef1f262 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: ../src/
-sources: ref/m1.ts
+sources: ref/m1.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 6c8aeb3190b..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 22f07c17544..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
index 512eba0e11a..f803a29f3bf 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["ref/m1.ts","test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 702b574b614..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"../src/","sources":["ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.json
index 71896f202b2..a5966ef08b8 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 5a3d45c1960..b05ffee34ca 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/sourceRootRelativePathModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: ../src/
-sources: ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: ../src/
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: ../src/
-sources: 
+sources: ref/m1.ts,test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 46c9f29e55a..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index b3972a3cfc1..00000000000
--- a/tests/baselines/reference/project/sourceRootRelativePathModuleSubfolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"../src/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AACnB,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/node/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/node/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/node/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/node/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/node/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/node/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSingleFileSpecifyOutputFile/node/sourceRootRelativePathSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSingleFileSpecifyOutputFile/node/sourceRootRelativePathSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSingleFileSpecifyOutputFile/node/sourceRootRelativePathSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/node/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/node/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/node/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index 5af28cf8560..13e9de8f87f 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
index a1d591a0497..94371fe696d 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
deleted file mode 100644
index cbb7eed4953..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.json
index 3270fe610aa..39cb44f229f 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.json
@@ -15,9 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.sourcemap.txt
index b1d3f293b7e..821236c5c85 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: 
-sources: m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: 
-sources: ../ref/m1.ts,../test.ts
+sources: ../ref/m1.ts,../ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -306,7 +134,7 @@ sourceFile:../ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:../ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
+sourceFile:../ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
 sourceFile:../test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:../test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:../test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:../test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:../test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:../test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:../test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
index a1d591a0497..a580c050d07 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
deleted file mode 100644
index 0826e9e95f3..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.json
index 3270fe610aa..39cb44f229f 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.json
@@ -15,9 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.sourcemap.txt
index 676e8f264ec..e37948398a3 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: 
-sources: m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: 
-sources: ../ref/m1.ts,../test.ts
+sources: ../ref/m1.ts,../ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -322,8 +151,8 @@ sourceFile:../test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:../test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:../test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:../test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:../test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:../test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:../test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index 1750a5975ae..81bb710c580 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
index 4f87045fd25..22aaecafe2d 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../ref/m1.ts","../ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index aabf49f904d..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../../ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 3a260af84a0..117a18c7c7a 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index a73c3b0852a..4394eb0748e 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: 
-sources: ../../../ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:../../../ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: outAndOutDirFile.js.map
 sourceRoot: 
-sources: ../ref/m1.ts,../test.ts
+sources: ../ref/m1.ts,../ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -306,7 +134,7 @@ sourceFile:../ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:../ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
+sourceFile:../ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/outAndOutDirFile.js
 sourceFile:../test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:../test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:../test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:../test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:../test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:../test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:../test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
index 4f87045fd25..2eab0f87324 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"","sources":["../ref/m1.ts","../ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index e31d90a8f0c..00000000000
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["../../../ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index 3a260af84a0..117a18c7c7a 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index 77ff10492be..9486ad5e3a7 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: 
-sources: ../../../ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:../../../ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: outAndOutDirFile.js.map
 sourceRoot: 
-sources: ../ref/m1.ts,../test.ts
+sources: ../ref/m1.ts,../ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -322,8 +151,8 @@ sourceFile:../test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:../test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:../test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:../test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:../test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:../test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:../test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:../test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..994e21ca032 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,45 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..c532c3846d9 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../../outputdir_module_multifolder_ref/m2.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICNU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
deleted file mode 100644
index cbb7eed4953..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile1.js b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 51755e4c9a3..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/sourcemapModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/sourcemapModuleMultifolderSpecifyOutputFile.json
index 3d2df95ad66..7ba960c4bef 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/sourcemapModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/sourcemapModuleMultifolderSpecifyOutputFile.json
@@ -15,15 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/sourcemapModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/sourcemapModuleMultifolderSpecifyOutputFile.sourcemap.txt
index 74ecef44103..6c8bdf4da74 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/sourcemapModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/sourcemapModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: 
-sources: m1.ts
+sources: ../ref/m1.ts,../../outputdir_module_multifolder_ref/m2.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:m1.ts
+emittedFile:bin/test.js
+sourceFile:../ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
+sourceFile:../../outputdir_module_multifolder_ref/m2.ts
+-------------------------------------------------------------------
 >>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: 
-sources: m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
 >>>    exports.m2_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -193,24 +187,24 @@ sourceFile:m2.ts
 3 >                  = 
 4 >                    10
 5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
+1 >Emitted(16, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(16, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(16, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(16, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(16, 24) Source(1, 23) + SourceIndex(1)
 ---
 >>>    var m2_c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(2, 1) + SourceIndex(1)
 ---
 >>>        function m2_c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
+1->Emitted(18, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -220,16 +214,16 @@ sourceFile:m2.ts
   >    public m2_c1_p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
+1->Emitted(19, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(19, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
 ---
 >>>        return m2_c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
+1->Emitted(20, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(20, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
 ---
 >>>    })();
 1 >^^^^
@@ -243,10 +237,10 @@ sourceFile:m2.ts
 4 >     export class m2_c1 {
   >         public m2_c1_p1: number;
   >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(21, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_c1 = m2_c1;
 1->^^^^
@@ -260,10 +254,10 @@ sourceFile:m2.ts
   >                     public m2_c1_p1: number;
   >                 }
 4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(22, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(22, 27) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_instance1 = new m2_c1();
 1->^^^^
@@ -282,20 +276,20 @@ sourceFile:m2.ts
 5 >                               m2_c1
 6 >                                    ()
 7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
+1->Emitted(23, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(23, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(23, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(23, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(23, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(23, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(23, 40) Source(6, 39) + SourceIndex(1)
 ---
 >>>    function m2_f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(7, 1) + SourceIndex(1)
 ---
 >>>        return exports.m2_instance1;
 1->^^^^^^^^
@@ -309,11 +303,11 @@ sourceFile:m2.ts
 3 >               
 4 >               m2_instance1
 5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
+1->Emitted(25, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(25, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(25, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(25, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(25, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
 ---
 >>>    }
 1 >^^^^
@@ -322,8 +316,8 @@ sourceFile:m2.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
+1 >Emitted(26, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(26, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
 ---
 >>>    exports.m2_f1 = m2_f1;
 1->^^^^
@@ -336,23 +330,17 @@ sourceFile:m2.ts
   >                     return m2_instance1;
   >                 }
 4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(27, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(27, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(27, 27) Source(9, 2) + SourceIndex(1)
 ---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
+sourceFile:../test.ts
+-------------------------------------------------------------------
 >>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+>>>define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -367,24 +355,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(3, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(3, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(3, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(3, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(3, 20) + SourceIndex(0)
+1 >Emitted(30, 5) Source(3, 12) + SourceIndex(2)
+2 >Emitted(30, 15) Source(3, 14) + SourceIndex(2)
+3 >Emitted(30, 18) Source(3, 17) + SourceIndex(2)
+4 >Emitted(30, 20) Source(3, 19) + SourceIndex(2)
+5 >Emitted(30, 21) Source(3, 20) + SourceIndex(2)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(4, 1) + SourceIndex(0)
+1->Emitted(31, 5) Source(4, 1) + SourceIndex(2)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(4, 1) + SourceIndex(0) name (c1)
+1->Emitted(32, 9) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -394,16 +382,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(6, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(33, 9) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(33, 10) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(6, 2) + SourceIndex(0) name (c1)
+1->Emitted(34, 9) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(34, 18) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -417,10 +405,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(4, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(6, 2) + SourceIndex(0)
+1 >Emitted(35, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(35, 6) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(35, 6) Source(4, 1) + SourceIndex(2)
+4 >Emitted(35, 10) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -434,10 +422,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(4, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(4, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(6, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(6, 2) + SourceIndex(0)
+1->Emitted(36, 5) Source(4, 14) + SourceIndex(2)
+2 >Emitted(36, 15) Source(4, 16) + SourceIndex(2)
+3 >Emitted(36, 20) Source(6, 2) + SourceIndex(2)
+4 >Emitted(36, 21) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -456,20 +444,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(8, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(8, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(8, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(8, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(8, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(8, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(8, 33) + SourceIndex(0)
+1->Emitted(37, 5) Source(8, 12) + SourceIndex(2)
+2 >Emitted(37, 22) Source(8, 21) + SourceIndex(2)
+3 >Emitted(37, 25) Source(8, 24) + SourceIndex(2)
+4 >Emitted(37, 29) Source(8, 28) + SourceIndex(2)
+5 >Emitted(37, 31) Source(8, 30) + SourceIndex(2)
+6 >Emitted(37, 33) Source(8, 32) + SourceIndex(2)
+7 >Emitted(37, 34) Source(8, 33) + SourceIndex(2)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(9, 1) + SourceIndex(0)
+1 >Emitted(38, 5) Source(9, 1) + SourceIndex(2)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -483,11 +471,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(10, 22) + SourceIndex(0) name (f1)
+1->Emitted(39, 9) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(39, 15) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(39, 16) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(39, 33) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(39, 34) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -496,8 +484,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(11, 2) + SourceIndex(0) name (f1)
+1 >Emitted(40, 5) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(40, 6) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -511,10 +499,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(9, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(9, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(11, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(11, 2) + SourceIndex(0)
+1->Emitted(41, 5) Source(9, 17) + SourceIndex(2)
+2 >Emitted(41, 15) Source(9, 19) + SourceIndex(2)
+3 >Emitted(41, 20) Source(11, 2) + SourceIndex(2)
+4 >Emitted(41, 21) Source(11, 2) + SourceIndex(2)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -534,13 +522,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(13, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(13, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(13, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(13, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(13, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(13, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(13, 26) + SourceIndex(0)
+1->Emitted(42, 5) Source(13, 12) + SourceIndex(2)
+2 >Emitted(42, 15) Source(13, 14) + SourceIndex(2)
+3 >Emitted(42, 18) Source(13, 17) + SourceIndex(2)
+4 >Emitted(42, 20) Source(13, 19) + SourceIndex(2)
+5 >Emitted(42, 21) Source(13, 20) + SourceIndex(2)
+6 >Emitted(42, 26) Source(13, 25) + SourceIndex(2)
+7 >Emitted(42, 27) Source(13, 26) + SourceIndex(2)
 ---
 >>>    exports.a3 = m2.m2_c1;
 1->^^^^
@@ -558,19 +546,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m2_c1
 7 >                         ;
-1->Emitted(15, 5) Source(14, 12) + SourceIndex(0)
-2 >Emitted(15, 15) Source(14, 14) + SourceIndex(0)
-3 >Emitted(15, 18) Source(14, 17) + SourceIndex(0)
-4 >Emitted(15, 20) Source(14, 19) + SourceIndex(0)
-5 >Emitted(15, 21) Source(14, 20) + SourceIndex(0)
-6 >Emitted(15, 26) Source(14, 25) + SourceIndex(0)
-7 >Emitted(15, 27) Source(14, 26) + SourceIndex(0)
+1->Emitted(43, 5) Source(14, 12) + SourceIndex(2)
+2 >Emitted(43, 15) Source(14, 14) + SourceIndex(2)
+3 >Emitted(43, 18) Source(14, 17) + SourceIndex(2)
+4 >Emitted(43, 20) Source(14, 19) + SourceIndex(2)
+5 >Emitted(43, 21) Source(14, 20) + SourceIndex(2)
+6 >Emitted(43, 26) Source(14, 25) + SourceIndex(2)
+7 >Emitted(43, 27) Source(14, 26) + SourceIndex(2)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 5cca04a0f25..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 462fa38ab42..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IAEW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..2974abdc1cc 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../../outputdir_module_multifolder_ref/m2.ts","../test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
deleted file mode 100644
index 0826e9e95f3..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"","sources":["m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile1.js b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile1.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 095951a67d0..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.json
index 3d2df95ad66..7ba960c4bef 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.json
@@ -15,15 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.sourcemap.txt
index f8d10678ca0..70054e8f1c6 100644
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/sourcemapModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,620 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: 
-sources: m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: 
-sources: m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: 
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-8 >                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>var m2 = require("../outputdir_module_multifolder_ref/m2");
-1->
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-6 >                                                         ^
-7 >                                                          ^
-1->
-  >
-2 >import 
-3 >    m2
-4 >       = require(
-5 >                 "../outputdir_module_multifolder_ref/m2"
-6 >                                                         )
-7 >                                                          ;
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
-2 >Emitted(2, 5) Source(2, 8) + SourceIndex(0)
-3 >Emitted(2, 7) Source(2, 10) + SourceIndex(0)
-4 >Emitted(2, 18) Source(2, 21) + SourceIndex(0)
-5 >Emitted(2, 58) Source(2, 61) + SourceIndex(0)
-6 >Emitted(2, 59) Source(2, 62) + SourceIndex(0)
-7 >Emitted(2, 60) Source(2, 63) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(3, 1) Source(3, 12) + SourceIndex(0)
-2 >Emitted(3, 11) Source(3, 14) + SourceIndex(0)
-3 >Emitted(3, 14) Source(3, 17) + SourceIndex(0)
-4 >Emitted(3, 16) Source(3, 19) + SourceIndex(0)
-5 >Emitted(3, 17) Source(3, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(4, 1) Source(4, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(6, 5) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(6, 6) Source(6, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 14) Source(6, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(8, 1) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(8, 2) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(8, 2) Source(4, 1) + SourceIndex(0)
-4 >Emitted(8, 6) Source(6, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(9, 1) Source(4, 14) + SourceIndex(0)
-2 >Emitted(9, 11) Source(4, 16) + SourceIndex(0)
-3 >Emitted(9, 16) Source(6, 2) + SourceIndex(0)
-4 >Emitted(9, 17) Source(6, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(10, 1) Source(8, 12) + SourceIndex(0)
-2 >Emitted(10, 18) Source(8, 21) + SourceIndex(0)
-3 >Emitted(10, 21) Source(8, 24) + SourceIndex(0)
-4 >Emitted(10, 25) Source(8, 28) + SourceIndex(0)
-5 >Emitted(10, 27) Source(8, 30) + SourceIndex(0)
-6 >Emitted(10, 29) Source(8, 32) + SourceIndex(0)
-7 >Emitted(10, 30) Source(8, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(12, 5) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(12, 11) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(12, 12) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(12, 29) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(12, 30) Source(10, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(13, 1) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(13, 2) Source(11, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(14, 1) Source(9, 17) + SourceIndex(0)
-2 >Emitted(14, 11) Source(9, 19) + SourceIndex(0)
-3 >Emitted(14, 16) Source(11, 2) + SourceIndex(0)
-4 >Emitted(14, 17) Source(11, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(15, 1) Source(13, 12) + SourceIndex(0)
-2 >Emitted(15, 11) Source(13, 14) + SourceIndex(0)
-3 >Emitted(15, 14) Source(13, 17) + SourceIndex(0)
-4 >Emitted(15, 16) Source(13, 19) + SourceIndex(0)
-5 >Emitted(15, 17) Source(13, 20) + SourceIndex(0)
-6 >Emitted(15, 22) Source(13, 25) + SourceIndex(0)
-7 >Emitted(15, 23) Source(13, 26) + SourceIndex(0)
----
->>>exports.a3 = m2.m2_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >export var 
-2 >a3
-3 >           = 
-4 >             m2
-5 >               .
-6 >                m2_c1
-7 >                     ;
-1->Emitted(16, 1) Source(14, 12) + SourceIndex(0)
-2 >Emitted(16, 11) Source(14, 14) + SourceIndex(0)
-3 >Emitted(16, 14) Source(14, 17) + SourceIndex(0)
-4 >Emitted(16, 16) Source(14, 19) + SourceIndex(0)
-5 >Emitted(16, 17) Source(14, 20) + SourceIndex(0)
-6 >Emitted(16, 22) Source(14, 25) + SourceIndex(0)
-7 >Emitted(16, 23) Source(14, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: 
+sources: ../ref/m1.ts,../../outputdir_module_multifolder_ref/m2.ts,../test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 14c09e444a5..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 3b3ef6b145c..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleMultifolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AAC9B,IAAO,EAAE,WAAW,wCAAwC,CAAC,CAAC;AACnD,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;AACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..f385e49ecd1 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..6377a26395e 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.js.map b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.js.map
deleted file mode 100644
index 51755e4c9a3..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/sourcemapModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/sourcemapModuleSimpleSpecifyOutputFile.json
index 9ff29662d40..c9889aff69b 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/sourcemapModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/sourcemapModuleSimpleSpecifyOutputFile.json
@@ -14,12 +14,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/sourcemapModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/sourcemapModuleSimpleSpecifyOutputFile.sourcemap.txt
index a1646bc14e5..71c0a41b2d1 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/sourcemapModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/sourcemapModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: 
-sources: m1.ts
+sources: ../m1.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:m1.ts
+emittedFile:bin/test.js
+sourceFile:../m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
+sourceFile:../test.ts
+-------------------------------------------------------------------
 >>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>define(["require", "exports", "m1"], function (require, exports, m1) {
+>>>define("test", ["require", "exports", "m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 372f1052b89..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 9bcc170386c..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..f491a9ec373 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../m1.ts","../test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.js.map b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.js.map
deleted file mode 100644
index 095951a67d0..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.json
index 9ff29662d40..c9889aff69b 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.json
@@ -14,12 +14,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.sourcemap.txt
index 4ff8b4fa8c7..056b7a1c7f2 100644
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/sourcemapModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: 
-sources: m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: 
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^
-6 >                     ^
-7 >                      ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "m1"
-6 >                     )
-7 >                      ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 22) Source(1, 25) + SourceIndex(0)
-6 >Emitted(1, 23) Source(1, 26) + SourceIndex(0)
-7 >Emitted(1, 24) Source(1, 27) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: 
+sources: ../m1.ts,../test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index c2e7dfa443b..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 7bae4ed7491..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSimpleSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,IAAI,CAAC,CAAC;AACf,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..18d212c7e69 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
index c1e0281a2ab..f77c1351b15 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 51755e4c9a3..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/sourcemapModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/sourcemapModuleSubfolderSpecifyOutputFile.json
index 9d200ef685d..da85c1bf06c 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/sourcemapModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/sourcemapModuleSubfolderSpecifyOutputFile.json
@@ -14,12 +14,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/sourcemapModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/sourcemapModuleSubfolderSpecifyOutputFile.sourcemap.txt
index d0abf20190f..9c12e1749ca 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/sourcemapModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/sourcemapModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: 
-sources: m1.ts
+sources: ../ref/m1.ts,../test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:m1.ts
+emittedFile:bin/test.js
+sourceFile:../ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
+sourceFile:../test.ts
+-------------------------------------------------------------------
 >>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1"], function (require, exports, m1) {
+>>>define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 6c8aeb3190b..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 9bcc170386c..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
index c1e0281a2ab..bfdacf69428 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"","sources":["../ref/m1.ts","../test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 095951a67d0..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.json
index 9d200ef685d..da85c1bf06c 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.json
@@ -14,12 +14,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 205f70497ad..282a64dbc6f 100644
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/sourcemapModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: 
-sources: m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: 
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: 
-sources: 
+sources: ../ref/m1.ts,../test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 46c9f29e55a..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 56d42d8bdfd..00000000000
--- a/tests/baselines/reference/project/sourcemapModuleSubfolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AACnB,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/node/sourcemapMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/node/sourcemapMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/node/sourcemapMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/node/sourcemapSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/node/sourcemapSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/node/sourcemapSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSingleFileSpecifyOutputFile/node/sourcemapSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapSingleFileSpecifyOutputFile/node/sourcemapSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSingleFileSpecifyOutputFile/node/sourcemapSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/node/sourcemapSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/node/sourcemapSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/node/sourcemapSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
index 5af28cf8560..13e9de8f87f 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
index 7a70d18105c..37bb9be8a95 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
deleted file mode 100644
index 04f168a6289..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.json
index 50a4518a1b0..7316c8b01c9 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
index d4cac643490..51a641cb750 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -306,7 +134,7 @@ sourceFile:ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/test.js
+sourceFile:ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
index d61b4c3b876..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
index 7a70d18105c..a6626039aa2 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
deleted file mode 100644
index 0ce68e169af..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.json
index 50a4518a1b0..7316c8b01c9 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.json
@@ -16,9 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m2.js.map",
-        "ref/m2.js",
-        "ref/m2.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
index cb96dcbf7d7..38aecc15857 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/test.js
@@ -322,8 +151,8 @@ sourceFile:test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
index 1750a5975ae..81bb710c580 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js
@@ -8,6 +8,20 @@ var m1_instance1 = new m1_c1();
 function m1_f1() {
     return m1_instance1;
 }
+define("ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
 /// <reference path='ref/m1.ts'/>
 /// <reference path='ref/m2.ts'/>
 var a1 = 10;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
index 53e31e30260..f3058d9f878 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 04f168a6289..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index b6ef6b5bd51..e165908b72c 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index d54fa316273..df760dc79b0 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,180 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
->>>    exports.m2_a1 = 10;
-1 >^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^
-5 >                      ^
-6 >                       ^^^^^^^^->
-1 >export var 
-2 >    m2_a1
-3 >                  = 
-4 >                    10
-5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
----
->>>    var m2_c1 = (function () {
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
----
->>>        function m2_c1() {
-1->^^^^^^^^
-2 >        ^^->
-1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>        }
-1->^^^^^^^^
-2 >        ^
-3 >         ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>        return m2_c1;
-1->^^^^^^^^
-2 >        ^^^^^^^^^^^^
-1->
-2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>    })();
-1 >^^^^
-2 >    ^
-3 >     
-4 >     ^^^^
-5 >         ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >    }
-3 >     
-4 >     export class m2_c1 {
-  >         public m2_c1_p1: number;
-  >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_c1 = m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-5 >                          ^^^^^^^^^^^^^^->
-1->
-2 >    m2_c1
-3 >                  {
-  >                     public m2_c1_p1: number;
-  >                 }
-4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
----
->>>    exports.m2_instance1 = new m2_c1();
-1->^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^
-3 >                        ^^^
-4 >                           ^^^^
-5 >                               ^^^^^
-6 >                                    ^^
-7 >                                      ^
-1->
-  >
-  >export var 
-2 >    m2_instance1
-3 >                         = 
-4 >                           new 
-5 >                               m2_c1
-6 >                                    ()
-7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
----
->>>    function m2_f1() {
-1 >^^^^
-2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
----
->>>        return exports.m2_instance1;
-1->^^^^^^^^
-2 >        ^^^^^^
-3 >              ^
-4 >               ^^^^^^^^^^^^^^^^^^^^
-5 >                                   ^
-1->export function m2_f1() {
-  >    
-2 >        return
-3 >               
-4 >               m2_instance1
-5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>    }
-1 >^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>    exports.m2_f1 = m2_f1;
-1->^^^^
-2 >    ^^^^^^^^^^^^^
-3 >                 ^^^^^^^^
-4 >                         ^
-1->
-2 >    m2_f1
-3 >                 () {
-  >                     return m2_instance1;
-  >                 }
-4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
----
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: outAndOutDirFile.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -306,7 +134,7 @@ sourceFile:ref/m1.ts
 >>>}
 1 >
 2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+3 > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
 2 >}
@@ -315,16 +143,182 @@ sourceFile:ref/m1.ts
 ---
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
+sourceFile:ref/m2.ts
+-------------------------------------------------------------------
+>>>define("ref/m2", ["require", "exports"], function (require, exports) {
+>>>    exports.m2_a1 = 10;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^
+4 >                    ^^
+5 >                      ^
+6 >                       ^^^^^^^^->
+1->export var 
+2 >    m2_a1
+3 >                  = 
+4 >                    10
+5 >                      ;
+1->Emitted(12, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(12, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(12, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(12, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(12, 24) Source(1, 23) + SourceIndex(1)
+---
+>>>    var m2_c1 = (function () {
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
+1->
+  >
+1->Emitted(13, 5) Source(2, 1) + SourceIndex(1)
+---
+>>>        function m2_c1() {
+1->^^^^^^^^
+2 >        ^^->
+1->
+1->Emitted(14, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
+---
+>>>        }
+1->^^^^^^^^
+2 >        ^
+3 >         ^^^^^^^^^^^^^->
+1->export class m2_c1 {
+  >    public m2_c1_p1: number;
+  >
+2 >        }
+1->Emitted(15, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(15, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
+---
+>>>        return m2_c1;
+1->^^^^^^^^
+2 >        ^^^^^^^^^^^^
+1->
+2 >        }
+1->Emitted(16, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(16, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
+---
+>>>    })();
+1 >^^^^
+2 >    ^
+3 >     
+4 >     ^^^^
+5 >         ^^^^^^^^^^^^^^^^^^->
+1 >
+2 >    }
+3 >     
+4 >     export class m2_c1 {
+  >         public m2_c1_p1: number;
+  >     }
+1 >Emitted(17, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(17, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(17, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(17, 10) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_c1 = m2_c1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+5 >                          ^^^^^^^^^^^^^^->
+1->
+2 >    m2_c1
+3 >                  {
+  >                     public m2_c1_p1: number;
+  >                 }
+4 >                         
+1->Emitted(18, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(18, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(18, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(18, 27) Source(4, 2) + SourceIndex(1)
+---
+>>>    exports.m2_instance1 = new m2_c1();
+1->^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^
+3 >                        ^^^
+4 >                           ^^^^
+5 >                               ^^^^^
+6 >                                    ^^
+7 >                                      ^
+1->
+  >
+  >export var 
+2 >    m2_instance1
+3 >                         = 
+4 >                           new 
+5 >                               m2_c1
+6 >                                    ()
+7 >                                      ;
+1->Emitted(19, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(19, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(19, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(19, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(19, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(19, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(19, 40) Source(6, 39) + SourceIndex(1)
+---
+>>>    function m2_f1() {
+1 >^^^^
+2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+1 >Emitted(20, 5) Source(7, 1) + SourceIndex(1)
+---
+>>>        return exports.m2_instance1;
+1->^^^^^^^^
+2 >        ^^^^^^
+3 >              ^
+4 >               ^^^^^^^^^^^^^^^^^^^^
+5 >                                   ^
+1->export function m2_f1() {
+  >    
+2 >        return
+3 >               
+4 >               m2_instance1
+5 >                                   ;
+1->Emitted(21, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(21, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(21, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(21, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(21, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
+---
+>>>    }
+1 >^^^^
+2 >    ^
+3 >     ^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+  >
+2 >    }
+1 >Emitted(22, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(22, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
+---
+>>>    exports.m2_f1 = m2_f1;
+1->^^^^
+2 >    ^^^^^^^^^^^^^
+3 >                 ^^^^^^^^
+4 >                         ^
+1->
+2 >    m2_f1
+3 >                 () {
+  >                     return m2_instance1;
+  >                 }
+4 >                         
+1->Emitted(23, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(23, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(23, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(23, 27) Source(9, 2) + SourceIndex(1)
+---
+-------------------------------------------------------------------
+emittedFile:bin/outAndOutDirFile.js
 sourceFile:test.ts
 -------------------------------------------------------------------
+>>>});
 >>>/// <reference path='ref/m1.ts'/>
-1->
+1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 3 >                                 ^->
-1->
+1 >
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1 >Emitted(25, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(25, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -332,8 +326,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(26, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(26, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -350,25 +344,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(27, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(27, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(27, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(27, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(27, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(27, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(28, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(29, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -378,16 +372,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(30, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(30, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(31, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(31, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -401,10 +395,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(32, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(32, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(32, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(32, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -425,21 +419,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(33, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(33, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(33, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(33, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(33, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(33, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(33, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(33, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(34, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -453,11 +447,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(35, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(35, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(35, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(35, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(35, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -466,7 +460,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(36, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(36, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
index 9b9cdd4a214..c3a64f5b6eb 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.d.ts
@@ -1,10 +1,17 @@
-/// <reference path="../outdir/outAndOutDirFolder/ref/m2.d.ts" />
 declare var m1_a1: number;
 declare class m1_c1 {
     m1_c1_p1: number;
 }
 declare var m1_instance1: m1_c1;
 declare function m1_f1(): m1_c1;
+declare module "ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
 declare var a1: number;
 declare class c1 {
     p1: number;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
index 53e31e30260..ba9f4ee590c 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/bin/outAndOutDirFile.js.map
@@ -1 +1 @@
-{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;ACRD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
+{"version":3,"file":"outAndOutDirFile.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","ref/m2.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":"AAAA,IAAI,KAAK,GAAG,EAAE,CAAC;AACf;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,YAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AAC/B;IACIE,MAAMA,CAACA,YAAYA,CAACA;AACxBA,CAACA;AERD,iCAAiC;AACjC,iCAAiC;AACjC,IAAI,EAAE,GAAG,EAAE,CAAC;AACZ;IAAAC;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAED,IAAI,SAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AACzB;IACIE,MAAMA,CAACA,SAASA,CAACA;AACrBA,CAACA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
deleted file mode 100644
index 0ce68e169af..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outdir/outAndOutDirFolder/ref/m2.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
new file mode 100644
index 00000000000..ea1bbf2ba6b
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
index b6ef6b5bd51..e165908b72c 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.json
@@ -17,9 +17,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "outdir/outAndOutDirFolder/ref/m2.js.map",
-        "outdir/outAndOutDirFolder/ref/m2.js",
-        "outdir/outAndOutDirFolder/ref/m2.d.ts",
         "bin/outAndOutDirFile.js.map",
         "bin/outAndOutDirFile.js",
         "bin/outAndOutDirFile.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
index 8bd8c2ac035..c8507ca7df8 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.sourcemap.txt
@@ -1,179 +1,8 @@
 ===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:outdir/outAndOutDirFolder/ref/m2.js
-sourceFile:ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: outAndOutDirFile.js
 mapUrl: outAndOutDirFile.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts,test.ts
+sources: ref/m1.ts,ref/m2.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
 emittedFile:bin/outAndOutDirFile.js
@@ -322,8 +151,8 @@ sourceFile:test.ts
 3 >                                 ^->
 1->
 2 >/// <reference path='ref/m1.ts'/>
-1->Emitted(11, 1) Source(1, 1) + SourceIndex(1)
-2 >Emitted(11, 34) Source(1, 34) + SourceIndex(1)
+1->Emitted(11, 1) Source(1, 1) + SourceIndex(2)
+2 >Emitted(11, 34) Source(1, 34) + SourceIndex(2)
 ---
 >>>/// <reference path='ref/m2.ts'/>
 1->
@@ -331,8 +160,8 @@ sourceFile:test.ts
 1->
   >
 2 >/// <reference path='ref/m2.ts'/>
-1->Emitted(12, 1) Source(2, 1) + SourceIndex(1)
-2 >Emitted(12, 34) Source(2, 34) + SourceIndex(1)
+1->Emitted(12, 1) Source(2, 1) + SourceIndex(2)
+2 >Emitted(12, 34) Source(2, 34) + SourceIndex(2)
 ---
 >>>var a1 = 10;
 1 >
@@ -349,25 +178,25 @@ sourceFile:test.ts
 4 >       = 
 5 >         10
 6 >           ;
-1 >Emitted(13, 1) Source(3, 1) + SourceIndex(1)
-2 >Emitted(13, 5) Source(3, 5) + SourceIndex(1)
-3 >Emitted(13, 7) Source(3, 7) + SourceIndex(1)
-4 >Emitted(13, 10) Source(3, 10) + SourceIndex(1)
-5 >Emitted(13, 12) Source(3, 12) + SourceIndex(1)
-6 >Emitted(13, 13) Source(3, 13) + SourceIndex(1)
+1 >Emitted(13, 1) Source(3, 1) + SourceIndex(2)
+2 >Emitted(13, 5) Source(3, 5) + SourceIndex(2)
+3 >Emitted(13, 7) Source(3, 7) + SourceIndex(2)
+4 >Emitted(13, 10) Source(3, 10) + SourceIndex(2)
+5 >Emitted(13, 12) Source(3, 12) + SourceIndex(2)
+6 >Emitted(13, 13) Source(3, 13) + SourceIndex(2)
 ---
 >>>var c1 = (function () {
 1->
 2 >^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(14, 1) Source(4, 1) + SourceIndex(1)
+1->Emitted(14, 1) Source(4, 1) + SourceIndex(2)
 ---
 >>>    function c1() {
 1->^^^^
 2 >    ^^->
 1->
-1->Emitted(15, 5) Source(4, 1) + SourceIndex(1) name (c1)
+1->Emitted(15, 5) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>    }
 1->^^^^
@@ -377,16 +206,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >    }
-1->Emitted(16, 5) Source(6, 1) + SourceIndex(1) name (c1.constructor)
-2 >Emitted(16, 6) Source(6, 2) + SourceIndex(1) name (c1.constructor)
+1->Emitted(16, 5) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(16, 6) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>    return c1;
 1->^^^^
 2 >    ^^^^^^^^^
 1->
 2 >    }
-1->Emitted(17, 5) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(17, 14) Source(6, 2) + SourceIndex(1) name (c1)
+1->Emitted(17, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(17, 14) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>})();
 1 >
@@ -400,10 +229,10 @@ sourceFile:test.ts
 4 > class c1 {
   >     public p1: number;
   > }
-1 >Emitted(18, 1) Source(6, 1) + SourceIndex(1) name (c1)
-2 >Emitted(18, 2) Source(6, 2) + SourceIndex(1) name (c1)
-3 >Emitted(18, 2) Source(4, 1) + SourceIndex(1)
-4 >Emitted(18, 6) Source(6, 2) + SourceIndex(1)
+1 >Emitted(18, 1) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(18, 2) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(18, 2) Source(4, 1) + SourceIndex(2)
+4 >Emitted(18, 6) Source(6, 2) + SourceIndex(2)
 ---
 >>>var instance1 = new c1();
 1->
@@ -424,21 +253,21 @@ sourceFile:test.ts
 6 >                    c1
 7 >                      ()
 8 >                        ;
-1->Emitted(19, 1) Source(8, 1) + SourceIndex(1)
-2 >Emitted(19, 5) Source(8, 5) + SourceIndex(1)
-3 >Emitted(19, 14) Source(8, 14) + SourceIndex(1)
-4 >Emitted(19, 17) Source(8, 17) + SourceIndex(1)
-5 >Emitted(19, 21) Source(8, 21) + SourceIndex(1)
-6 >Emitted(19, 23) Source(8, 23) + SourceIndex(1)
-7 >Emitted(19, 25) Source(8, 25) + SourceIndex(1)
-8 >Emitted(19, 26) Source(8, 26) + SourceIndex(1)
+1->Emitted(19, 1) Source(8, 1) + SourceIndex(2)
+2 >Emitted(19, 5) Source(8, 5) + SourceIndex(2)
+3 >Emitted(19, 14) Source(8, 14) + SourceIndex(2)
+4 >Emitted(19, 17) Source(8, 17) + SourceIndex(2)
+5 >Emitted(19, 21) Source(8, 21) + SourceIndex(2)
+6 >Emitted(19, 23) Source(8, 23) + SourceIndex(2)
+7 >Emitted(19, 25) Source(8, 25) + SourceIndex(2)
+8 >Emitted(19, 26) Source(8, 26) + SourceIndex(2)
 ---
 >>>function f1() {
 1 >
 2 >^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(20, 1) Source(9, 1) + SourceIndex(1)
+1 >Emitted(20, 1) Source(9, 1) + SourceIndex(2)
 ---
 >>>    return instance1;
 1->^^^^
@@ -452,11 +281,11 @@ sourceFile:test.ts
 3 >           
 4 >           instance1
 5 >                    ;
-1->Emitted(21, 5) Source(10, 5) + SourceIndex(1) name (f1)
-2 >Emitted(21, 11) Source(10, 11) + SourceIndex(1) name (f1)
-3 >Emitted(21, 12) Source(10, 12) + SourceIndex(1) name (f1)
-4 >Emitted(21, 21) Source(10, 21) + SourceIndex(1) name (f1)
-5 >Emitted(21, 22) Source(10, 22) + SourceIndex(1) name (f1)
+1->Emitted(21, 5) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(21, 11) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(21, 12) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(21, 21) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(21, 22) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>}
 1 >
@@ -465,7 +294,7 @@ sourceFile:test.ts
 1 >
   >
 2 >}
-1 >Emitted(22, 1) Source(11, 1) + SourceIndex(1) name (f1)
-2 >Emitted(22, 2) Source(11, 2) + SourceIndex(1) name (f1)
+1 >Emitted(22, 1) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(22, 2) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>//# sourceMappingURL=outAndOutDirFile.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..994e21ca032 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,45 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
+    exports.m2_a1 = 10;
+    var m2_c1 = (function () {
+        function m2_c1() {
+        }
+        return m2_c1;
+    })();
+    exports.m2_c1 = m2_c1;
+    exports.m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return exports.m2_instance1;
+    }
+    exports.m2_f1 = m2_f1;
+});
+define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+    exports.a3 = m2.m2_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
index d3e851981ec..85e465474d3 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/ref/m1.ts","outputdir_module_multifolder_ref/m2.ts","outputdir_module_multifolder/test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","m2_c1","m2_c1.constructor","m2_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICRU,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAC;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICNU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
deleted file mode 100644
index 3b00d82ab66..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
deleted file mode 100644
index 144ad24e2de..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m2_a1 = 10;
-    var m2_c1 = (function () {
-        function m2_c1() {
-        }
-        return m2_c1;
-    })();
-    exports.m2_c1 = m2_c1;
-    exports.m2_instance1 = new m2_c1();
-    function m2_f1() {
-        return exports.m2_instance1;
-    }
-    exports.m2_f1 = m2_f1;
-});
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 8c257bd1111..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/sourcerootUrlModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/sourcerootUrlModuleMultifolderSpecifyOutputFile.json
index cc2a6c9b1aa..27485e45ad9 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/sourcerootUrlModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/sourcerootUrlModuleMultifolderSpecifyOutputFile.json
@@ -16,15 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/sourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/sourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
index 86764c6d57a..d2331ef3579 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/sourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/sourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder/ref/m1.ts
+sources: outputdir_module_multifolder/ref/m1.ts,outputdir_module_multifolder_ref/m2.ts,outputdir_module_multifolder/test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder/ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:outputdir_module_multifolder/ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder_ref/m2.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:diskFile1.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder_ref/m2.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>});
+>>>define("../outputdir_module_multifolder_ref/m2", ["require", "exports"], function (require, exports) {
 >>>    exports.m2_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -193,24 +187,24 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 3 >                  = 
 4 >                    10
 5 >                      ;
-1 >Emitted(2, 5) Source(1, 12) + SourceIndex(0)
-2 >Emitted(2, 18) Source(1, 17) + SourceIndex(0)
-3 >Emitted(2, 21) Source(1, 20) + SourceIndex(0)
-4 >Emitted(2, 23) Source(1, 22) + SourceIndex(0)
-5 >Emitted(2, 24) Source(1, 23) + SourceIndex(0)
+1 >Emitted(16, 5) Source(1, 12) + SourceIndex(1)
+2 >Emitted(16, 18) Source(1, 17) + SourceIndex(1)
+3 >Emitted(16, 21) Source(1, 20) + SourceIndex(1)
+4 >Emitted(16, 23) Source(1, 22) + SourceIndex(1)
+5 >Emitted(16, 24) Source(1, 23) + SourceIndex(1)
 ---
 >>>    var m2_c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(2, 1) + SourceIndex(1)
 ---
 >>>        function m2_c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(2, 1) + SourceIndex(0) name (m2_c1)
+1->Emitted(18, 9) Source(2, 1) + SourceIndex(1) name (m2_c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -220,16 +214,16 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >    public m2_c1_p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(5, 10) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
+1->Emitted(19, 9) Source(4, 1) + SourceIndex(1) name (m2_c1.constructor)
+2 >Emitted(19, 10) Source(4, 2) + SourceIndex(1) name (m2_c1.constructor)
 ---
 >>>        return m2_c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 21) Source(4, 2) + SourceIndex(0) name (m2_c1)
+1->Emitted(20, 9) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(20, 21) Source(4, 2) + SourceIndex(1) name (m2_c1)
 ---
 >>>    })();
 1 >^^^^
@@ -243,10 +237,10 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 4 >     export class m2_c1 {
   >         public m2_c1_p1: number;
   >     }
-1 >Emitted(7, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(7, 6) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(7, 6) Source(2, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(4, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(4, 1) + SourceIndex(1) name (m2_c1)
+2 >Emitted(21, 6) Source(4, 2) + SourceIndex(1) name (m2_c1)
+3 >Emitted(21, 6) Source(2, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_c1 = m2_c1;
 1->^^^^
@@ -260,10 +254,10 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >                     public m2_c1_p1: number;
   >                 }
 4 >                         
-1->Emitted(8, 5) Source(2, 14) + SourceIndex(0)
-2 >Emitted(8, 18) Source(2, 19) + SourceIndex(0)
-3 >Emitted(8, 26) Source(4, 2) + SourceIndex(0)
-4 >Emitted(8, 27) Source(4, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(2, 14) + SourceIndex(1)
+2 >Emitted(22, 18) Source(2, 19) + SourceIndex(1)
+3 >Emitted(22, 26) Source(4, 2) + SourceIndex(1)
+4 >Emitted(22, 27) Source(4, 2) + SourceIndex(1)
 ---
 >>>    exports.m2_instance1 = new m2_c1();
 1->^^^^
@@ -282,20 +276,20 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 5 >                               m2_c1
 6 >                                    ()
 7 >                                      ;
-1->Emitted(9, 5) Source(6, 12) + SourceIndex(0)
-2 >Emitted(9, 25) Source(6, 24) + SourceIndex(0)
-3 >Emitted(9, 28) Source(6, 27) + SourceIndex(0)
-4 >Emitted(9, 32) Source(6, 31) + SourceIndex(0)
-5 >Emitted(9, 37) Source(6, 36) + SourceIndex(0)
-6 >Emitted(9, 39) Source(6, 38) + SourceIndex(0)
-7 >Emitted(9, 40) Source(6, 39) + SourceIndex(0)
+1->Emitted(23, 5) Source(6, 12) + SourceIndex(1)
+2 >Emitted(23, 25) Source(6, 24) + SourceIndex(1)
+3 >Emitted(23, 28) Source(6, 27) + SourceIndex(1)
+4 >Emitted(23, 32) Source(6, 31) + SourceIndex(1)
+5 >Emitted(23, 37) Source(6, 36) + SourceIndex(1)
+6 >Emitted(23, 39) Source(6, 38) + SourceIndex(1)
+7 >Emitted(23, 40) Source(6, 39) + SourceIndex(1)
 ---
 >>>    function m2_f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(7, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(7, 1) + SourceIndex(1)
 ---
 >>>        return exports.m2_instance1;
 1->^^^^^^^^
@@ -309,11 +303,11 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 3 >               
 4 >               m2_instance1
 5 >                                   ;
-1->Emitted(11, 9) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 15) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(11, 16) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(11, 36) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(11, 37) Source(8, 25) + SourceIndex(0) name (m2_f1)
+1->Emitted(25, 9) Source(8, 5) + SourceIndex(1) name (m2_f1)
+2 >Emitted(25, 15) Source(8, 11) + SourceIndex(1) name (m2_f1)
+3 >Emitted(25, 16) Source(8, 12) + SourceIndex(1) name (m2_f1)
+4 >Emitted(25, 36) Source(8, 24) + SourceIndex(1) name (m2_f1)
+5 >Emitted(25, 37) Source(8, 25) + SourceIndex(1) name (m2_f1)
 ---
 >>>    }
 1 >^^^^
@@ -322,8 +316,8 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(12, 6) Source(9, 2) + SourceIndex(0) name (m2_f1)
+1 >Emitted(26, 5) Source(9, 1) + SourceIndex(1) name (m2_f1)
+2 >Emitted(26, 6) Source(9, 2) + SourceIndex(1) name (m2_f1)
 ---
 >>>    exports.m2_f1 = m2_f1;
 1->^^^^
@@ -336,23 +330,17 @@ sourceFile:outputdir_module_multifolder_ref/m2.ts
   >                     return m2_instance1;
   >                 }
 4 >                         
-1->Emitted(13, 5) Source(7, 17) + SourceIndex(0)
-2 >Emitted(13, 18) Source(7, 22) + SourceIndex(0)
-3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
-4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(7, 17) + SourceIndex(1)
+2 >Emitted(27, 18) Source(7, 22) + SourceIndex(1)
+3 >Emitted(27, 26) Source(9, 2) + SourceIndex(1)
+4 >Emitted(27, 27) Source(9, 2) + SourceIndex(1)
 ---
->>>});
->>>//# sourceMappingURL=m2.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder/test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:outputdir_module_multifolder/test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -367,24 +355,24 @@ sourceFile:outputdir_module_multifolder/test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(3, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(3, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(3, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(3, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(3, 20) + SourceIndex(0)
+1 >Emitted(30, 5) Source(3, 12) + SourceIndex(2)
+2 >Emitted(30, 15) Source(3, 14) + SourceIndex(2)
+3 >Emitted(30, 18) Source(3, 17) + SourceIndex(2)
+4 >Emitted(30, 20) Source(3, 19) + SourceIndex(2)
+5 >Emitted(30, 21) Source(3, 20) + SourceIndex(2)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(4, 1) + SourceIndex(0)
+1->Emitted(31, 5) Source(4, 1) + SourceIndex(2)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(4, 1) + SourceIndex(0) name (c1)
+1->Emitted(32, 9) Source(4, 1) + SourceIndex(2) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -394,16 +382,16 @@ sourceFile:outputdir_module_multifolder/test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(6, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(33, 9) Source(6, 1) + SourceIndex(2) name (c1.constructor)
+2 >Emitted(33, 10) Source(6, 2) + SourceIndex(2) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(6, 2) + SourceIndex(0) name (c1)
+1->Emitted(34, 9) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(34, 18) Source(6, 2) + SourceIndex(2) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -417,10 +405,10 @@ sourceFile:outputdir_module_multifolder/test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(4, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(6, 2) + SourceIndex(0)
+1 >Emitted(35, 5) Source(6, 1) + SourceIndex(2) name (c1)
+2 >Emitted(35, 6) Source(6, 2) + SourceIndex(2) name (c1)
+3 >Emitted(35, 6) Source(4, 1) + SourceIndex(2)
+4 >Emitted(35, 10) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -434,10 +422,10 @@ sourceFile:outputdir_module_multifolder/test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(4, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(4, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(6, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(6, 2) + SourceIndex(0)
+1->Emitted(36, 5) Source(4, 14) + SourceIndex(2)
+2 >Emitted(36, 15) Source(4, 16) + SourceIndex(2)
+3 >Emitted(36, 20) Source(6, 2) + SourceIndex(2)
+4 >Emitted(36, 21) Source(6, 2) + SourceIndex(2)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -456,20 +444,20 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(8, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(8, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(8, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(8, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(8, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(8, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(8, 33) + SourceIndex(0)
+1->Emitted(37, 5) Source(8, 12) + SourceIndex(2)
+2 >Emitted(37, 22) Source(8, 21) + SourceIndex(2)
+3 >Emitted(37, 25) Source(8, 24) + SourceIndex(2)
+4 >Emitted(37, 29) Source(8, 28) + SourceIndex(2)
+5 >Emitted(37, 31) Source(8, 30) + SourceIndex(2)
+6 >Emitted(37, 33) Source(8, 32) + SourceIndex(2)
+7 >Emitted(37, 34) Source(8, 33) + SourceIndex(2)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(9, 1) + SourceIndex(0)
+1 >Emitted(38, 5) Source(9, 1) + SourceIndex(2)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -483,11 +471,11 @@ sourceFile:outputdir_module_multifolder/test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(10, 22) + SourceIndex(0) name (f1)
+1->Emitted(39, 9) Source(10, 5) + SourceIndex(2) name (f1)
+2 >Emitted(39, 15) Source(10, 11) + SourceIndex(2) name (f1)
+3 >Emitted(39, 16) Source(10, 12) + SourceIndex(2) name (f1)
+4 >Emitted(39, 33) Source(10, 21) + SourceIndex(2) name (f1)
+5 >Emitted(39, 34) Source(10, 22) + SourceIndex(2) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -496,8 +484,8 @@ sourceFile:outputdir_module_multifolder/test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(11, 2) + SourceIndex(0) name (f1)
+1 >Emitted(40, 5) Source(11, 1) + SourceIndex(2) name (f1)
+2 >Emitted(40, 6) Source(11, 2) + SourceIndex(2) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -511,10 +499,10 @@ sourceFile:outputdir_module_multifolder/test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(9, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(9, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(11, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(11, 2) + SourceIndex(0)
+1->Emitted(41, 5) Source(9, 17) + SourceIndex(2)
+2 >Emitted(41, 15) Source(9, 19) + SourceIndex(2)
+3 >Emitted(41, 20) Source(11, 2) + SourceIndex(2)
+4 >Emitted(41, 21) Source(11, 2) + SourceIndex(2)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -534,13 +522,13 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(13, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(13, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(13, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(13, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(13, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(13, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(13, 26) + SourceIndex(0)
+1->Emitted(42, 5) Source(13, 12) + SourceIndex(2)
+2 >Emitted(42, 15) Source(13, 14) + SourceIndex(2)
+3 >Emitted(42, 18) Source(13, 17) + SourceIndex(2)
+4 >Emitted(42, 20) Source(13, 19) + SourceIndex(2)
+5 >Emitted(42, 21) Source(13, 20) + SourceIndex(2)
+6 >Emitted(42, 26) Source(13, 25) + SourceIndex(2)
+7 >Emitted(42, 27) Source(13, 26) + SourceIndex(2)
 ---
 >>>    exports.a3 = m2.m2_c1;
 1->^^^^
@@ -558,19 +546,13 @@ sourceFile:outputdir_module_multifolder/test.ts
 5 >                   .
 6 >                    m2_c1
 7 >                         ;
-1->Emitted(15, 5) Source(14, 12) + SourceIndex(0)
-2 >Emitted(15, 15) Source(14, 14) + SourceIndex(0)
-3 >Emitted(15, 18) Source(14, 17) + SourceIndex(0)
-4 >Emitted(15, 20) Source(14, 19) + SourceIndex(0)
-5 >Emitted(15, 21) Source(14, 20) + SourceIndex(0)
-6 >Emitted(15, 26) Source(14, 25) + SourceIndex(0)
-7 >Emitted(15, 27) Source(14, 26) + SourceIndex(0)
+1->Emitted(43, 5) Source(14, 12) + SourceIndex(2)
+2 >Emitted(43, 15) Source(14, 14) + SourceIndex(2)
+3 >Emitted(43, 18) Source(14, 17) + SourceIndex(2)
+4 >Emitted(43, 20) Source(14, 19) + SourceIndex(2)
+5 >Emitted(43, 21) Source(14, 20) + SourceIndex(2)
+6 >Emitted(43, 26) Source(14, 25) + SourceIndex(2)
+7 >Emitted(43, 27) Source(14, 26) + SourceIndex(2)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 5cca04a0f25..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-define(["require", "exports", "ref/m1", "../outputdir_module_multifolder_ref/m2"], function (require, exports, m1, m2) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-    exports.a3 = m2.m2_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index 8612cd0d108..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IAEW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;IACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..9b6af66589a 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,28 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "../outputdir_module_multifolder_ref/m2" {
+    export var m2_a1: number;
+    export class m2_c1 {
+        m2_c1_p1: number;
+    }
+    export var m2_instance1: m2_c1;
+    export function m2_f1(): m2_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+    export var a3: typeof m2.m2_c1;
+}
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
index d3e851981ec..f84040526ba 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/ref/m1.ts","outputdir_module_multifolder_ref/m2.ts","outputdir_module_multifolder/test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
deleted file mode 100644
index 058e405b606..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile0.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m2.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder_ref/m2.ts"],"names":["m2_c1","m2_c1.constructor","m2_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js
deleted file mode 100644
index ec0a73b5af8..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m2_a1 = 10;
-var m2_c1 = (function () {
-    function m2_c1() {
-    }
-    return m2_c1;
-})();
-exports.m2_c1 = m2_c1;
-exports.m2_instance1 = new m2_c1();
-function m2_f1() {
-    return exports.m2_instance1;
-}
-exports.m2_f1 = m2_f1;
-//# sourceMappingURL=m2.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
deleted file mode 100644
index c09a3c0c32a..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/diskFile2.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m2_a1: number;
-export declare class m2_c1 {
-    m2_c1_p1: number;
-}
-export declare var m2_instance1: m2_c1;
-export declare function m2_f1(): m2_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index e7f54a4a2e1..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..247f9e4f2f2
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,39 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    import m2 = require("../outputdir_module_multifolder_ref/m2");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
+    export var a3 = m2.m2_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.json
index cc2a6c9b1aa..27485e45ad9 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.json
@@ -16,15 +16,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "../outputdir_module_multifolder_ref/m2.js.map",
-        "../outputdir_module_multifolder_ref/m2.js",
-        "../outputdir_module_multifolder_ref/m2.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
index eb2dff17042..95f7d3cee8f 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/sourcerootUrlModuleMultifolderSpecifyOutputFile.sourcemap.txt
@@ -1,620 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder/ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:outputdir_module_multifolder/ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: m2.js
-mapUrl: m2.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder_ref/m2.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:diskFile1.js
-sourceFile:outputdir_module_multifolder_ref/m2.ts
--------------------------------------------------------------------
->>>exports.m2_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m2_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m2_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m2_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m2_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m2_c1 {
-  >    public m2_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m2_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m2_c1.constructor)
----
->>>    return m2_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m2_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m2_c1 {
-  >     public m2_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m2_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m2_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_c1 = m2_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m2_c1
-3 >              {
-  >                 public m2_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m2_instance1 = new m2_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m2_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m2_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m2_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m2_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m2_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m2_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m2_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m2_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m2_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m2_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m2_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m2_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m2_f1)
----
->>>exports.m2_f1 = m2_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m2_f1
-3 >             () {
-  >                 return m2_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m2.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: outputdir_module_multifolder/test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:outputdir_module_multifolder/test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-8 >                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>var m2 = require("../outputdir_module_multifolder_ref/m2");
-1->
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-6 >                                                         ^
-7 >                                                          ^
-1->
-  >
-2 >import 
-3 >    m2
-4 >       = require(
-5 >                 "../outputdir_module_multifolder_ref/m2"
-6 >                                                         )
-7 >                                                          ;
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
-2 >Emitted(2, 5) Source(2, 8) + SourceIndex(0)
-3 >Emitted(2, 7) Source(2, 10) + SourceIndex(0)
-4 >Emitted(2, 18) Source(2, 21) + SourceIndex(0)
-5 >Emitted(2, 58) Source(2, 61) + SourceIndex(0)
-6 >Emitted(2, 59) Source(2, 62) + SourceIndex(0)
-7 >Emitted(2, 60) Source(2, 63) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(3, 1) Source(3, 12) + SourceIndex(0)
-2 >Emitted(3, 11) Source(3, 14) + SourceIndex(0)
-3 >Emitted(3, 14) Source(3, 17) + SourceIndex(0)
-4 >Emitted(3, 16) Source(3, 19) + SourceIndex(0)
-5 >Emitted(3, 17) Source(3, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(4, 1) Source(4, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(6, 5) Source(6, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(6, 6) Source(6, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(7, 5) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 14) Source(6, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(8, 1) Source(6, 1) + SourceIndex(0) name (c1)
-2 >Emitted(8, 2) Source(6, 2) + SourceIndex(0) name (c1)
-3 >Emitted(8, 2) Source(4, 1) + SourceIndex(0)
-4 >Emitted(8, 6) Source(6, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(9, 1) Source(4, 14) + SourceIndex(0)
-2 >Emitted(9, 11) Source(4, 16) + SourceIndex(0)
-3 >Emitted(9, 16) Source(6, 2) + SourceIndex(0)
-4 >Emitted(9, 17) Source(6, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(10, 1) Source(8, 12) + SourceIndex(0)
-2 >Emitted(10, 18) Source(8, 21) + SourceIndex(0)
-3 >Emitted(10, 21) Source(8, 24) + SourceIndex(0)
-4 >Emitted(10, 25) Source(8, 28) + SourceIndex(0)
-5 >Emitted(10, 27) Source(8, 30) + SourceIndex(0)
-6 >Emitted(10, 29) Source(8, 32) + SourceIndex(0)
-7 >Emitted(10, 30) Source(8, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(12, 5) Source(10, 5) + SourceIndex(0) name (f1)
-2 >Emitted(12, 11) Source(10, 11) + SourceIndex(0) name (f1)
-3 >Emitted(12, 12) Source(10, 12) + SourceIndex(0) name (f1)
-4 >Emitted(12, 29) Source(10, 21) + SourceIndex(0) name (f1)
-5 >Emitted(12, 30) Source(10, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(13, 1) Source(11, 1) + SourceIndex(0) name (f1)
-2 >Emitted(13, 2) Source(11, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(14, 1) Source(9, 17) + SourceIndex(0)
-2 >Emitted(14, 11) Source(9, 19) + SourceIndex(0)
-3 >Emitted(14, 16) Source(11, 2) + SourceIndex(0)
-4 >Emitted(14, 17) Source(11, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(15, 1) Source(13, 12) + SourceIndex(0)
-2 >Emitted(15, 11) Source(13, 14) + SourceIndex(0)
-3 >Emitted(15, 14) Source(13, 17) + SourceIndex(0)
-4 >Emitted(15, 16) Source(13, 19) + SourceIndex(0)
-5 >Emitted(15, 17) Source(13, 20) + SourceIndex(0)
-6 >Emitted(15, 22) Source(13, 25) + SourceIndex(0)
-7 >Emitted(15, 23) Source(13, 26) + SourceIndex(0)
----
->>>exports.a3 = m2.m2_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >export var 
-2 >a3
-3 >           = 
-4 >             m2
-5 >               .
-6 >                m2_c1
-7 >                     ;
-1->Emitted(16, 1) Source(14, 12) + SourceIndex(0)
-2 >Emitted(16, 11) Source(14, 14) + SourceIndex(0)
-3 >Emitted(16, 14) Source(14, 17) + SourceIndex(0)
-4 >Emitted(16, 16) Source(14, 19) + SourceIndex(0)
-5 >Emitted(16, 17) Source(14, 20) + SourceIndex(0)
-6 >Emitted(16, 22) Source(14, 25) + SourceIndex(0)
-7 >Emitted(16, 23) Source(14, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
+sources: outputdir_module_multifolder/ref/m1.ts,outputdir_module_multifolder_ref/m2.ts,outputdir_module_multifolder/test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 4afd4e69f2d..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,10 +0,0 @@
-import m1 = require("ref/m1");
-import m2 = require("../outputdir_module_multifolder_ref/m2");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
-export declare var a3: typeof m2.m2_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 14c09e444a5..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,17 +0,0 @@
-var m1 = require("ref/m1");
-var m2 = require("../outputdir_module_multifolder_ref/m2");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-exports.a3 = m2.m2_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 4ac74c2fcdb..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleMultifolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["outputdir_module_multifolder/test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AAC9B,IAAO,EAAE,WAAW,wCAAwC,CAAC,CAAC;AACnD,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC;AACd,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..f385e49ecd1 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
index d3e851981ec..2ace469f902 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map
deleted file mode 100644
index 6751f2f82cd..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/sourcerootUrlModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/sourcerootUrlModuleSimpleSpecifyOutputFile.json
index 5419c5a8225..4d92e8a8951 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/sourcerootUrlModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/sourcerootUrlModuleSimpleSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/sourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/sourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
index 3e447368494..e0c060eb889 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/sourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/sourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: m1.ts
+sources: m1.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:m1.js
+emittedFile:bin/test.js
 sourceFile:m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 372f1052b89..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index a57b57d2b17..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..df062274b3e 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
index d3e851981ec..3b75f2878c9 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["m1.ts","test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map
deleted file mode 100644
index ca45773f423..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..12592331fb5
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.json b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.json
index 5419c5a8225..4d92e8a8951 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "m1.js.map",
-        "m1.js",
-        "m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
index 4d3c5799e27..dfbb5f48fff 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/sourcerootUrlModuleSimpleSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:m1.js
-sourceFile:m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^
-6 >                     ^
-7 >                      ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "m1"
-6 >                     )
-7 >                      ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 22) Source(1, 25) + SourceIndex(0)
-6 >Emitted(1, 23) Source(1, 26) + SourceIndex(0)
-7 >Emitted(1, 24) Source(1, 27) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
+sources: m1.ts,test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index 250d2615a79..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js
deleted file mode 100644
index c2e7dfa443b..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index 41d3e11e995..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSimpleSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,IAAI,CAAC,CAAC;AACf,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
index 6f3fefb9498..18d212c7e69 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js
@@ -1 +1,30 @@
+define("ref/m1", ["require", "exports"], function (require, exports) {
+    exports.m1_a1 = 10;
+    var m1_c1 = (function () {
+        function m1_c1() {
+        }
+        return m1_c1;
+    })();
+    exports.m1_c1 = m1_c1;
+    exports.m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return exports.m1_instance1;
+    }
+    exports.m1_f1 = m1_f1;
+});
+define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
+    exports.a1 = 10;
+    var c1 = (function () {
+        function c1() {
+        }
+        return c1;
+    })();
+    exports.c1 = c1;
+    exports.instance1 = new c1();
+    function f1() {
+        return exports.instance1;
+    }
+    exports.f1 = f1;
+    exports.a2 = m1.m1_c1;
+});
 //# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
index d3e851981ec..29e01bc0bc6 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1","c1","c1.constructor","f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA;;;ICPU,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAC;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
deleted file mode 100644
index bbaba444ba2..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js
+++ /dev/null
@@ -1,15 +0,0 @@
-define(["require", "exports"], function (require, exports) {
-    exports.m1_a1 = 10;
-    var m1_c1 = (function () {
-        function m1_c1() {
-        }
-        return m1_c1;
-    })();
-    exports.m1_c1 = m1_c1;
-    exports.m1_instance1 = new m1_c1();
-    function m1_f1() {
-        return exports.m1_instance1;
-    }
-    exports.m1_f1 = m1_f1;
-});
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
deleted file mode 100644
index 6c5413f630e..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":";IAAW,aAAK,GAAG,EAAE,CAAC;IACtB;QAAAA;QAEAC,CAACA;QAADD,YAACA;IAADA,CAACA,AAFD,IAEC;IAFY,aAAK,QAEjB,CAAA;IAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;IACtC;QACIE,MAAMA,CAACA,oBAAYA,CAACA;IACxBA,CAACA;IAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/sourcerootUrlModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/sourcerootUrlModuleSubfolderSpecifyOutputFile.json
index d80dacb3444..e1f6d3c6e36 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/sourcerootUrlModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/sourcerootUrlModuleSubfolderSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/sourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/sourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
index 54c26748c78..54624487a57 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/sourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/sourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,14 +1,14 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
+JsFile: test.js
+mapUrl: test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts
+sources: ref/m1.ts,test.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:ref/m1.js
+emittedFile:bin/test.js
 sourceFile:ref/m1.ts
 -------------------------------------------------------------------
->>>define(["require", "exports"], function (require, exports) {
+>>>define("ref/m1", ["require", "exports"], function (require, exports) {
 >>>    exports.m1_a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^^^^
@@ -169,18 +169,12 @@ sourceFile:ref/m1.ts
 3 >Emitted(13, 26) Source(9, 2) + SourceIndex(0)
 4 >Emitted(13, 27) Source(9, 2) + SourceIndex(0)
 ---
->>>});
->>>//# sourceMappingURL=m1.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: test.ts
-===================================================================
 -------------------------------------------------------------------
-emittedFile:test.js
+emittedFile:bin/test.js
 sourceFile:test.ts
 -------------------------------------------------------------------
->>>define(["require", "exports", "ref/m1"], function (require, exports, m1) {
+>>>});
+>>>define("test", ["require", "exports", "ref/m1"], function (require, exports, m1) {
 >>>    exports.a1 = 10;
 1 >^^^^
 2 >    ^^^^^^^^^^
@@ -194,24 +188,24 @@ sourceFile:test.ts
 3 >               = 
 4 >                 10
 5 >                   ;
-1 >Emitted(2, 5) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 15) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 18) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 20) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 21) Source(2, 20) + SourceIndex(0)
+1 >Emitted(16, 5) Source(2, 12) + SourceIndex(1)
+2 >Emitted(16, 15) Source(2, 14) + SourceIndex(1)
+3 >Emitted(16, 18) Source(2, 17) + SourceIndex(1)
+4 >Emitted(16, 20) Source(2, 19) + SourceIndex(1)
+5 >Emitted(16, 21) Source(2, 20) + SourceIndex(1)
 ---
 >>>    var c1 = (function () {
 1->^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^->
 1->
   >
-1->Emitted(3, 5) Source(3, 1) + SourceIndex(0)
+1->Emitted(17, 5) Source(3, 1) + SourceIndex(1)
 ---
 >>>        function c1() {
 1->^^^^^^^^
 2 >        ^^->
 1->
-1->Emitted(4, 9) Source(3, 1) + SourceIndex(0) name (c1)
+1->Emitted(18, 9) Source(3, 1) + SourceIndex(1) name (c1)
 ---
 >>>        }
 1->^^^^^^^^
@@ -221,16 +215,16 @@ sourceFile:test.ts
   >    public p1: number;
   >
 2 >        }
-1->Emitted(5, 9) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 10) Source(5, 2) + SourceIndex(0) name (c1.constructor)
+1->Emitted(19, 9) Source(5, 1) + SourceIndex(1) name (c1.constructor)
+2 >Emitted(19, 10) Source(5, 2) + SourceIndex(1) name (c1.constructor)
 ---
 >>>        return c1;
 1->^^^^^^^^
 2 >        ^^^^^^^^^
 1->
 2 >        }
-1->Emitted(6, 9) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 18) Source(5, 2) + SourceIndex(0) name (c1)
+1->Emitted(20, 9) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(20, 18) Source(5, 2) + SourceIndex(1) name (c1)
 ---
 >>>    })();
 1 >^^^^
@@ -244,10 +238,10 @@ sourceFile:test.ts
 4 >     export class c1 {
   >         public p1: number;
   >     }
-1 >Emitted(7, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 6) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 6) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 10) Source(5, 2) + SourceIndex(0)
+1 >Emitted(21, 5) Source(5, 1) + SourceIndex(1) name (c1)
+2 >Emitted(21, 6) Source(5, 2) + SourceIndex(1) name (c1)
+3 >Emitted(21, 6) Source(3, 1) + SourceIndex(1)
+4 >Emitted(21, 10) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.c1 = c1;
 1->^^^^
@@ -261,10 +255,10 @@ sourceFile:test.ts
   >                  public p1: number;
   >              }
 4 >                   
-1->Emitted(8, 5) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 15) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 20) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 21) Source(5, 2) + SourceIndex(0)
+1->Emitted(22, 5) Source(3, 14) + SourceIndex(1)
+2 >Emitted(22, 15) Source(3, 16) + SourceIndex(1)
+3 >Emitted(22, 20) Source(5, 2) + SourceIndex(1)
+4 >Emitted(22, 21) Source(5, 2) + SourceIndex(1)
 ---
 >>>    exports.instance1 = new c1();
 1->^^^^
@@ -283,20 +277,20 @@ sourceFile:test.ts
 5 >                            c1
 6 >                              ()
 7 >                                ;
-1->Emitted(9, 5) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 22) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 25) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 29) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 31) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 33) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 34) Source(7, 33) + SourceIndex(0)
+1->Emitted(23, 5) Source(7, 12) + SourceIndex(1)
+2 >Emitted(23, 22) Source(7, 21) + SourceIndex(1)
+3 >Emitted(23, 25) Source(7, 24) + SourceIndex(1)
+4 >Emitted(23, 29) Source(7, 28) + SourceIndex(1)
+5 >Emitted(23, 31) Source(7, 30) + SourceIndex(1)
+6 >Emitted(23, 33) Source(7, 32) + SourceIndex(1)
+7 >Emitted(23, 34) Source(7, 33) + SourceIndex(1)
 ---
 >>>    function f1() {
 1 >^^^^
 2 >    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >
-1 >Emitted(10, 5) Source(8, 1) + SourceIndex(0)
+1 >Emitted(24, 5) Source(8, 1) + SourceIndex(1)
 ---
 >>>        return exports.instance1;
 1->^^^^^^^^
@@ -310,11 +304,11 @@ sourceFile:test.ts
 3 >               
 4 >               instance1
 5 >                                ;
-1->Emitted(11, 9) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 15) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 16) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 33) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 34) Source(9, 22) + SourceIndex(0) name (f1)
+1->Emitted(25, 9) Source(9, 5) + SourceIndex(1) name (f1)
+2 >Emitted(25, 15) Source(9, 11) + SourceIndex(1) name (f1)
+3 >Emitted(25, 16) Source(9, 12) + SourceIndex(1) name (f1)
+4 >Emitted(25, 33) Source(9, 21) + SourceIndex(1) name (f1)
+5 >Emitted(25, 34) Source(9, 22) + SourceIndex(1) name (f1)
 ---
 >>>    }
 1 >^^^^
@@ -323,8 +317,8 @@ sourceFile:test.ts
 1 >
   >
 2 >    }
-1 >Emitted(12, 5) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 6) Source(10, 2) + SourceIndex(0) name (f1)
+1 >Emitted(26, 5) Source(10, 1) + SourceIndex(1) name (f1)
+2 >Emitted(26, 6) Source(10, 2) + SourceIndex(1) name (f1)
 ---
 >>>    exports.f1 = f1;
 1->^^^^
@@ -338,10 +332,10 @@ sourceFile:test.ts
   >                  return instance1;
   >              }
 4 >                   
-1->Emitted(13, 5) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 15) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 20) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 21) Source(10, 2) + SourceIndex(0)
+1->Emitted(27, 5) Source(8, 17) + SourceIndex(1)
+2 >Emitted(27, 15) Source(8, 19) + SourceIndex(1)
+3 >Emitted(27, 20) Source(10, 2) + SourceIndex(1)
+4 >Emitted(27, 21) Source(10, 2) + SourceIndex(1)
 ---
 >>>    exports.a2 = m1.m1_c1;
 1->^^^^
@@ -360,19 +354,13 @@ sourceFile:test.ts
 5 >                   .
 6 >                    m1_c1
 7 >                         ;
-1->Emitted(14, 5) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 15) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 18) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 20) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 21) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 26) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 27) Source(12, 26) + SourceIndex(0)
+1->Emitted(28, 5) Source(12, 12) + SourceIndex(1)
+2 >Emitted(28, 15) Source(12, 14) + SourceIndex(1)
+3 >Emitted(28, 18) Source(12, 17) + SourceIndex(1)
+4 >Emitted(28, 20) Source(12, 19) + SourceIndex(1)
+5 >Emitted(28, 21) Source(12, 20) + SourceIndex(1)
+6 >Emitted(28, 26) Source(12, 25) + SourceIndex(1)
+7 >Emitted(28, 27) Source(12, 26) + SourceIndex(1)
 ---
 >>>});
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
-===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js
deleted file mode 100644
index 6c8aeb3190b..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js
+++ /dev/null
@@ -1,16 +0,0 @@
-define(["require", "exports", "ref/m1"], function (require, exports, m1) {
-    exports.a1 = 10;
-    var c1 = (function () {
-        function c1() {
-        }
-        return c1;
-    })();
-    exports.c1 = c1;
-    exports.instance1 = new c1();
-    function f1() {
-        return exports.instance1;
-    }
-    exports.f1 = f1;
-    exports.a2 = m1.m1_c1;
-});
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map
deleted file mode 100644
index a57b57d2b17..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/amd/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":";IACW,UAAE,GAAG,EAAE,CAAC;IACnB;QAAAA;QAEAC,CAACA;QAADD,SAACA;IAADA,CAACA,AAFD,IAEC;IAFY,UAAE,KAEd,CAAA;IAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;IAChC;QACIE,MAAMA,CAACA,iBAASA,CAACA;IACrBA,CAACA;IAFe,UAAE,KAEjB,CAAA;IAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
index e69de29bb2d..18eee0fd4df 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.d.ts
@@ -0,0 +1,18 @@
+declare module "ref/m1" {
+    export var m1_a1: number;
+    export class m1_c1 {
+        m1_c1_p1: number;
+    }
+    export var m1_instance1: m1_c1;
+    export function m1_f1(): m1_c1;
+}
+declare module "test" {
+    import m1 = require("ref/m1");
+    export var a1: number;
+    export class c1 {
+        p1: number;
+    }
+    export var instance1: c1;
+    export function f1(): c1;
+    export var a2: typeof m1.m1_c1;
+}
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
index d3e851981ec..4409af8d0a7 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/bin/test.js.map
@@ -1 +1 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":[],"names":[],"mappings":""}
\ No newline at end of file
+{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts","test.ts"],"names":[],"mappings":""}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
deleted file mode 100644
index 4a53b24b156..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.d.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-export declare var m1_a1: number;
-export declare class m1_c1 {
-    m1_c1_p1: number;
-}
-export declare var m1_instance1: m1_c1;
-export declare function m1_f1(): m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js
deleted file mode 100644
index 1b4470e2b37..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js
+++ /dev/null
@@ -1,13 +0,0 @@
-exports.m1_a1 = 10;
-var m1_c1 = (function () {
-    function m1_c1() {
-    }
-    return m1_c1;
-})();
-exports.m1_c1 = m1_c1;
-exports.m1_instance1 = new m1_c1();
-function m1_f1() {
-    return exports.m1_instance1;
-}
-exports.m1_f1 = m1_f1;
-//# sourceMappingURL=m1.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
deleted file mode 100644
index 35e7e9a48dd..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/ref/m1.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"m1.js","sourceRoot":"http://typescript.codeplex.com/","sources":["ref/m1.ts"],"names":["m1_c1","m1_c1.constructor","m1_f1"],"mappings":"AAAW,aAAK,GAAG,EAAE,CAAC;AACtB;IAAAA;IAEAC,CAACA;IAADD,YAACA;AAADA,CAACA,AAFD,IAEC;AAFY,aAAK,QAEjB,CAAA;AAEU,oBAAY,GAAG,IAAI,KAAK,EAAE,CAAC;AACtC;IACIE,MAAMA,CAACA,oBAAYA,CAACA;AACxBA,CAACA;AAFe,aAAK,QAEpB,CAAA"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..42154149020
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,27 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    export var m1_a1 = 10;
+    export class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    export var m1_instance1 = new m1_c1();
+    export function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    import m1 = require("ref/m1");
+    export var a1 = 10;
+    export class c1 {
+        public p1: number;
+    }
+    
+    export var instance1 = new c1();
+    export function f1() {
+        return instance1;
+    }
+    
+    export var a2 = m1.m1_c1;
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.json b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.json
index d80dacb3444..e1f6d3c6e36 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.json
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.json
@@ -15,12 +15,6 @@
         "test.ts"
     ],
     "emittedFiles": [
-        "ref/m1.js.map",
-        "ref/m1.js",
-        "ref/m1.d.ts",
-        "test.js.map",
-        "test.js",
-        "test.d.ts",
         "bin/test.js.map",
         "bin/test.js",
         "bin/test.d.ts"
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
index cf41966a818..2903ad0141c 100644
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
+++ b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/sourcerootUrlModuleSubfolderSpecifyOutputFile.sourcemap.txt
@@ -1,399 +1,7 @@
 ===================================================================
-JsFile: m1.js
-mapUrl: m1.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: ref/m1.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:ref/m1.js
-sourceFile:ref/m1.ts
--------------------------------------------------------------------
->>>exports.m1_a1 = 10;
-1 >
-2 >^^^^^^^^^^^^^
-3 >             ^^^
-4 >                ^^
-5 >                  ^
-6 >                   ^^^^^^^^->
-1 >export var 
-2 >m1_a1
-3 >              = 
-4 >                10
-5 >                  ;
-1 >Emitted(1, 1) Source(1, 12) + SourceIndex(0)
-2 >Emitted(1, 14) Source(1, 17) + SourceIndex(0)
-3 >Emitted(1, 17) Source(1, 20) + SourceIndex(0)
-4 >Emitted(1, 19) Source(1, 22) + SourceIndex(0)
-5 >Emitted(1, 20) Source(1, 23) + SourceIndex(0)
----
->>>var m1_c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(2, 1) Source(2, 1) + SourceIndex(0)
----
->>>    function m1_c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (m1_c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^^^^->
-1->export class m1_c1 {
-  >    public m1_c1_p1: number;
-  >
-2 >    }
-1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (m1_c1.constructor)
-2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (m1_c1.constructor)
----
->>>    return m1_c1;
-1->^^^^
-2 >    ^^^^^^^^^^^^
-1->
-2 >    }
-1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(5, 17) Source(4, 2) + SourceIndex(0) name (m1_c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class m1_c1 {
-  >     public m1_c1_p1: number;
-  > }
-1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (m1_c1)
-2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (m1_c1)
-3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
-4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_c1 = m1_c1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^^^^^^^^->
-1->
-2 >m1_c1
-3 >              {
-  >                 public m1_c1_p1: number;
-  >             }
-4 >                     
-1->Emitted(7, 1) Source(2, 14) + SourceIndex(0)
-2 >Emitted(7, 14) Source(2, 19) + SourceIndex(0)
-3 >Emitted(7, 22) Source(4, 2) + SourceIndex(0)
-4 >Emitted(7, 23) Source(4, 2) + SourceIndex(0)
----
->>>exports.m1_instance1 = new m1_c1();
-1->
-2 >^^^^^^^^^^^^^^^^^^^^
-3 >                    ^^^
-4 >                       ^^^^
-5 >                           ^^^^^
-6 >                                ^^
-7 >                                  ^
-1->
-  >
-  >export var 
-2 >m1_instance1
-3 >                     = 
-4 >                       new 
-5 >                           m1_c1
-6 >                                ()
-7 >                                  ;
-1->Emitted(8, 1) Source(6, 12) + SourceIndex(0)
-2 >Emitted(8, 21) Source(6, 24) + SourceIndex(0)
-3 >Emitted(8, 24) Source(6, 27) + SourceIndex(0)
-4 >Emitted(8, 28) Source(6, 31) + SourceIndex(0)
-5 >Emitted(8, 33) Source(6, 36) + SourceIndex(0)
-6 >Emitted(8, 35) Source(6, 38) + SourceIndex(0)
-7 >Emitted(8, 36) Source(6, 39) + SourceIndex(0)
----
->>>function m1_f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(9, 1) Source(7, 1) + SourceIndex(0)
----
->>>    return exports.m1_instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^^^^
-5 >                               ^
-1->export function m1_f1() {
-  >    
-2 >    return
-3 >           
-4 >           m1_instance1
-5 >                               ;
-1->Emitted(10, 5) Source(8, 5) + SourceIndex(0) name (m1_f1)
-2 >Emitted(10, 11) Source(8, 11) + SourceIndex(0) name (m1_f1)
-3 >Emitted(10, 12) Source(8, 12) + SourceIndex(0) name (m1_f1)
-4 >Emitted(10, 32) Source(8, 24) + SourceIndex(0) name (m1_f1)
-5 >Emitted(10, 33) Source(8, 25) + SourceIndex(0) name (m1_f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(11, 1) Source(9, 1) + SourceIndex(0) name (m1_f1)
-2 >Emitted(11, 2) Source(9, 2) + SourceIndex(0) name (m1_f1)
----
->>>exports.m1_f1 = m1_f1;
-1->
-2 >^^^^^^^^^^^^^
-3 >             ^^^^^^^^
-4 >                     ^
-5 >                      ^^^^^^^->
-1->
-2 >m1_f1
-3 >             () {
-  >                 return m1_instance1;
-  >             }
-4 >                     
-1->Emitted(12, 1) Source(7, 17) + SourceIndex(0)
-2 >Emitted(12, 14) Source(7, 22) + SourceIndex(0)
-3 >Emitted(12, 22) Source(9, 2) + SourceIndex(0)
-4 >Emitted(12, 23) Source(9, 2) + SourceIndex(0)
----
->>>//# sourceMappingURL=m1.js.map===================================================================
 JsFile: test.js
 mapUrl: test.js.map
 sourceRoot: http://typescript.codeplex.com/
-sources: test.ts
-===================================================================
--------------------------------------------------------------------
-emittedFile:test.js
-sourceFile:test.ts
--------------------------------------------------------------------
->>>var m1 = require("ref/m1");
-1 >
-2 >^^^^
-3 >    ^^
-4 >      ^^^^^^^^^^^
-5 >                 ^^^^^^^^
-6 >                         ^
-7 >                          ^
-1 >
-2 >import 
-3 >    m1
-4 >       = require(
-5 >                 "ref/m1"
-6 >                         )
-7 >                          ;
-1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
-2 >Emitted(1, 5) Source(1, 8) + SourceIndex(0)
-3 >Emitted(1, 7) Source(1, 10) + SourceIndex(0)
-4 >Emitted(1, 18) Source(1, 21) + SourceIndex(0)
-5 >Emitted(1, 26) Source(1, 29) + SourceIndex(0)
-6 >Emitted(1, 27) Source(1, 30) + SourceIndex(0)
-7 >Emitted(1, 28) Source(1, 31) + SourceIndex(0)
----
->>>exports.a1 = 10;
-1 >
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^^^^->
-1 >
-  >export var 
-2 >a1
-3 >           = 
-4 >             10
-5 >               ;
-1 >Emitted(2, 1) Source(2, 12) + SourceIndex(0)
-2 >Emitted(2, 11) Source(2, 14) + SourceIndex(0)
-3 >Emitted(2, 14) Source(2, 17) + SourceIndex(0)
-4 >Emitted(2, 16) Source(2, 19) + SourceIndex(0)
-5 >Emitted(2, 17) Source(2, 20) + SourceIndex(0)
----
->>>var c1 = (function () {
-1->
-2 >^^^^^^^^^^^^^^^^^^^^->
-1->
-  >
-1->Emitted(3, 1) Source(3, 1) + SourceIndex(0)
----
->>>    function c1() {
-1->^^^^
-2 >    ^^->
-1->
-1->Emitted(4, 5) Source(3, 1) + SourceIndex(0) name (c1)
----
->>>    }
-1->^^^^
-2 >    ^
-3 >     ^^^^^^^^^^->
-1->export class c1 {
-  >    public p1: number;
-  >
-2 >    }
-1->Emitted(5, 5) Source(5, 1) + SourceIndex(0) name (c1.constructor)
-2 >Emitted(5, 6) Source(5, 2) + SourceIndex(0) name (c1.constructor)
----
->>>    return c1;
-1->^^^^
-2 >    ^^^^^^^^^
-1->
-2 >    }
-1->Emitted(6, 5) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(6, 14) Source(5, 2) + SourceIndex(0) name (c1)
----
->>>})();
-1 >
-2 >^
-3 > 
-4 > ^^^^
-5 >     ^^^^^^^^^^^^->
-1 >
-2 >}
-3 > 
-4 > export class c1 {
-  >     public p1: number;
-  > }
-1 >Emitted(7, 1) Source(5, 1) + SourceIndex(0) name (c1)
-2 >Emitted(7, 2) Source(5, 2) + SourceIndex(0) name (c1)
-3 >Emitted(7, 2) Source(3, 1) + SourceIndex(0)
-4 >Emitted(7, 6) Source(5, 2) + SourceIndex(0)
----
->>>exports.c1 = c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^^^^^^^^->
-1->
-2 >c1
-3 >           {
-  >              public p1: number;
-  >          }
-4 >               
-1->Emitted(8, 1) Source(3, 14) + SourceIndex(0)
-2 >Emitted(8, 11) Source(3, 16) + SourceIndex(0)
-3 >Emitted(8, 16) Source(5, 2) + SourceIndex(0)
-4 >Emitted(8, 17) Source(5, 2) + SourceIndex(0)
----
->>>exports.instance1 = new c1();
-1->
-2 >^^^^^^^^^^^^^^^^^
-3 >                 ^^^
-4 >                    ^^^^
-5 >                        ^^
-6 >                          ^^
-7 >                            ^
-1->
-  >
-  >export var 
-2 >instance1
-3 >                  = 
-4 >                    new 
-5 >                        c1
-6 >                          ()
-7 >                            ;
-1->Emitted(9, 1) Source(7, 12) + SourceIndex(0)
-2 >Emitted(9, 18) Source(7, 21) + SourceIndex(0)
-3 >Emitted(9, 21) Source(7, 24) + SourceIndex(0)
-4 >Emitted(9, 25) Source(7, 28) + SourceIndex(0)
-5 >Emitted(9, 27) Source(7, 30) + SourceIndex(0)
-6 >Emitted(9, 29) Source(7, 32) + SourceIndex(0)
-7 >Emitted(9, 30) Source(7, 33) + SourceIndex(0)
----
->>>function f1() {
-1 >
-2 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
-1 >
-  >
-1 >Emitted(10, 1) Source(8, 1) + SourceIndex(0)
----
->>>    return exports.instance1;
-1->^^^^
-2 >    ^^^^^^
-3 >          ^
-4 >           ^^^^^^^^^^^^^^^^^
-5 >                            ^
-1->export function f1() {
-  >    
-2 >    return
-3 >           
-4 >           instance1
-5 >                            ;
-1->Emitted(11, 5) Source(9, 5) + SourceIndex(0) name (f1)
-2 >Emitted(11, 11) Source(9, 11) + SourceIndex(0) name (f1)
-3 >Emitted(11, 12) Source(9, 12) + SourceIndex(0) name (f1)
-4 >Emitted(11, 29) Source(9, 21) + SourceIndex(0) name (f1)
-5 >Emitted(11, 30) Source(9, 22) + SourceIndex(0) name (f1)
----
->>>}
-1 >
-2 >^
-3 > ^^^^^^^^^^^^^^^^->
-1 >
-  >
-2 >}
-1 >Emitted(12, 1) Source(10, 1) + SourceIndex(0) name (f1)
-2 >Emitted(12, 2) Source(10, 2) + SourceIndex(0) name (f1)
----
->>>exports.f1 = f1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^^^
-4 >               ^
-5 >                ^^^^^^^->
-1->
-2 >f1
-3 >          () {
-  >              return instance1;
-  >          }
-4 >               
-1->Emitted(13, 1) Source(8, 17) + SourceIndex(0)
-2 >Emitted(13, 11) Source(8, 19) + SourceIndex(0)
-3 >Emitted(13, 16) Source(10, 2) + SourceIndex(0)
-4 >Emitted(13, 17) Source(10, 2) + SourceIndex(0)
----
->>>exports.a2 = m1.m1_c1;
-1->
-2 >^^^^^^^^^^
-3 >          ^^^
-4 >             ^^
-5 >               ^
-6 >                ^^^^^
-7 >                     ^
-8 >                      ^^^^^^^^^->
-1->
-  >
-  >export var 
-2 >a2
-3 >           = 
-4 >             m1
-5 >               .
-6 >                m1_c1
-7 >                     ;
-1->Emitted(14, 1) Source(12, 12) + SourceIndex(0)
-2 >Emitted(14, 11) Source(12, 14) + SourceIndex(0)
-3 >Emitted(14, 14) Source(12, 17) + SourceIndex(0)
-4 >Emitted(14, 16) Source(12, 19) + SourceIndex(0)
-5 >Emitted(14, 17) Source(12, 20) + SourceIndex(0)
-6 >Emitted(14, 22) Source(12, 25) + SourceIndex(0)
-7 >Emitted(14, 23) Source(12, 26) + SourceIndex(0)
----
->>>//# sourceMappingURL=test.js.map===================================================================
-JsFile: test.js
-mapUrl: test.js.map
-sourceRoot: http://typescript.codeplex.com/
-sources: 
+sources: ref/m1.ts,test.ts
 ===================================================================
 >>>//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts
deleted file mode 100644
index a61d8541048..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.d.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import m1 = require("ref/m1");
-export declare var a1: number;
-export declare class c1 {
-    p1: number;
-}
-export declare var instance1: c1;
-export declare function f1(): c1;
-export declare var a2: typeof m1.m1_c1;
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js
deleted file mode 100644
index 46c9f29e55a..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js
+++ /dev/null
@@ -1,15 +0,0 @@
-var m1 = require("ref/m1");
-exports.a1 = 10;
-var c1 = (function () {
-    function c1() {
-    }
-    return c1;
-})();
-exports.c1 = c1;
-exports.instance1 = new c1();
-function f1() {
-    return exports.instance1;
-}
-exports.f1 = f1;
-exports.a2 = m1.m1_c1;
-//# sourceMappingURL=test.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map b/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map
deleted file mode 100644
index d0638b6c34c..00000000000
--- a/tests/baselines/reference/project/sourcerootUrlModuleSubfolderSpecifyOutputFile/node/test.js.map
+++ /dev/null
@@ -1 +0,0 @@
-{"version":3,"file":"test.js","sourceRoot":"http://typescript.codeplex.com/","sources":["test.ts"],"names":["c1","c1.constructor","f1"],"mappings":"AAAA,IAAO,EAAE,WAAW,QAAQ,CAAC,CAAC;AACnB,UAAE,GAAG,EAAE,CAAC;AACnB;IAAAA;IAEAC,CAACA;IAADD,SAACA;AAADA,CAACA,AAFD,IAEC;AAFY,UAAE,KAEd,CAAA;AAEU,iBAAS,GAAG,IAAI,EAAE,EAAE,CAAC;AAChC;IACIE,MAAMA,CAACA,iBAASA,CAACA;AACrBA,CAACA;AAFe,UAAE,KAEjB,CAAA;AAEU,UAAE,GAAG,EAAE,CAAC,KAAK,CAAC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/node/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/node/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53a35eb2c84
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/node/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,36 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/node/sourcerootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/node/sourcerootUrlSimpleSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..53fc18f86c7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/node/sourcerootUrlSimpleSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSingleFileSpecifyOutputFile/node/sourcerootUrlSingleFileSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlSingleFileSpecifyOutputFile/node/sourcerootUrlSingleFileSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..eb358c3b79d
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSingleFileSpecifyOutputFile/node/sourcerootUrlSingleFileSpecifyOutputFile.errors.txt
@@ -0,0 +1,14 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== test.ts (0 errors) ====
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/node/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/node/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt
new file mode 100644
index 00000000000..376cfa761b8
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/node/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -0,0 +1,25 @@
+error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+
+
+!!! error TS6082: Only 'amd' and 'system' modules are supported alongside --outFile.
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (0 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/thisTypeAndConstraints.js b/tests/baselines/reference/thisTypeAndConstraints.js
new file mode 100644
index 00000000000..d62ebe6917c
--- /dev/null
+++ b/tests/baselines/reference/thisTypeAndConstraints.js
@@ -0,0 +1,50 @@
+//// [thisTypeAndConstraints.ts]
+class A {
+    self() {
+        return this;
+    }
+}
+
+function f<T extends A>(x: T) {
+    function g<U extends T>(x: U) {
+        x = x.self();
+    }
+    x = x.self();
+}
+
+class B<T extends A> {
+    foo(x: T) {
+        x = x.self();
+    }
+    bar<U extends T>(x: U) {
+        x = x.self();
+    }
+}
+
+
+//// [thisTypeAndConstraints.js]
+var A = (function () {
+    function A() {
+    }
+    A.prototype.self = function () {
+        return this;
+    };
+    return A;
+})();
+function f(x) {
+    function g(x) {
+        x = x.self();
+    }
+    x = x.self();
+}
+var B = (function () {
+    function B() {
+    }
+    B.prototype.foo = function (x) {
+        x = x.self();
+    };
+    B.prototype.bar = function (x) {
+        x = x.self();
+    };
+    return B;
+})();
diff --git a/tests/baselines/reference/thisTypeAndConstraints.symbols b/tests/baselines/reference/thisTypeAndConstraints.symbols
new file mode 100644
index 00000000000..5f93df22c1a
--- /dev/null
+++ b/tests/baselines/reference/thisTypeAndConstraints.symbols
@@ -0,0 +1,70 @@
+=== tests/cases/conformance/types/thisType/thisTypeAndConstraints.ts ===
+class A {
+>A : Symbol(A, Decl(thisTypeAndConstraints.ts, 0, 0))
+
+    self() {
+>self : Symbol(self, Decl(thisTypeAndConstraints.ts, 0, 9))
+
+        return this;
+>this : Symbol(A, Decl(thisTypeAndConstraints.ts, 0, 0))
+    }
+}
+
+function f<T extends A>(x: T) {
+>f : Symbol(f, Decl(thisTypeAndConstraints.ts, 4, 1))
+>T : Symbol(T, Decl(thisTypeAndConstraints.ts, 6, 11))
+>A : Symbol(A, Decl(thisTypeAndConstraints.ts, 0, 0))
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 6, 24))
+>T : Symbol(T, Decl(thisTypeAndConstraints.ts, 6, 11))
+
+    function g<U extends T>(x: U) {
+>g : Symbol(g, Decl(thisTypeAndConstraints.ts, 6, 31))
+>U : Symbol(U, Decl(thisTypeAndConstraints.ts, 7, 15))
+>T : Symbol(T, Decl(thisTypeAndConstraints.ts, 6, 11))
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 7, 28))
+>U : Symbol(U, Decl(thisTypeAndConstraints.ts, 7, 15))
+
+        x = x.self();
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 7, 28))
+>x.self : Symbol(A.self, Decl(thisTypeAndConstraints.ts, 0, 9))
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 7, 28))
+>self : Symbol(A.self, Decl(thisTypeAndConstraints.ts, 0, 9))
+    }
+    x = x.self();
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 6, 24))
+>x.self : Symbol(A.self, Decl(thisTypeAndConstraints.ts, 0, 9))
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 6, 24))
+>self : Symbol(A.self, Decl(thisTypeAndConstraints.ts, 0, 9))
+}
+
+class B<T extends A> {
+>B : Symbol(B, Decl(thisTypeAndConstraints.ts, 11, 1))
+>T : Symbol(T, Decl(thisTypeAndConstraints.ts, 13, 8))
+>A : Symbol(A, Decl(thisTypeAndConstraints.ts, 0, 0))
+
+    foo(x: T) {
+>foo : Symbol(foo, Decl(thisTypeAndConstraints.ts, 13, 22))
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 14, 8))
+>T : Symbol(T, Decl(thisTypeAndConstraints.ts, 13, 8))
+
+        x = x.self();
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 14, 8))
+>x.self : Symbol(A.self, Decl(thisTypeAndConstraints.ts, 0, 9))
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 14, 8))
+>self : Symbol(A.self, Decl(thisTypeAndConstraints.ts, 0, 9))
+    }
+    bar<U extends T>(x: U) {
+>bar : Symbol(bar, Decl(thisTypeAndConstraints.ts, 16, 5))
+>U : Symbol(U, Decl(thisTypeAndConstraints.ts, 17, 8))
+>T : Symbol(T, Decl(thisTypeAndConstraints.ts, 13, 8))
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 17, 21))
+>U : Symbol(U, Decl(thisTypeAndConstraints.ts, 17, 8))
+
+        x = x.self();
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 17, 21))
+>x.self : Symbol(A.self, Decl(thisTypeAndConstraints.ts, 0, 9))
+>x : Symbol(x, Decl(thisTypeAndConstraints.ts, 17, 21))
+>self : Symbol(A.self, Decl(thisTypeAndConstraints.ts, 0, 9))
+    }
+}
+
diff --git a/tests/baselines/reference/thisTypeAndConstraints.types b/tests/baselines/reference/thisTypeAndConstraints.types
new file mode 100644
index 00000000000..af7a06e83cf
--- /dev/null
+++ b/tests/baselines/reference/thisTypeAndConstraints.types
@@ -0,0 +1,78 @@
+=== tests/cases/conformance/types/thisType/thisTypeAndConstraints.ts ===
+class A {
+>A : A
+
+    self() {
+>self : () => this
+
+        return this;
+>this : this
+    }
+}
+
+function f<T extends A>(x: T) {
+>f : <T extends A>(x: T) => void
+>T : T
+>A : A
+>x : T
+>T : T
+
+    function g<U extends T>(x: U) {
+>g : <U extends T>(x: U) => void
+>U : U
+>T : T
+>x : U
+>U : U
+
+        x = x.self();
+>x = x.self() : U
+>x : U
+>x.self() : U
+>x.self : () => U
+>x : U
+>self : () => U
+    }
+    x = x.self();
+>x = x.self() : T
+>x : T
+>x.self() : T
+>x.self : () => T
+>x : T
+>self : () => T
+}
+
+class B<T extends A> {
+>B : B<T>
+>T : T
+>A : A
+
+    foo(x: T) {
+>foo : (x: T) => void
+>x : T
+>T : T
+
+        x = x.self();
+>x = x.self() : T
+>x : T
+>x.self() : T
+>x.self : () => T
+>x : T
+>self : () => T
+    }
+    bar<U extends T>(x: U) {
+>bar : <U extends T>(x: U) => void
+>U : U
+>T : T
+>x : U
+>U : U
+
+        x = x.self();
+>x = x.self() : U
+>x : U
+>x.self() : U
+>x.self : () => U
+>x : U
+>self : () => U
+    }
+}
+
diff --git a/tests/baselines/reference/thisTypeInClasses.errors.txt b/tests/baselines/reference/thisTypeInClasses.errors.txt
deleted file mode 100644
index db2ae1b5793..00000000000
--- a/tests/baselines/reference/thisTypeInClasses.errors.txt
+++ /dev/null
@@ -1,57 +0,0 @@
-tests/cases/conformance/types/thisType/thisTypeInClasses.ts(4,20): error TS2526: A 'this' type is available only in a non-static member of a class or interface.
-
-
-==== tests/cases/conformance/types/thisType/thisTypeInClasses.ts (1 errors) ====
-    class C1 {
-        x: this;
-        f(x: this): this { return undefined; }
-        constructor(x: this) { }
-                       ~~~~
-!!! error TS2526: A 'this' type is available only in a non-static member of a class or interface.
-    }
-    
-    class C2 {
-        [x: string]: this;
-    }
-    
-    interface Foo<T> {
-        x: T;
-        y: this;
-    }
-    
-    class C3 {
-        a: this[];
-        b: [this, this];
-        c: this | Date;
-        d: this & Date;
-        e: (((this)));
-        f: (x: this) => this;
-        g: new (x: this) => this;
-        h: Foo<this>;
-        i: Foo<this | (() => this)>;
-        j: (x: any) => x is this;
-    }
-    
-    declare class C4 {
-        x: this;
-        f(x: this): this;
-    }
-    
-    class C5 {
-        foo() {
-            let f1 = (x: this): this => this;
-            let f2 = (x: this) => this;
-            let f3 = (x: this) => (y: this) => this;
-            let f4 = (x: this) => {
-                let g = (y: this) => {
-                    return () => this;
-                }
-                return g(this);
-            }
-        }
-        bar() {
-            let x1 = <this>undefined;
-            let x2 = undefined as this;
-        }
-    }
-    
\ No newline at end of file
diff --git a/tests/baselines/reference/thisTypeInClasses.js b/tests/baselines/reference/thisTypeInClasses.js
index 93344fa62cb..52ad452aa56 100644
--- a/tests/baselines/reference/thisTypeInClasses.js
+++ b/tests/baselines/reference/thisTypeInClasses.js
@@ -2,7 +2,6 @@
 class C1 {
     x: this;
     f(x: this): this { return undefined; }
-    constructor(x: this) { }
 }
 
 class C2 {
@@ -53,7 +52,7 @@ class C5 {
 
 //// [thisTypeInClasses.js]
 var C1 = (function () {
-    function C1(x) {
+    function C1() {
     }
     C1.prototype.f = function (x) { return undefined; };
     return C1;
diff --git a/tests/baselines/reference/thisTypeInClasses.symbols b/tests/baselines/reference/thisTypeInClasses.symbols
index 04ed47b09ff..0915d6e5e6b 100644
--- a/tests/baselines/reference/thisTypeInClasses.symbols
+++ b/tests/baselines/reference/thisTypeInClasses.symbols
@@ -9,131 +9,128 @@ class C1 {
 >f : Symbol(f, Decl(thisTypeInClasses.ts, 1, 12))
 >x : Symbol(x, Decl(thisTypeInClasses.ts, 2, 6))
 >undefined : Symbol(undefined)
-
-    constructor(x: this) { }
->x : Symbol(x, Decl(thisTypeInClasses.ts, 3, 16))
 }
 
 class C2 {
->C2 : Symbol(C2, Decl(thisTypeInClasses.ts, 4, 1))
+>C2 : Symbol(C2, Decl(thisTypeInClasses.ts, 3, 1))
 
     [x: string]: this;
->x : Symbol(x, Decl(thisTypeInClasses.ts, 7, 5))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 6, 5))
 }
 
 interface Foo<T> {
->Foo : Symbol(Foo, Decl(thisTypeInClasses.ts, 8, 1))
->T : Symbol(T, Decl(thisTypeInClasses.ts, 10, 14))
+>Foo : Symbol(Foo, Decl(thisTypeInClasses.ts, 7, 1))
+>T : Symbol(T, Decl(thisTypeInClasses.ts, 9, 14))
 
     x: T;
->x : Symbol(x, Decl(thisTypeInClasses.ts, 10, 18))
->T : Symbol(T, Decl(thisTypeInClasses.ts, 10, 14))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 9, 18))
+>T : Symbol(T, Decl(thisTypeInClasses.ts, 9, 14))
 
     y: this;
->y : Symbol(y, Decl(thisTypeInClasses.ts, 11, 9))
+>y : Symbol(y, Decl(thisTypeInClasses.ts, 10, 9))
 }
 
 class C3 {
->C3 : Symbol(C3, Decl(thisTypeInClasses.ts, 13, 1))
+>C3 : Symbol(C3, Decl(thisTypeInClasses.ts, 12, 1))
 
     a: this[];
->a : Symbol(a, Decl(thisTypeInClasses.ts, 15, 10))
+>a : Symbol(a, Decl(thisTypeInClasses.ts, 14, 10))
 
     b: [this, this];
->b : Symbol(b, Decl(thisTypeInClasses.ts, 16, 14))
+>b : Symbol(b, Decl(thisTypeInClasses.ts, 15, 14))
 
     c: this | Date;
->c : Symbol(c, Decl(thisTypeInClasses.ts, 17, 20))
+>c : Symbol(c, Decl(thisTypeInClasses.ts, 16, 20))
 >Date : Symbol(Date, Decl(lib.d.ts, --, --), Decl(lib.d.ts, --, --))
 
     d: this & Date;
->d : Symbol(d, Decl(thisTypeInClasses.ts, 18, 19))
+>d : Symbol(d, Decl(thisTypeInClasses.ts, 17, 19))
 >Date : Symbol(Date, Decl(lib.d.ts, --, --), Decl(lib.d.ts, --, --))
 
     e: (((this)));
->e : Symbol(e, Decl(thisTypeInClasses.ts, 19, 19))
+>e : Symbol(e, Decl(thisTypeInClasses.ts, 18, 19))
 
     f: (x: this) => this;
->f : Symbol(f, Decl(thisTypeInClasses.ts, 20, 18))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 21, 8))
+>f : Symbol(f, Decl(thisTypeInClasses.ts, 19, 18))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 20, 8))
 
     g: new (x: this) => this;
->g : Symbol(g, Decl(thisTypeInClasses.ts, 21, 25))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 22, 12))
+>g : Symbol(g, Decl(thisTypeInClasses.ts, 20, 25))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 21, 12))
 
     h: Foo<this>;
->h : Symbol(h, Decl(thisTypeInClasses.ts, 22, 29))
->Foo : Symbol(Foo, Decl(thisTypeInClasses.ts, 8, 1))
+>h : Symbol(h, Decl(thisTypeInClasses.ts, 21, 29))
+>Foo : Symbol(Foo, Decl(thisTypeInClasses.ts, 7, 1))
 
     i: Foo<this | (() => this)>;
->i : Symbol(i, Decl(thisTypeInClasses.ts, 23, 17))
->Foo : Symbol(Foo, Decl(thisTypeInClasses.ts, 8, 1))
+>i : Symbol(i, Decl(thisTypeInClasses.ts, 22, 17))
+>Foo : Symbol(Foo, Decl(thisTypeInClasses.ts, 7, 1))
 
     j: (x: any) => x is this;
->j : Symbol(j, Decl(thisTypeInClasses.ts, 24, 32))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 25, 8))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 25, 8))
+>j : Symbol(j, Decl(thisTypeInClasses.ts, 23, 32))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 24, 8))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 24, 8))
 }
 
 declare class C4 {
->C4 : Symbol(C4, Decl(thisTypeInClasses.ts, 26, 1))
+>C4 : Symbol(C4, Decl(thisTypeInClasses.ts, 25, 1))
 
     x: this;
->x : Symbol(x, Decl(thisTypeInClasses.ts, 28, 18))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 27, 18))
 
     f(x: this): this;
->f : Symbol(f, Decl(thisTypeInClasses.ts, 29, 12))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 30, 6))
+>f : Symbol(f, Decl(thisTypeInClasses.ts, 28, 12))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 29, 6))
 }
 
 class C5 {
->C5 : Symbol(C5, Decl(thisTypeInClasses.ts, 31, 1))
+>C5 : Symbol(C5, Decl(thisTypeInClasses.ts, 30, 1))
 
     foo() {
->foo : Symbol(foo, Decl(thisTypeInClasses.ts, 33, 10))
+>foo : Symbol(foo, Decl(thisTypeInClasses.ts, 32, 10))
 
         let f1 = (x: this): this => this;
->f1 : Symbol(f1, Decl(thisTypeInClasses.ts, 35, 11))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 35, 18))
->this : Symbol(C5, Decl(thisTypeInClasses.ts, 31, 1))
->this : Symbol(C5, Decl(thisTypeInClasses.ts, 31, 1))
+>f1 : Symbol(f1, Decl(thisTypeInClasses.ts, 34, 11))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 34, 18))
+>this : Symbol(C5, Decl(thisTypeInClasses.ts, 30, 1))
+>this : Symbol(C5, Decl(thisTypeInClasses.ts, 30, 1))
 
         let f2 = (x: this) => this;
->f2 : Symbol(f2, Decl(thisTypeInClasses.ts, 36, 11))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 36, 18))
->this : Symbol(C5, Decl(thisTypeInClasses.ts, 31, 1))
+>f2 : Symbol(f2, Decl(thisTypeInClasses.ts, 35, 11))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 35, 18))
+>this : Symbol(C5, Decl(thisTypeInClasses.ts, 30, 1))
 
         let f3 = (x: this) => (y: this) => this;
->f3 : Symbol(f3, Decl(thisTypeInClasses.ts, 37, 11))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 37, 18))
->y : Symbol(y, Decl(thisTypeInClasses.ts, 37, 31))
->this : Symbol(C5, Decl(thisTypeInClasses.ts, 31, 1))
+>f3 : Symbol(f3, Decl(thisTypeInClasses.ts, 36, 11))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 36, 18))
+>y : Symbol(y, Decl(thisTypeInClasses.ts, 36, 31))
+>this : Symbol(C5, Decl(thisTypeInClasses.ts, 30, 1))
 
         let f4 = (x: this) => {
->f4 : Symbol(f4, Decl(thisTypeInClasses.ts, 38, 11))
->x : Symbol(x, Decl(thisTypeInClasses.ts, 38, 18))
+>f4 : Symbol(f4, Decl(thisTypeInClasses.ts, 37, 11))
+>x : Symbol(x, Decl(thisTypeInClasses.ts, 37, 18))
 
             let g = (y: this) => {
->g : Symbol(g, Decl(thisTypeInClasses.ts, 39, 15))
->y : Symbol(y, Decl(thisTypeInClasses.ts, 39, 21))
+>g : Symbol(g, Decl(thisTypeInClasses.ts, 38, 15))
+>y : Symbol(y, Decl(thisTypeInClasses.ts, 38, 21))
 
                 return () => this;
->this : Symbol(C5, Decl(thisTypeInClasses.ts, 31, 1))
+>this : Symbol(C5, Decl(thisTypeInClasses.ts, 30, 1))
             }
             return g(this);
->g : Symbol(g, Decl(thisTypeInClasses.ts, 39, 15))
->this : Symbol(C5, Decl(thisTypeInClasses.ts, 31, 1))
+>g : Symbol(g, Decl(thisTypeInClasses.ts, 38, 15))
+>this : Symbol(C5, Decl(thisTypeInClasses.ts, 30, 1))
         }
     }
     bar() {
->bar : Symbol(bar, Decl(thisTypeInClasses.ts, 44, 5))
+>bar : Symbol(bar, Decl(thisTypeInClasses.ts, 43, 5))
 
         let x1 = <this>undefined;
->x1 : Symbol(x1, Decl(thisTypeInClasses.ts, 46, 11))
+>x1 : Symbol(x1, Decl(thisTypeInClasses.ts, 45, 11))
 >undefined : Symbol(undefined)
 
         let x2 = undefined as this;
->x2 : Symbol(x2, Decl(thisTypeInClasses.ts, 47, 11))
+>x2 : Symbol(x2, Decl(thisTypeInClasses.ts, 46, 11))
 >undefined : Symbol(undefined)
     }
 }
diff --git a/tests/baselines/reference/thisTypeInClasses.types b/tests/baselines/reference/thisTypeInClasses.types
index ddfdfb277a9..512359decd9 100644
--- a/tests/baselines/reference/thisTypeInClasses.types
+++ b/tests/baselines/reference/thisTypeInClasses.types
@@ -9,9 +9,6 @@ class C1 {
 >f : (x: this) => this
 >x : this
 >undefined : undefined
-
-    constructor(x: this) { }
->x : this
 }
 
 class C2 {
diff --git a/tests/baselines/reference/typeGuardOfFormInstanceOf.js b/tests/baselines/reference/typeGuardOfFormInstanceOf.js
index cab04365c19..1431b4b9c60 100644
--- a/tests/baselines/reference/typeGuardOfFormInstanceOf.js
+++ b/tests/baselines/reference/typeGuardOfFormInstanceOf.js
@@ -14,21 +14,58 @@ class C2 {
 class D1 extends C1 {
     p3: number;
 }
+class C3 {
+    p4: number;
+}
 var str: string;
 var num: number;
 var strOrNum: string | number;
 
-var c1Orc2: C1 | C2;
-str = c1Orc2 instanceof C1 && c1Orc2.p1; // C1
-num = c1Orc2 instanceof C2 && c1Orc2.p2; // C2
-str = c1Orc2 instanceof D1 && c1Orc2.p1; // D1
-num = c1Orc2 instanceof D1 && c1Orc2.p3; // D1
+var ctor1: C1 | C2;
+str = ctor1 instanceof C1 && ctor1.p1; // C1
+num = ctor1 instanceof C2 && ctor1.p2; // C2
+str = ctor1 instanceof D1 && ctor1.p1; // D1
+num = ctor1 instanceof D1 && ctor1.p3; // D1
 
-var c2Ord1: C2 | D1;
-num = c2Ord1 instanceof C2 && c2Ord1.p2; // C2
-num = c2Ord1 instanceof D1 && c2Ord1.p3; // D1
-str = c2Ord1 instanceof D1 && c2Ord1.p1; // D1
-var r2: D1 | C2 = c2Ord1 instanceof C1 && c2Ord1; // C2 | D1
+var ctor2: C2 | D1;
+num = ctor2 instanceof C2 && ctor2.p2; // C2
+num = ctor2 instanceof D1 && ctor2.p3; // D1
+str = ctor2 instanceof D1 && ctor2.p1; // D1
+var r2: D1 | C2 = ctor2 instanceof C1 && ctor2; // C2 | D1
+
+var ctor3: C1 | C2;
+if (ctor3 instanceof C1) {
+    ctor3.p1; // C1
+}
+else {
+    ctor3.p2; // C2
+}
+
+var ctor4: C1 | C2 | C3;
+if (ctor4 instanceof C1) {
+    ctor4.p1; // C1
+}
+else if (ctor4 instanceof C2) {
+    ctor4.p2; // C2
+}
+else {
+    ctor4.p4; // C3
+}
+
+var ctor5: C1 | D1 | C2;
+if (ctor5 instanceof C1) {
+    ctor5.p1; // C1
+}
+else {
+    ctor5.p2; // C2
+}
+
+var ctor6: C1 | C2 | C3;
+if (ctor6 instanceof C1 || ctor6 instanceof C2) {
+}
+else {
+    ctor6.p4; // C3
+}
 
 //// [typeGuardOfFormInstanceOf.js]
 // A type guard of the form x instanceof C, where C is of a subtype of the global type 'Function' 
@@ -58,16 +95,51 @@ var D1 = (function (_super) {
     }
     return D1;
 })(C1);
+var C3 = (function () {
+    function C3() {
+    }
+    return C3;
+})();
 var str;
 var num;
 var strOrNum;
-var c1Orc2;
-str = c1Orc2 instanceof C1 && c1Orc2.p1; // C1
-num = c1Orc2 instanceof C2 && c1Orc2.p2; // C2
-str = c1Orc2 instanceof D1 && c1Orc2.p1; // D1
-num = c1Orc2 instanceof D1 && c1Orc2.p3; // D1
-var c2Ord1;
-num = c2Ord1 instanceof C2 && c2Ord1.p2; // C2
-num = c2Ord1 instanceof D1 && c2Ord1.p3; // D1
-str = c2Ord1 instanceof D1 && c2Ord1.p1; // D1
-var r2 = c2Ord1 instanceof C1 && c2Ord1; // C2 | D1
+var ctor1;
+str = ctor1 instanceof C1 && ctor1.p1; // C1
+num = ctor1 instanceof C2 && ctor1.p2; // C2
+str = ctor1 instanceof D1 && ctor1.p1; // D1
+num = ctor1 instanceof D1 && ctor1.p3; // D1
+var ctor2;
+num = ctor2 instanceof C2 && ctor2.p2; // C2
+num = ctor2 instanceof D1 && ctor2.p3; // D1
+str = ctor2 instanceof D1 && ctor2.p1; // D1
+var r2 = ctor2 instanceof C1 && ctor2; // C2 | D1
+var ctor3;
+if (ctor3 instanceof C1) {
+    ctor3.p1; // C1
+}
+else {
+    ctor3.p2; // C2
+}
+var ctor4;
+if (ctor4 instanceof C1) {
+    ctor4.p1; // C1
+}
+else if (ctor4 instanceof C2) {
+    ctor4.p2; // C2
+}
+else {
+    ctor4.p4; // C3
+}
+var ctor5;
+if (ctor5 instanceof C1) {
+    ctor5.p1; // C1
+}
+else {
+    ctor5.p2; // C2
+}
+var ctor6;
+if (ctor6 instanceof C1 || ctor6 instanceof C2) {
+}
+else {
+    ctor6.p4; // C3
+}
diff --git a/tests/baselines/reference/typeGuardOfFormInstanceOf.symbols b/tests/baselines/reference/typeGuardOfFormInstanceOf.symbols
index 7a48d87e963..0dd2844f6ad 100644
--- a/tests/baselines/reference/typeGuardOfFormInstanceOf.symbols
+++ b/tests/baselines/reference/typeGuardOfFormInstanceOf.symbols
@@ -24,86 +24,184 @@ class D1 extends C1 {
     p3: number;
 >p3 : Symbol(p3, Decl(typeGuardOfFormInstanceOf.ts, 12, 21))
 }
+class C3 {
+>C3 : Symbol(C3, Decl(typeGuardOfFormInstanceOf.ts, 14, 1))
+
+    p4: number;
+>p4 : Symbol(p4, Decl(typeGuardOfFormInstanceOf.ts, 15, 10))
+}
 var str: string;
->str : Symbol(str, Decl(typeGuardOfFormInstanceOf.ts, 15, 3))
+>str : Symbol(str, Decl(typeGuardOfFormInstanceOf.ts, 18, 3))
 
 var num: number;
->num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 16, 3))
+>num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
 
 var strOrNum: string | number;
->strOrNum : Symbol(strOrNum, Decl(typeGuardOfFormInstanceOf.ts, 17, 3))
+>strOrNum : Symbol(strOrNum, Decl(typeGuardOfFormInstanceOf.ts, 20, 3))
 
-var c1Orc2: C1 | C2;
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+var ctor1: C1 | C2;
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
 >C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
 
-str = c1Orc2 instanceof C1 && c1Orc2.p1; // C1
->str : Symbol(str, Decl(typeGuardOfFormInstanceOf.ts, 15, 3))
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+str = ctor1 instanceof C1 && ctor1.p1; // C1
+>str : Symbol(str, Decl(typeGuardOfFormInstanceOf.ts, 18, 3))
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
->c1Orc2.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+>ctor1.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
 
-num = c1Orc2 instanceof C2 && c1Orc2.p2; // C2
->num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 16, 3))
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+num = ctor1 instanceof C2 && ctor1.p2; // C2
+>num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
->c1Orc2.p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+>ctor1.p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
 
-str = c1Orc2 instanceof D1 && c1Orc2.p1; // D1
->str : Symbol(str, Decl(typeGuardOfFormInstanceOf.ts, 15, 3))
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+str = ctor1 instanceof D1 && ctor1.p1; // D1
+>str : Symbol(str, Decl(typeGuardOfFormInstanceOf.ts, 18, 3))
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >D1 : Symbol(D1, Decl(typeGuardOfFormInstanceOf.ts, 11, 1))
->c1Orc2.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+>ctor1.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
 
-num = c1Orc2 instanceof D1 && c1Orc2.p3; // D1
->num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 16, 3))
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+num = ctor1 instanceof D1 && ctor1.p3; // D1
+>num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >D1 : Symbol(D1, Decl(typeGuardOfFormInstanceOf.ts, 11, 1))
->c1Orc2.p3 : Symbol(D1.p3, Decl(typeGuardOfFormInstanceOf.ts, 12, 21))
->c1Orc2 : Symbol(c1Orc2, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+>ctor1.p3 : Symbol(D1.p3, Decl(typeGuardOfFormInstanceOf.ts, 12, 21))
+>ctor1 : Symbol(ctor1, Decl(typeGuardOfFormInstanceOf.ts, 22, 3))
 >p3 : Symbol(D1.p3, Decl(typeGuardOfFormInstanceOf.ts, 12, 21))
 
-var c2Ord1: C2 | D1;
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+var ctor2: C2 | D1;
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 >C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
 >D1 : Symbol(D1, Decl(typeGuardOfFormInstanceOf.ts, 11, 1))
 
-num = c2Ord1 instanceof C2 && c2Ord1.p2; // C2
->num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 16, 3))
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+num = ctor2 instanceof C2 && ctor2.p2; // C2
+>num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 >C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
->c2Ord1.p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+>ctor2.p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 >p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
 
-num = c2Ord1 instanceof D1 && c2Ord1.p3; // D1
->num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 16, 3))
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+num = ctor2 instanceof D1 && ctor2.p3; // D1
+>num : Symbol(num, Decl(typeGuardOfFormInstanceOf.ts, 19, 3))
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 >D1 : Symbol(D1, Decl(typeGuardOfFormInstanceOf.ts, 11, 1))
->c2Ord1.p3 : Symbol(D1.p3, Decl(typeGuardOfFormInstanceOf.ts, 12, 21))
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+>ctor2.p3 : Symbol(D1.p3, Decl(typeGuardOfFormInstanceOf.ts, 12, 21))
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 >p3 : Symbol(D1.p3, Decl(typeGuardOfFormInstanceOf.ts, 12, 21))
 
-str = c2Ord1 instanceof D1 && c2Ord1.p1; // D1
->str : Symbol(str, Decl(typeGuardOfFormInstanceOf.ts, 15, 3))
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+str = ctor2 instanceof D1 && ctor2.p1; // D1
+>str : Symbol(str, Decl(typeGuardOfFormInstanceOf.ts, 18, 3))
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 >D1 : Symbol(D1, Decl(typeGuardOfFormInstanceOf.ts, 11, 1))
->c2Ord1.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+>ctor2.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 >p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
 
-var r2: D1 | C2 = c2Ord1 instanceof C1 && c2Ord1; // C2 | D1
->r2 : Symbol(r2, Decl(typeGuardOfFormInstanceOf.ts, 29, 3))
+var r2: D1 | C2 = ctor2 instanceof C1 && ctor2; // C2 | D1
+>r2 : Symbol(r2, Decl(typeGuardOfFormInstanceOf.ts, 32, 3))
 >D1 : Symbol(D1, Decl(typeGuardOfFormInstanceOf.ts, 11, 1))
 >C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 >C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
->c2Ord1 : Symbol(c2Ord1, Decl(typeGuardOfFormInstanceOf.ts, 25, 3))
+>ctor2 : Symbol(ctor2, Decl(typeGuardOfFormInstanceOf.ts, 28, 3))
 
+var ctor3: C1 | C2;
+>ctor3 : Symbol(ctor3, Decl(typeGuardOfFormInstanceOf.ts, 34, 3))
+>C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
+>C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
+
+if (ctor3 instanceof C1) {
+>ctor3 : Symbol(ctor3, Decl(typeGuardOfFormInstanceOf.ts, 34, 3))
+>C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
+
+    ctor3.p1; // C1
+>ctor3.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+>ctor3 : Symbol(ctor3, Decl(typeGuardOfFormInstanceOf.ts, 34, 3))
+>p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+}
+else {
+    ctor3.p2; // C2
+>ctor3.p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
+>ctor3 : Symbol(ctor3, Decl(typeGuardOfFormInstanceOf.ts, 34, 3))
+>p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
+}
+
+var ctor4: C1 | C2 | C3;
+>ctor4 : Symbol(ctor4, Decl(typeGuardOfFormInstanceOf.ts, 42, 3))
+>C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
+>C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
+>C3 : Symbol(C3, Decl(typeGuardOfFormInstanceOf.ts, 14, 1))
+
+if (ctor4 instanceof C1) {
+>ctor4 : Symbol(ctor4, Decl(typeGuardOfFormInstanceOf.ts, 42, 3))
+>C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
+
+    ctor4.p1; // C1
+>ctor4.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+>ctor4 : Symbol(ctor4, Decl(typeGuardOfFormInstanceOf.ts, 42, 3))
+>p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+}
+else if (ctor4 instanceof C2) {
+>ctor4 : Symbol(ctor4, Decl(typeGuardOfFormInstanceOf.ts, 42, 3))
+>C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
+
+    ctor4.p2; // C2
+>ctor4.p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
+>ctor4 : Symbol(ctor4, Decl(typeGuardOfFormInstanceOf.ts, 42, 3))
+>p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
+}
+else {
+    ctor4.p4; // C3
+>ctor4.p4 : Symbol(C3.p4, Decl(typeGuardOfFormInstanceOf.ts, 15, 10))
+>ctor4 : Symbol(ctor4, Decl(typeGuardOfFormInstanceOf.ts, 42, 3))
+>p4 : Symbol(C3.p4, Decl(typeGuardOfFormInstanceOf.ts, 15, 10))
+}
+
+var ctor5: C1 | D1 | C2;
+>ctor5 : Symbol(ctor5, Decl(typeGuardOfFormInstanceOf.ts, 53, 3))
+>C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
+>D1 : Symbol(D1, Decl(typeGuardOfFormInstanceOf.ts, 11, 1))
+>C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
+
+if (ctor5 instanceof C1) {
+>ctor5 : Symbol(ctor5, Decl(typeGuardOfFormInstanceOf.ts, 53, 3))
+>C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
+
+    ctor5.p1; // C1
+>ctor5.p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+>ctor5 : Symbol(ctor5, Decl(typeGuardOfFormInstanceOf.ts, 53, 3))
+>p1 : Symbol(C1.p1, Decl(typeGuardOfFormInstanceOf.ts, 6, 10))
+}
+else {
+    ctor5.p2; // C2
+>ctor5.p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
+>ctor5 : Symbol(ctor5, Decl(typeGuardOfFormInstanceOf.ts, 53, 3))
+>p2 : Symbol(C2.p2, Decl(typeGuardOfFormInstanceOf.ts, 9, 10))
+}
+
+var ctor6: C1 | C2 | C3;
+>ctor6 : Symbol(ctor6, Decl(typeGuardOfFormInstanceOf.ts, 61, 3))
+>C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
+>C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
+>C3 : Symbol(C3, Decl(typeGuardOfFormInstanceOf.ts, 14, 1))
+
+if (ctor6 instanceof C1 || ctor6 instanceof C2) {
+>ctor6 : Symbol(ctor6, Decl(typeGuardOfFormInstanceOf.ts, 61, 3))
+>C1 : Symbol(C1, Decl(typeGuardOfFormInstanceOf.ts, 0, 0))
+>ctor6 : Symbol(ctor6, Decl(typeGuardOfFormInstanceOf.ts, 61, 3))
+>C2 : Symbol(C2, Decl(typeGuardOfFormInstanceOf.ts, 8, 1))
+}
+else {
+    ctor6.p4; // C3
+>ctor6.p4 : Symbol(C3.p4, Decl(typeGuardOfFormInstanceOf.ts, 15, 10))
+>ctor6 : Symbol(ctor6, Decl(typeGuardOfFormInstanceOf.ts, 61, 3))
+>p4 : Symbol(C3.p4, Decl(typeGuardOfFormInstanceOf.ts, 15, 10))
+}
diff --git a/tests/baselines/reference/typeGuardOfFormInstanceOf.types b/tests/baselines/reference/typeGuardOfFormInstanceOf.types
index c824e907733..6b83b57dcb5 100644
--- a/tests/baselines/reference/typeGuardOfFormInstanceOf.types
+++ b/tests/baselines/reference/typeGuardOfFormInstanceOf.types
@@ -24,6 +24,12 @@ class D1 extends C1 {
     p3: number;
 >p3 : number
 }
+class C3 {
+>C3 : C3
+
+    p4: number;
+>p4 : number
+}
 var str: string;
 >str : string
 
@@ -33,100 +39,199 @@ var num: number;
 var strOrNum: string | number;
 >strOrNum : string | number
 
-var c1Orc2: C1 | C2;
->c1Orc2 : C1 | C2
+var ctor1: C1 | C2;
+>ctor1 : C1 | C2
 >C1 : C1
 >C2 : C2
 
-str = c1Orc2 instanceof C1 && c1Orc2.p1; // C1
->str = c1Orc2 instanceof C1 && c1Orc2.p1 : string
+str = ctor1 instanceof C1 && ctor1.p1; // C1
+>str = ctor1 instanceof C1 && ctor1.p1 : string
 >str : string
->c1Orc2 instanceof C1 && c1Orc2.p1 : string
->c1Orc2 instanceof C1 : boolean
->c1Orc2 : C1 | C2
+>ctor1 instanceof C1 && ctor1.p1 : string
+>ctor1 instanceof C1 : boolean
+>ctor1 : C1 | C2
 >C1 : typeof C1
->c1Orc2.p1 : string
->c1Orc2 : C1
+>ctor1.p1 : string
+>ctor1 : C1
 >p1 : string
 
-num = c1Orc2 instanceof C2 && c1Orc2.p2; // C2
->num = c1Orc2 instanceof C2 && c1Orc2.p2 : number
+num = ctor1 instanceof C2 && ctor1.p2; // C2
+>num = ctor1 instanceof C2 && ctor1.p2 : number
 >num : number
->c1Orc2 instanceof C2 && c1Orc2.p2 : number
->c1Orc2 instanceof C2 : boolean
->c1Orc2 : C1 | C2
+>ctor1 instanceof C2 && ctor1.p2 : number
+>ctor1 instanceof C2 : boolean
+>ctor1 : C1 | C2
 >C2 : typeof C2
->c1Orc2.p2 : number
->c1Orc2 : C2
+>ctor1.p2 : number
+>ctor1 : C2
 >p2 : number
 
-str = c1Orc2 instanceof D1 && c1Orc2.p1; // D1
->str = c1Orc2 instanceof D1 && c1Orc2.p1 : string
+str = ctor1 instanceof D1 && ctor1.p1; // D1
+>str = ctor1 instanceof D1 && ctor1.p1 : string
 >str : string
->c1Orc2 instanceof D1 && c1Orc2.p1 : string
->c1Orc2 instanceof D1 : boolean
->c1Orc2 : C1 | C2
+>ctor1 instanceof D1 && ctor1.p1 : string
+>ctor1 instanceof D1 : boolean
+>ctor1 : C1 | C2
 >D1 : typeof D1
->c1Orc2.p1 : string
->c1Orc2 : D1
+>ctor1.p1 : string
+>ctor1 : D1
 >p1 : string
 
-num = c1Orc2 instanceof D1 && c1Orc2.p3; // D1
->num = c1Orc2 instanceof D1 && c1Orc2.p3 : number
+num = ctor1 instanceof D1 && ctor1.p3; // D1
+>num = ctor1 instanceof D1 && ctor1.p3 : number
 >num : number
->c1Orc2 instanceof D1 && c1Orc2.p3 : number
->c1Orc2 instanceof D1 : boolean
->c1Orc2 : C1 | C2
+>ctor1 instanceof D1 && ctor1.p3 : number
+>ctor1 instanceof D1 : boolean
+>ctor1 : C1 | C2
 >D1 : typeof D1
->c1Orc2.p3 : number
->c1Orc2 : D1
+>ctor1.p3 : number
+>ctor1 : D1
 >p3 : number
 
-var c2Ord1: C2 | D1;
->c2Ord1 : C2 | D1
+var ctor2: C2 | D1;
+>ctor2 : C2 | D1
 >C2 : C2
 >D1 : D1
 
-num = c2Ord1 instanceof C2 && c2Ord1.p2; // C2
->num = c2Ord1 instanceof C2 && c2Ord1.p2 : number
+num = ctor2 instanceof C2 && ctor2.p2; // C2
+>num = ctor2 instanceof C2 && ctor2.p2 : number
 >num : number
->c2Ord1 instanceof C2 && c2Ord1.p2 : number
->c2Ord1 instanceof C2 : boolean
->c2Ord1 : C2 | D1
+>ctor2 instanceof C2 && ctor2.p2 : number
+>ctor2 instanceof C2 : boolean
+>ctor2 : C2 | D1
 >C2 : typeof C2
->c2Ord1.p2 : number
->c2Ord1 : C2
+>ctor2.p2 : number
+>ctor2 : C2
 >p2 : number
 
-num = c2Ord1 instanceof D1 && c2Ord1.p3; // D1
->num = c2Ord1 instanceof D1 && c2Ord1.p3 : number
+num = ctor2 instanceof D1 && ctor2.p3; // D1
+>num = ctor2 instanceof D1 && ctor2.p3 : number
 >num : number
->c2Ord1 instanceof D1 && c2Ord1.p3 : number
->c2Ord1 instanceof D1 : boolean
->c2Ord1 : C2 | D1
+>ctor2 instanceof D1 && ctor2.p3 : number
+>ctor2 instanceof D1 : boolean
+>ctor2 : C2 | D1
 >D1 : typeof D1
->c2Ord1.p3 : number
->c2Ord1 : D1
+>ctor2.p3 : number
+>ctor2 : D1
 >p3 : number
 
-str = c2Ord1 instanceof D1 && c2Ord1.p1; // D1
->str = c2Ord1 instanceof D1 && c2Ord1.p1 : string
+str = ctor2 instanceof D1 && ctor2.p1; // D1
+>str = ctor2 instanceof D1 && ctor2.p1 : string
 >str : string
->c2Ord1 instanceof D1 && c2Ord1.p1 : string
->c2Ord1 instanceof D1 : boolean
->c2Ord1 : C2 | D1
+>ctor2 instanceof D1 && ctor2.p1 : string
+>ctor2 instanceof D1 : boolean
+>ctor2 : C2 | D1
 >D1 : typeof D1
->c2Ord1.p1 : string
->c2Ord1 : D1
+>ctor2.p1 : string
+>ctor2 : D1
 >p1 : string
 
-var r2: D1 | C2 = c2Ord1 instanceof C1 && c2Ord1; // C2 | D1
+var r2: D1 | C2 = ctor2 instanceof C1 && ctor2; // C2 | D1
 >r2 : D1 | C2
 >D1 : D1
 >C2 : C2
->c2Ord1 instanceof C1 && c2Ord1 : D1
->c2Ord1 instanceof C1 : boolean
->c2Ord1 : C2 | D1
+>ctor2 instanceof C1 && ctor2 : D1
+>ctor2 instanceof C1 : boolean
+>ctor2 : C2 | D1
 >C1 : typeof C1
->c2Ord1 : D1
+>ctor2 : D1
 
+var ctor3: C1 | C2;
+>ctor3 : C1 | C2
+>C1 : C1
+>C2 : C2
+
+if (ctor3 instanceof C1) {
+>ctor3 instanceof C1 : boolean
+>ctor3 : C1 | C2
+>C1 : typeof C1
+
+    ctor3.p1; // C1
+>ctor3.p1 : string
+>ctor3 : C1
+>p1 : string
+}
+else {
+    ctor3.p2; // C2
+>ctor3.p2 : number
+>ctor3 : C2
+>p2 : number
+}
+
+var ctor4: C1 | C2 | C3;
+>ctor4 : C1 | C2 | C3
+>C1 : C1
+>C2 : C2
+>C3 : C3
+
+if (ctor4 instanceof C1) {
+>ctor4 instanceof C1 : boolean
+>ctor4 : C1 | C2 | C3
+>C1 : typeof C1
+
+    ctor4.p1; // C1
+>ctor4.p1 : string
+>ctor4 : C1
+>p1 : string
+}
+else if (ctor4 instanceof C2) {
+>ctor4 instanceof C2 : boolean
+>ctor4 : C2 | C3
+>C2 : typeof C2
+
+    ctor4.p2; // C2
+>ctor4.p2 : number
+>ctor4 : C2
+>p2 : number
+}
+else {
+    ctor4.p4; // C3
+>ctor4.p4 : number
+>ctor4 : C3
+>p4 : number
+}
+
+var ctor5: C1 | D1 | C2;
+>ctor5 : C1 | D1 | C2
+>C1 : C1
+>D1 : D1
+>C2 : C2
+
+if (ctor5 instanceof C1) {
+>ctor5 instanceof C1 : boolean
+>ctor5 : C1 | D1 | C2
+>C1 : typeof C1
+
+    ctor5.p1; // C1
+>ctor5.p1 : string
+>ctor5 : C1
+>p1 : string
+}
+else {
+    ctor5.p2; // C2
+>ctor5.p2 : number
+>ctor5 : C2
+>p2 : number
+}
+
+var ctor6: C1 | C2 | C3;
+>ctor6 : C1 | C2 | C3
+>C1 : C1
+>C2 : C2
+>C3 : C3
+
+if (ctor6 instanceof C1 || ctor6 instanceof C2) {
+>ctor6 instanceof C1 || ctor6 instanceof C2 : boolean
+>ctor6 instanceof C1 : boolean
+>ctor6 : C1 | C2 | C3
+>C1 : typeof C1
+>ctor6 instanceof C2 : boolean
+>ctor6 : C2 | C3
+>C2 : typeof C2
+}
+else {
+    ctor6.p4; // C3
+>ctor6.p4 : number
+>ctor6 : C3
+>p4 : number
+}
diff --git a/tests/baselines/reference/typeParameterEquality.js b/tests/baselines/reference/typeParameterEquality.js
new file mode 100644
index 00000000000..b77e534b354
--- /dev/null
+++ b/tests/baselines/reference/typeParameterEquality.js
@@ -0,0 +1,11 @@
+//// [typeParameterEquality.ts]
+class C {
+    get x(): <T>(a: T) => T { return null; }
+    set x(p: <U>(a: U) => U) {}
+}
+
+//// [typeParameterEquality.js]
+class C {
+    get x() { return null; }
+    set x(p) { }
+}
diff --git a/tests/baselines/reference/typeParameterEquality.symbols b/tests/baselines/reference/typeParameterEquality.symbols
new file mode 100644
index 00000000000..562d6277d93
--- /dev/null
+++ b/tests/baselines/reference/typeParameterEquality.symbols
@@ -0,0 +1,19 @@
+=== tests/cases/compiler/typeParameterEquality.ts ===
+class C {
+>C : Symbol(C, Decl(typeParameterEquality.ts, 0, 0))
+
+    get x(): <T>(a: T) => T { return null; }
+>x : Symbol(x, Decl(typeParameterEquality.ts, 0, 9), Decl(typeParameterEquality.ts, 1, 44))
+>T : Symbol(T, Decl(typeParameterEquality.ts, 1, 14))
+>a : Symbol(a, Decl(typeParameterEquality.ts, 1, 17))
+>T : Symbol(T, Decl(typeParameterEquality.ts, 1, 14))
+>T : Symbol(T, Decl(typeParameterEquality.ts, 1, 14))
+
+    set x(p: <U>(a: U) => U) {}
+>x : Symbol(x, Decl(typeParameterEquality.ts, 0, 9), Decl(typeParameterEquality.ts, 1, 44))
+>p : Symbol(p, Decl(typeParameterEquality.ts, 2, 10))
+>U : Symbol(U, Decl(typeParameterEquality.ts, 2, 14))
+>a : Symbol(a, Decl(typeParameterEquality.ts, 2, 17))
+>U : Symbol(U, Decl(typeParameterEquality.ts, 2, 14))
+>U : Symbol(U, Decl(typeParameterEquality.ts, 2, 14))
+}
diff --git a/tests/baselines/reference/typeParameterEquality.types b/tests/baselines/reference/typeParameterEquality.types
new file mode 100644
index 00000000000..2e51c3a51e6
--- /dev/null
+++ b/tests/baselines/reference/typeParameterEquality.types
@@ -0,0 +1,20 @@
+=== tests/cases/compiler/typeParameterEquality.ts ===
+class C {
+>C : C
+
+    get x(): <T>(a: T) => T { return null; }
+>x : <T>(a: T) => T
+>T : T
+>a : T
+>T : T
+>T : T
+>null : null
+
+    set x(p: <U>(a: U) => U) {}
+>x : <T>(a: T) => T
+>p : <U>(a: U) => U
+>U : U
+>a : U
+>U : U
+>U : U
+}
diff --git a/tests/cases/compiler/outModuleConcatAmd.ts b/tests/cases/compiler/outModuleConcatAmd.ts
new file mode 100644
index 00000000000..411a13e72a2
--- /dev/null
+++ b/tests/cases/compiler/outModuleConcatAmd.ts
@@ -0,0 +1,12 @@
+// @target: ES5
+// @sourcemap: true
+// @declaration: true
+// @module: amd
+// @outFile: all.js
+
+// @Filename: ref/a.ts
+export class A { }
+
+// @Filename: b.ts
+import {A} from "./ref/a";
+export class B extends A { }
\ No newline at end of file
diff --git a/tests/cases/compiler/outModuleConcatCommonjs.ts b/tests/cases/compiler/outModuleConcatCommonjs.ts
new file mode 100644
index 00000000000..0cb57bd11e7
--- /dev/null
+++ b/tests/cases/compiler/outModuleConcatCommonjs.ts
@@ -0,0 +1,14 @@
+// @target: ES5
+// @sourcemap: true
+// @declaration: true
+// @module: commonjs
+// @outFile: all.js
+
+// This should be an error
+
+// @Filename: ref/a.ts
+export class A { }
+
+// @Filename: b.ts
+import {A} from "./ref/a";
+export class B extends A { }
\ No newline at end of file
diff --git a/tests/cases/compiler/outModuleConcatES6.ts b/tests/cases/compiler/outModuleConcatES6.ts
new file mode 100644
index 00000000000..e98514e9adc
--- /dev/null
+++ b/tests/cases/compiler/outModuleConcatES6.ts
@@ -0,0 +1,14 @@
+// @target: ES6
+// @sourcemap: true
+// @declaration: true
+// @module: es6
+// @outFile: all.js
+
+// This should be an error
+
+// @Filename: ref/a.ts
+export class A { }
+
+// @Filename: b.ts
+import {A} from "./ref/a";
+export class B extends A { }
\ No newline at end of file
diff --git a/tests/cases/compiler/outModuleConcatSystem.ts b/tests/cases/compiler/outModuleConcatSystem.ts
new file mode 100644
index 00000000000..c8d9b4e9737
--- /dev/null
+++ b/tests/cases/compiler/outModuleConcatSystem.ts
@@ -0,0 +1,12 @@
+// @target: ES5
+// @sourcemap: true
+// @declaration: true
+// @module: system
+// @outFile: all.js
+
+// @Filename: ref/a.ts
+export class A { }
+
+// @Filename: b.ts
+import {A} from "./ref/a";
+export class B extends A { }
\ No newline at end of file
diff --git a/tests/cases/compiler/outModuleConcatUmd.ts b/tests/cases/compiler/outModuleConcatUmd.ts
new file mode 100644
index 00000000000..fa4a4a519c6
--- /dev/null
+++ b/tests/cases/compiler/outModuleConcatUmd.ts
@@ -0,0 +1,14 @@
+// @target: ES5
+// @sourcemap: true
+// @declaration: true
+// @module: umd
+// @outFile: all.js
+
+// This should error
+
+// @Filename: ref/a.ts
+export class A { }
+
+// @Filename: b.ts
+import {A} from "./ref/a";
+export class B extends A { }
\ No newline at end of file
diff --git a/tests/cases/compiler/outModuleTripleSlashRefs.ts b/tests/cases/compiler/outModuleTripleSlashRefs.ts
new file mode 100644
index 00000000000..fdeb4f93453
--- /dev/null
+++ b/tests/cases/compiler/outModuleTripleSlashRefs.ts
@@ -0,0 +1,33 @@
+// @target: ES5
+// @sourcemap: true
+// @declaration: true
+// @module: amd
+// @outFile: all.js
+
+// @Filename: ref/a.ts
+/// <reference path="./b.ts" />
+export class A {
+	member: typeof GlobalFoo;
+}
+
+// @Filename: ref/b.ts
+/// <reference path="./c.d.ts" />
+class Foo {
+	member: Bar;
+}
+declare var GlobalFoo: Foo;
+
+// @Filename: ref/c.d.ts
+/// <reference path="./d.d.ts" />
+declare class Bar {
+	member: Baz;
+}
+
+// @Filename: ref/d.d.ts
+declare class Baz {
+	member: number;
+}
+
+// @Filename: b.ts
+import {A} from "./ref/a";
+export class B extends A { }
diff --git a/tests/cases/compiler/typeParameterEquality.ts b/tests/cases/compiler/typeParameterEquality.ts
new file mode 100644
index 00000000000..aa136aa3655
--- /dev/null
+++ b/tests/cases/compiler/typeParameterEquality.ts
@@ -0,0 +1,5 @@
+// @target: es6
+class C {
+    get x(): <T>(a: T) => T { return null; }
+    set x(p: <U>(a: U) => U) {}
+}
\ No newline at end of file
diff --git a/tests/cases/conformance/expressions/typeGuards/typeGuardOfFormInstanceOf.ts b/tests/cases/conformance/expressions/typeGuards/typeGuardOfFormInstanceOf.ts
index 233909f44aa..31514fca749 100644
--- a/tests/cases/conformance/expressions/typeGuards/typeGuardOfFormInstanceOf.ts
+++ b/tests/cases/conformance/expressions/typeGuards/typeGuardOfFormInstanceOf.ts
@@ -13,18 +13,55 @@ class C2 {
 class D1 extends C1 {
     p3: number;
 }
+class C3 {
+    p4: number;
+}
 var str: string;
 var num: number;
 var strOrNum: string | number;
 
-var c1Orc2: C1 | C2;
-str = c1Orc2 instanceof C1 && c1Orc2.p1; // C1
-num = c1Orc2 instanceof C2 && c1Orc2.p2; // C2
-str = c1Orc2 instanceof D1 && c1Orc2.p1; // D1
-num = c1Orc2 instanceof D1 && c1Orc2.p3; // D1
+var ctor1: C1 | C2;
+str = ctor1 instanceof C1 && ctor1.p1; // C1
+num = ctor1 instanceof C2 && ctor1.p2; // C2
+str = ctor1 instanceof D1 && ctor1.p1; // D1
+num = ctor1 instanceof D1 && ctor1.p3; // D1
+
+var ctor2: C2 | D1;
+num = ctor2 instanceof C2 && ctor2.p2; // C2
+num = ctor2 instanceof D1 && ctor2.p3; // D1
+str = ctor2 instanceof D1 && ctor2.p1; // D1
+var r2: D1 | C2 = ctor2 instanceof C1 && ctor2; // C2 | D1
 
-var c2Ord1: C2 | D1;
-num = c2Ord1 instanceof C2 && c2Ord1.p2; // C2
-num = c2Ord1 instanceof D1 && c2Ord1.p3; // D1
-str = c2Ord1 instanceof D1 && c2Ord1.p1; // D1
-var r2: D1 | C2 = c2Ord1 instanceof C1 && c2Ord1; // C2 | D1
\ No newline at end of file
+var ctor3: C1 | C2;
+if (ctor3 instanceof C1) {
+    ctor3.p1; // C1
+}
+else {
+    ctor3.p2; // C2
+}
+
+var ctor4: C1 | C2 | C3;
+if (ctor4 instanceof C1) {
+    ctor4.p1; // C1
+}
+else if (ctor4 instanceof C2) {
+    ctor4.p2; // C2
+}
+else {
+    ctor4.p4; // C3
+}
+
+var ctor5: C1 | D1 | C2;
+if (ctor5 instanceof C1) {
+    ctor5.p1; // C1
+}
+else {
+    ctor5.p2; // C2
+}
+
+var ctor6: C1 | C2 | C3;
+if (ctor6 instanceof C1 || ctor6 instanceof C2) {
+}
+else {
+    ctor6.p4; // C3
+}
\ No newline at end of file
diff --git a/tests/cases/conformance/types/thisType/thisTypeAndConstraints.ts b/tests/cases/conformance/types/thisType/thisTypeAndConstraints.ts
new file mode 100644
index 00000000000..f46b251c3b2
--- /dev/null
+++ b/tests/cases/conformance/types/thisType/thisTypeAndConstraints.ts
@@ -0,0 +1,21 @@
+class A {
+    self() {
+        return this;
+    }
+}
+
+function f<T extends A>(x: T) {
+    function g<U extends T>(x: U) {
+        x = x.self();
+    }
+    x = x.self();
+}
+
+class B<T extends A> {
+    foo(x: T) {
+        x = x.self();
+    }
+    bar<U extends T>(x: U) {
+        x = x.self();
+    }
+}
diff --git a/tests/cases/conformance/types/thisType/thisTypeInClasses.ts b/tests/cases/conformance/types/thisType/thisTypeInClasses.ts
index 17dc13cf558..6c650341fbe 100644
--- a/tests/cases/conformance/types/thisType/thisTypeInClasses.ts
+++ b/tests/cases/conformance/types/thisType/thisTypeInClasses.ts
@@ -1,7 +1,6 @@
 class C1 {
     x: this;
     f(x: this): this { return undefined; }
-    constructor(x: this) { }
 }
 
 class C2 {