diff --git a/src/compiler/commandLineParser.ts b/src/compiler/commandLineParser.ts
index 3c3bb14174d..5336b01bb14 100644
--- a/src/compiler/commandLineParser.ts
+++ b/src/compiler/commandLineParser.ts
@@ -502,41 +502,30 @@ namespace ts {
             else {
                 const filesSeen: Map<boolean> = {};
                 const exclude = json["exclude"] instanceof Array ? map(<string[]>json["exclude"], normalizeSlashes) : undefined;
-                const extensionsByPriority = getSupportedExtensions(options);
-                for (let extensionsIndex = 0; extensionsIndex < extensionsByPriority.length; extensionsIndex++) {
-                    const currentExtension = extensionsByPriority[extensionsIndex];
-                    const filesInDirWithExtension = host.readDirectory(basePath, currentExtension, exclude);
-                    // Get list of conflicting extensions, conflicting extension is
-                    // - extension that is lower priority than current extension and 
-                    // - extension also is current extension (ends with "." + currentExtension)
-                    const conflictingExtensions: string[] = [];
-                    for (let i = extensionsIndex + 1; i < extensionsByPriority.length; i++) {
-                        const extension = extensionsByPriority[i]; // lower priority extension
-                        if (fileExtensionIs(extension, currentExtension)) { // also has current extension
-                            conflictingExtensions.push(extension);
-                        }
-                    }
+                const supportedExtensions = getSupportedExtensions(options);
+                Debug.assert(indexOf(supportedExtensions, ".ts") < indexOf(supportedExtensions, ".d.ts"), "Changed priority of extensions to pick");
 
-                    // Add the files to fileNames list if the file is not any of conflicting extension
+                // Get files of supported extensions in their order of resolution
+                for (const extension of supportedExtensions) {
+                    const filesInDirWithExtension = host.readDirectory(basePath, extension, exclude);
                     for (const fileName of filesInDirWithExtension) {
-                        let hasConflictingExtension = false;
-                        for (const conflictingExtension of conflictingExtensions) {
-                            // eg. 'f.d.ts' will match '.ts' extension but really should be process later with '.d.ts' files
-                            if (fileExtensionIs(fileName, conflictingExtension)) {
-                                hasConflictingExtension = true;
-                                break;
+                        // .ts extension would read the .d.ts extension files too but since .d.ts is lower priority extension, 
+                        // lets pick them when its turn comes up
+                        if (extension === ".ts" && fileExtensionIs(fileName, ".d.ts")) {
+                            continue;
+                        }
+
+                        // If this is one of the output extension (which would be .d.ts and .js if we are allowing compilation of js files)
+                        // do not include this file if we included .ts or .tsx file with same base name as it could be output of the earlier compilation
+                        if (extension === ".d.ts" || (options.allowJs && extension === ".js")) {
+                            const baseName = fileName.substr(0, fileName.length - extension.length);
+                            if (hasProperty(filesSeen, baseName + ".ts") || hasProperty(filesSeen, baseName + ".tsx")) {
+                                continue;
                             }
                         }
 
-                        if (!hasConflictingExtension) {
-                            // Add the file only if there is no higher priority extension file already included
-                            // eg. when a.d.ts and a.js are present in the folder, include only a.d.ts not a.js
-                            const baseName = fileName.substr(0, fileName.length - currentExtension.length);
-                            if (!hasProperty(filesSeen, baseName)) {
-                                filesSeen[baseName] = true;
-                                fileNames.push(fileName);
-                            }
-                        }
+                        filesSeen[fileName] = true;
+                        fileNames.push(fileName);
                     }
                 }
             }
diff --git a/src/compiler/core.ts b/src/compiler/core.ts
index 5b0eedfc1f9..b773cdfaf45 100644
--- a/src/compiler/core.ts
+++ b/src/compiler/core.ts
@@ -297,8 +297,8 @@ namespace ts {
         return <T>result;
     }
 
-    export function extend<T1, T2>(first: Map<T1>, second: Map<T2>): Map<T1 & T2> {
-        const result: Map<T1 & T2> = {};
+    export function extend<T1 extends Map<{}>, T2 extends Map<{}>>(first: T1 , second: T2): T1 & T2 {
+        const result: T1 & T2 = <any>{};
         for (const id in first) {
             (result as any)[id] = first[id];
         }
diff --git a/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/amd/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.errors.txt b/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/amd/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.errors.txt
index 8da5b629ca8..ac25edc1bd5 100644
--- a/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/amd/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.errors.txt
+++ b/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/amd/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.errors.txt
@@ -1,6 +1,10 @@
 error TS5053: Option 'allowJs' cannot be specified with option 'declaration'.
+error TS5055: Cannot write file 'SameNameDTsNotSpecifiedWithAllowJs/a.js' because it would overwrite input file.
 
 
 !!! error TS5053: Option 'allowJs' cannot be specified with option 'declaration'.
+!!! error TS5055: Cannot write file 'SameNameDTsNotSpecifiedWithAllowJs/a.js' because it would overwrite input file.
 ==== SameNameDTsNotSpecifiedWithAllowJs/a.d.ts (0 errors) ====
-    declare var a: number;
\ No newline at end of file
+    declare var a: number;
+==== SameNameDTsNotSpecifiedWithAllowJs/a.js (0 errors) ====
+    var test1 = 10; // Shouldnt get compiled
\ No newline at end of file
diff --git a/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/amd/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.json b/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/amd/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.json
index 77e1f227030..b4c3fb8f51b 100644
--- a/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/amd/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.json
+++ b/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/amd/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.json
@@ -6,7 +6,8 @@
     "project": "SameNameDTsNotSpecifiedWithAllowJs",
     "resolvedInputFiles": [
         "lib.d.ts",
-        "SameNameDTsNotSpecifiedWithAllowJs/a.d.ts"
+        "SameNameDTsNotSpecifiedWithAllowJs/a.d.ts",
+        "SameNameDTsNotSpecifiedWithAllowJs/a.js"
     ],
     "emittedFiles": []
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/node/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.errors.txt b/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/node/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.errors.txt
index 8da5b629ca8..ac25edc1bd5 100644
--- a/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/node/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.errors.txt
+++ b/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/node/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.errors.txt
@@ -1,6 +1,10 @@
 error TS5053: Option 'allowJs' cannot be specified with option 'declaration'.
+error TS5055: Cannot write file 'SameNameDTsNotSpecifiedWithAllowJs/a.js' because it would overwrite input file.
 
 
 !!! error TS5053: Option 'allowJs' cannot be specified with option 'declaration'.
+!!! error TS5055: Cannot write file 'SameNameDTsNotSpecifiedWithAllowJs/a.js' because it would overwrite input file.
 ==== SameNameDTsNotSpecifiedWithAllowJs/a.d.ts (0 errors) ====
-    declare var a: number;
\ No newline at end of file
+    declare var a: number;
+==== SameNameDTsNotSpecifiedWithAllowJs/a.js (0 errors) ====
+    var test1 = 10; // Shouldnt get compiled
\ No newline at end of file
diff --git a/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/node/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.json b/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/node/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.json
index 77e1f227030..b4c3fb8f51b 100644
--- a/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/node/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.json
+++ b/tests/baselines/reference/project/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs/node/jsFileCompilationSameNameDtsNotSpecifiedWithAllowJs.json
@@ -6,7 +6,8 @@
     "project": "SameNameDTsNotSpecifiedWithAllowJs",
     "resolvedInputFiles": [
         "lib.d.ts",
-        "SameNameDTsNotSpecifiedWithAllowJs/a.d.ts"
+        "SameNameDTsNotSpecifiedWithAllowJs/a.d.ts",
+        "SameNameDTsNotSpecifiedWithAllowJs/a.js"
     ],
     "emittedFiles": []
 }
\ No newline at end of file