Fixes the tests that got disabled when generating config set es2016 expecting to find libFile and remove incorrect affects flag from listFilesOnly (#51243)

* Fix the existing test

* Remove affectsEmit from listFilesOnly

src/testRunner/unittests/tsc/helpers.ts

@@ -6,6 +6,10 @@ namespace ts {
         storeFilesChangingSignatureDuringEmit?: boolean;
     };
 
+    export function compilerOptionsToConfigJson(options: CompilerOptions) {
+        return optionMapToObject(serializeCompilerOptions(options));
+    }
+
     export const noChangeRun: TestTscEdit = {
         subScenario: "no-change-run",
         modifyFs: noop

src/testRunner/unittests/tsc/listFilesOnly.ts

@@ -19,5 +19,26 @@ namespace ts {
             }),
             commandLineArgs: ["/src/test.ts", "--listFilesOnly"]
         });
+
+        verifyTscWithEdits({
+            scenario: "listFilesOnly",
+            subScenario: "combined with incremental",
+            fs: () => loadProjectFromFiles({
+                "/src/test.ts": `export const x = 1;`,
+                "/src/tsconfig.json": "{}"
+            }),
+            commandLineArgs: ["-p", "/src", "--incremental", "--listFilesOnly"],
+            edits: [
+                {
+                    ...noChangeRun,
+                    commandLineArgs: ["-p", "/src", "--incremental"],
+                },
+                noChangeRun,
+                {
+                    ...noChangeRun,
+                    commandLineArgs: ["-p", "/src", "--incremental"],
+                }
+            ]
+        });
     });
 }

src/testRunner/unittests/tscWatch/programUpdates.ts

@@ -1164,7 +1164,9 @@ declare const eval: any`
                         };
                         const tsconfig: File = {
                             path: `${projectRoot}/tsconfig.json`,
-                            content: generateTSConfig(options, emptyArray, "\n")
+                            content: JSON.stringify({
+                                compilerOptions: compilerOptionsToConfigJson(options)
+                            })
                         };
                         return createWatchedSystem([file1, file2, libFile, tsconfig], { currentDirectory: projectRoot });
                     },