Merge pull request #5471 from Microsoft/jsFileCompilation

Compilation of Js Files

src/compiler/checker.ts

@@ -11034,6 +11034,7 @@ namespace ts {
 
             const symbol = getSymbolOfNode(node);
             const firstDeclaration = getDeclarationOfKind(symbol, node.kind);
+
             // Only type check the symbol once
             if (node === firstDeclaration) {
                 checkFunctionOrConstructorSymbol(symbol);
@@ -12064,7 +12065,14 @@ namespace ts {
                 const symbol = getSymbolOfNode(node);
                 const localSymbol = node.localSymbol || symbol;
 
-                const firstDeclaration = getDeclarationOfKind(localSymbol, node.kind);
+                // Since the javascript won't do semantic analysis like typescript, 
+                // if the javascript file comes before the typescript file and both contain same name functions, 
+                // checkFunctionOrConstructorSymbol wouldn't be called if we didnt ignore javascript function.
+                const firstDeclaration = forEach(localSymbol.declarations,
+                    // Get first non javascript function declaration
+                    declaration => declaration.kind === node.kind && !isSourceFileJavaScript(getSourceFile(declaration)) ?
+                        declaration : undefined);
+
                 // Only type check the symbol once
                 if (node === firstDeclaration) {
                     checkFunctionOrConstructorSymbol(localSymbol);

src/compiler/commandLineParser.ts

@@ -279,6 +279,11 @@ namespace ts {
             name: "forceConsistentCasingInFileNames",
             type: "boolean",
             description: Diagnostics.Disallow_inconsistently_cased_references_to_the_same_file
+        },
+        {
+            name: "allowJs",
+            type: "boolean",
+            description: Diagnostics.Allow_javascript_files_to_be_compiled,
         }
     ];
 
@@ -474,15 +479,16 @@ namespace ts {
       * @param basePath A root directory to resolve relative path entries in the config
       *    file to. e.g. outDir
       */
-    export function parseJsonConfigFileContent(json: any, host: ParseConfigHost, basePath: string): ParsedCommandLine {
-        const { options, errors } = convertCompilerOptionsFromJson(json["compilerOptions"], basePath);
+    export function parseJsonConfigFileContent(json: any, host: ParseConfigHost, basePath: string, existingOptions: CompilerOptions = {}): ParsedCommandLine {
+        const { options: optionsFromJsonConfigFile, errors } = convertCompilerOptionsFromJson(json["compilerOptions"], basePath);
 
+        const options = extend(existingOptions, optionsFromJsonConfigFile);
         return {
             options,
             fileNames: getFileNames(),
             errors
         };
-
+
         function getFileNames(): string[] {
             let fileNames: string[] = [];
             if (hasProperty(json, "files")) {
@@ -494,23 +500,32 @@ namespace ts {
                 }
             }
             else {
+                const filesSeen: Map<boolean> = {};
                 const exclude = json["exclude"] instanceof Array ? map(<string[]>json["exclude"], normalizeSlashes) : undefined;
-                const sysFiles = host.readDirectory(basePath, ".ts", exclude).concat(host.readDirectory(basePath, ".tsx", exclude));
-                for (let i = 0; i < sysFiles.length; i++) {
-                    const name = sysFiles[i];
-                    if (fileExtensionIs(name, ".d.ts")) {
-                        const baseName = name.substr(0, name.length - ".d.ts".length);
-                        if (!contains(sysFiles, baseName + ".tsx") && !contains(sysFiles, baseName + ".ts")) {
-                            fileNames.push(name);
+                const supportedExtensions = getSupportedExtensions(options);
+                Debug.assert(indexOf(supportedExtensions, ".ts") < indexOf(supportedExtensions, ".d.ts"), "Changed priority of extensions to pick");
+
+                // 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) {
+                        // .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;
                         }
-                    }
-                    else if (fileExtensionIs(name, ".ts")) {
-                        if (!contains(sysFiles, name + "x")) {
-                            fileNames.push(name);
+
+                        // 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 && contains(supportedJavascriptExtensions, extension))) {
+                            const baseName = fileName.substr(0, fileName.length - extension.length);
+                            if (hasProperty(filesSeen, baseName + ".ts") || hasProperty(filesSeen, baseName + ".tsx")) {
+                                continue;
+                            }
                         }
-                    }
-                    else {
-                        fileNames.push(name);
+
+                        filesSeen[fileName] = true;
+                        fileNames.push(fileName);
                     }
                 }
             }

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];
         }
@@ -714,7 +714,7 @@ namespace ts {
     }
 
     export function getBaseFileName(path: string) {
-        if (!path) {
+        if (path === undefined) {
             return undefined;
         }
         const i = path.lastIndexOf(directorySeparator);
@@ -738,13 +738,18 @@ namespace ts {
     /**
      *  List of supported extensions in order of file resolution precedence.
      */
-    export const supportedExtensions = [".ts", ".tsx", ".d.ts"];
-    export const supportedJsExtensions = supportedExtensions.concat(".js", ".jsx");
+    export const supportedTypeScriptExtensions = [".ts", ".tsx", ".d.ts"];
+    export const supportedJavascriptExtensions = [".js", ".jsx"];
+    const allSupportedExtensions  = supportedTypeScriptExtensions.concat(supportedJavascriptExtensions);
 
-    export function isSupportedSourceFileName(fileName: string) {
+    export function getSupportedExtensions(options?: CompilerOptions): string[] {
+        return options && options.allowJs ? allSupportedExtensions : supportedTypeScriptExtensions;
+    }
+
+    export function isSupportedSourceFileName(fileName: string, compilerOptions?: CompilerOptions) {
         if (!fileName) { return false; }
 
-        for (const extension of supportedExtensions) {
+        for (const extension of getSupportedExtensions(compilerOptions)) {
             if (fileExtensionIs(fileName, extension)) {
                 return true;
             }
@@ -855,4 +860,4 @@ namespace ts {
         }
         return copiedList;
     }
-}
+}

src/compiler/declarationEmitter.ts

@@ -31,13 +31,17 @@ namespace ts {
     }
 
     export function getDeclarationDiagnostics(host: EmitHost, resolver: EmitResolver, targetSourceFile: SourceFile): Diagnostic[] {
-        const diagnostics: Diagnostic[] = [];
-        const jsFilePath = getOwnEmitOutputFilePath(targetSourceFile, host, ".js");
-        emitDeclarations(host, resolver, diagnostics, jsFilePath, targetSourceFile);
-        return diagnostics;
+        const declarationDiagnostics = createDiagnosticCollection();
+        forEachExpectedEmitFile(host, getDeclarationDiagnosticsFromFile, targetSourceFile);
+        return declarationDiagnostics.getDiagnostics(targetSourceFile.fileName);
+
+        function getDeclarationDiagnosticsFromFile({ declarationFilePath }, sources: SourceFile[], isBundledEmit: boolean) {
+            emitDeclarations(host, resolver, declarationDiagnostics, declarationFilePath, sources, isBundledEmit);
+        }
     }
 
-    function emitDeclarations(host: EmitHost, resolver: EmitResolver, diagnostics: Diagnostic[], jsFilePath: string, root?: SourceFile): DeclarationEmit {
+    function emitDeclarations(host: EmitHost, resolver: EmitResolver, emitterDiagnostics: DiagnosticCollection, declarationFilePath: string,
+        sourceFiles: SourceFile[], isBundledEmit: boolean): DeclarationEmit {
         const newLine = host.getNewLine();
         const compilerOptions = host.getCompilerOptions();
 
@@ -58,7 +62,7 @@ namespace ts {
         let errorNameNode: DeclarationName;
         const emitJsDocComments = compilerOptions.removeComments ? function (declaration: Node) { } : writeJsDocComments;
         const emit = compilerOptions.stripInternal ? stripInternal : emitNode;
-        let noDeclare = !root;
+        let noDeclare: boolean;
 
         let moduleElementDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[] = [];
         let asynchronousSubModuleDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[];
@@ -68,105 +72,78 @@ namespace ts {
         // and we could be collecting these paths from multiple files into single one with --out option
         let referencePathsOutput = "";
 
-        if (root) {
-            // Emitting just a single file, so emit references in this file only
+        // Emit references corresponding to each file
+        const emittedReferencedFiles: SourceFile[] = [];
+        let addedGlobalFileReference = false;
+        let allSourcesModuleElementDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[] = [];
+        forEach(sourceFiles, sourceFile => {
+            // Dont emit for javascript file
+            if (isSourceFileJavaScript(sourceFile)) {
+                return;
+            }
+
+            // Check what references need to be added
             if (!compilerOptions.noResolve) {
-                let addedGlobalFileReference = false;
-                forEach(root.referencedFiles, fileReference => {
-                    const referencedFile = tryResolveScriptReference(host, root, fileReference);
+                forEach(sourceFile.referencedFiles, fileReference => {
+                    const referencedFile = tryResolveScriptReference(host, sourceFile, fileReference);
 
-                    // All the references that are not going to be part of same file
-                    if (referencedFile && ((referencedFile.flags & NodeFlags.DeclarationFile) || // This is a declare file reference
-                        shouldEmitToOwnFile(referencedFile, compilerOptions) || // This is referenced file is emitting its own js file
-                        !addedGlobalFileReference)) { // Or the global out file corresponding to this reference was not added
-
-                        writeReferencePath(referencedFile);
-                        if (!isExternalModuleOrDeclarationFile(referencedFile)) {
+                    // Emit reference in dts, if the file reference was not already emitted
+                    if (referencedFile && !contains(emittedReferencedFiles, referencedFile)) {
+                        // Add a reference to generated dts file,
+                        // global file reference is added only 
+                        //  - if it is not bundled emit (because otherwise it would be self reference)
+                        //  - and it is not already added
+                        if (writeReferencePath(referencedFile, !isBundledEmit && !addedGlobalFileReference)) {
                             addedGlobalFileReference = true;
                         }
+                        emittedReferencedFiles.push(referencedFile);
                     }
                 });
             }
 
-            emitSourceFile(root);
+            if (!isBundledEmit || !isExternalModule(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) {
+                    if (aliasEmitInfo.isVisible && !aliasEmitInfo.asynchronousOutput) {
                         Debug.assert(aliasEmitInfo.node.kind === SyntaxKind.ImportDeclaration);
                         createAndSetNewTextWriterWithSymbolWriter();
-                        Debug.assert(aliasEmitInfo.indent === 0);
+                        Debug.assert(aliasEmitInfo.indent === 0 || (aliasEmitInfo.indent === 1 && isBundledEmit));
+                        for (let i = 0; i < aliasEmitInfo.indent; i++) {
+                            increaseIndent();
+                        }
                         writeImportDeclaration(<ImportDeclaration>aliasEmitInfo.node);
                         aliasEmitInfo.asynchronousOutput = writer.getText();
+                        for (let i = 0; i < aliasEmitInfo.indent; i++) {
+                            decreaseIndent();
+                        }
                     }
                 });
                 setWriter(oldWriter);
+
+                allSourcesModuleElementDeclarationEmitInfo = allSourcesModuleElementDeclarationEmitInfo.concat(moduleElementDeclarationEmitInfo);
+                moduleElementDeclarationEmitInfo = [];
             }
-        }
-        else {
-            // Emit references corresponding to this file
-            const emittedReferencedFiles: SourceFile[] = [];
-            let prevModuleElementDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[] = [];
-            forEach(host.getSourceFiles(), 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, emit that reference
-                            if (referencedFile && (isDeclarationFile(referencedFile) &&
-                                !contains(emittedReferencedFiles, referencedFile))) { // If the file reference was not already emitted
-
-                                writeReferencePath(referencedFile);
-                                emittedReferencedFiles.push(referencedFile);
-                            }
-                        });
-                    }
-                }
-
-                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 {
             reportedDeclarationError,
-            moduleElementDeclarationEmitInfo,
+            moduleElementDeclarationEmitInfo: allSourcesModuleElementDeclarationEmitInfo,
             synchronousDeclarationOutput: writer.getText(),
             referencePathsOutput,
         };
@@ -278,14 +255,14 @@ namespace ts {
                 const errorInfo = writer.getSymbolAccessibilityDiagnostic(symbolAccesibilityResult);
                 if (errorInfo) {
                     if (errorInfo.typeName) {
-                        diagnostics.push(createDiagnosticForNode(symbolAccesibilityResult.errorNode || errorInfo.errorNode,
+                        emitterDiagnostics.add(createDiagnosticForNode(symbolAccesibilityResult.errorNode || errorInfo.errorNode,
                             errorInfo.diagnosticMessage,
                             getTextOfNodeFromSourceText(currentText, errorInfo.typeName),
                             symbolAccesibilityResult.errorSymbolName,
                             symbolAccesibilityResult.errorModuleName));
                     }
                     else {
-                        diagnostics.push(createDiagnosticForNode(symbolAccesibilityResult.errorNode || errorInfo.errorNode,
+                        emitterDiagnostics.add(createDiagnosticForNode(symbolAccesibilityResult.errorNode || errorInfo.errorNode,
                             errorInfo.diagnosticMessage,
                             symbolAccesibilityResult.errorSymbolName,
                             symbolAccesibilityResult.errorModuleName));
@@ -300,7 +277,8 @@ namespace ts {
 
         function reportInaccessibleThisError() {
             if (errorNameNode) {
-                diagnostics.push(createDiagnosticForNode(errorNameNode, Diagnostics.The_inferred_type_of_0_references_an_inaccessible_this_type_A_type_annotation_is_necessary,
+                reportedDeclarationError = true;
+                emitterDiagnostics.add(createDiagnosticForNode(errorNameNode, Diagnostics.The_inferred_type_of_0_references_an_inaccessible_this_type_A_type_annotation_is_necessary,
                     declarationNameToString(errorNameNode)));
             }
         }
@@ -743,7 +721,7 @@ namespace ts {
         }
 
         function emitExternalModuleSpecifier(moduleSpecifier: Expression) {
-            if (moduleSpecifier.kind === SyntaxKind.StringLiteral && (!root) && (compilerOptions.out || compilerOptions.outFile)) {
+            if (moduleSpecifier.kind === SyntaxKind.StringLiteral && isBundledEmit) {
                 const moduleName = getExternalModuleNameFromDeclaration(host, resolver, moduleSpecifier.parent as (ImportEqualsDeclaration | ImportDeclaration | ExportDeclaration));
                 if (moduleName) {
                     write("\"");
@@ -1643,34 +1621,58 @@ namespace ts {
             }
         }
 
-        function writeReferencePath(referencedFile: SourceFile) {
-            let declFileName = referencedFile.flags & NodeFlags.DeclarationFile
-                ? referencedFile.fileName // Declaration file, use declaration file name
-                : shouldEmitToOwnFile(referencedFile, compilerOptions)
-                    ? getOwnEmitOutputFilePath(referencedFile, host, ".d.ts") // Own output file so get the .d.ts file
-                    : removeFileExtension(compilerOptions.outFile || compilerOptions.out) + ".d.ts"; // Global out file
+        /**
+         * Adds the reference to referenced file, returns true if global file reference was emitted
+         * @param referencedFile
+         * @param addBundledFileReference Determines if global file reference corresponding to bundled file should be emitted or not
+         */
+        function writeReferencePath(referencedFile: SourceFile, addBundledFileReference: boolean): boolean {
+            let declFileName: string;
+            let addedBundledEmitReference = false;
+            if (isDeclarationFile(referencedFile)) {
+                // Declaration file, use declaration file name
+                declFileName = referencedFile.fileName;
+            }
+            else {
+                // Get the declaration file path
+                forEachExpectedEmitFile(host, getDeclFileName, referencedFile);
+            }
 
-            declFileName = getRelativePathToDirectoryOrUrl(
-                getDirectoryPath(normalizeSlashes(jsFilePath)),
-                declFileName,
-                host.getCurrentDirectory(),
-                host.getCanonicalFileName,
-            /*isAbsolutePathAnUrl*/ false);
+            if (declFileName) {
+                declFileName = getRelativePathToDirectoryOrUrl(
+                    getDirectoryPath(normalizeSlashes(declarationFilePath)),
+                    declFileName,
+                    host.getCurrentDirectory(),
+                    host.getCanonicalFileName,
+                    /*isAbsolutePathAnUrl*/ false);
 
-            referencePathsOutput += "/// <reference path=\"" + declFileName + "\" />" + newLine;
+                referencePathsOutput += "/// <reference path=\"" + declFileName + "\" />" + newLine;
+            }
+            return addedBundledEmitReference;
+
+            function getDeclFileName(emitFileNames: EmitFileNames, sourceFiles: SourceFile[], isBundledEmit: boolean) {
+                // Dont add reference path to this file if it is a bundled emit and caller asked not emit bundled file path
+                if (isBundledEmit && !addBundledFileReference) {
+                    return;
+                }
+
+                Debug.assert(!!emitFileNames.declarationFilePath || isSourceFileJavaScript(referencedFile), "Declaration file is not present only for javascript files");
+                declFileName = emitFileNames.declarationFilePath || emitFileNames.jsFilePath;
+                addedBundledEmitReference = isBundledEmit;
+            }
         }
     }
 
     /* @internal */
-    export function writeDeclarationFile(jsFilePath: string, sourceFile: SourceFile, host: EmitHost, resolver: EmitResolver, diagnostics: Diagnostic[]) {
-        const emitDeclarationResult = emitDeclarations(host, resolver, diagnostics, jsFilePath, sourceFile);
-        // TODO(shkamat): Should we not write any declaration file if any of them can produce error,
-        // or should we just not write this file like we are doing now
-        if (!emitDeclarationResult.reportedDeclarationError) {
+    export function writeDeclarationFile(declarationFilePath: string, sourceFiles: SourceFile[], isBundledEmit: boolean, host: EmitHost, resolver: EmitResolver, emitterDiagnostics: DiagnosticCollection) {
+        const emitDeclarationResult = emitDeclarations(host, resolver, emitterDiagnostics, declarationFilePath, sourceFiles, isBundledEmit);
+        const emitSkipped = emitDeclarationResult.reportedDeclarationError || host.isEmitBlocked(declarationFilePath);
+        if (!emitSkipped) {
             const declarationOutput = emitDeclarationResult.referencePathsOutput
                 + getDeclarationOutput(emitDeclarationResult.synchronousDeclarationOutput, emitDeclarationResult.moduleElementDeclarationEmitInfo);
-            writeFile(host, diagnostics, removeFileExtension(jsFilePath) + ".d.ts", declarationOutput, host.getCompilerOptions().emitBOM);
+            writeFile(host, emitterDiagnostics, declarationFilePath, declarationOutput, host.getCompilerOptions().emitBOM);
         }
+        return emitSkipped;
 
         function getDeclarationOutput(synchronousDeclarationOutput: string, moduleElementDeclarationEmitInfo: ModuleElementDeclarationEmitInfo[]) {
             let appliedSyncOutputPos = 0;

src/compiler/diagnosticMessages.json

@@ -2060,6 +2060,14 @@
         "category": "Error",
         "code": 5054
     },
+    "Cannot write file '{0}' because it would overwrite input file.": {
+        "category": "Error",
+        "code": 5055
+    },
+    "Cannot write file '{0}' because it would be overwritten by multiple input files.": {
+        "category": "Error",
+        "code": 5056
+    },
 
     "Concatenate and emit output to single file.": {
         "category": "Message",
@@ -2322,6 +2330,11 @@
         "category": "Error",
         "code": 6082
     },
+    "Allow javascript files to be compiled.": {
+        "category": "Message",
+        "code": 6083
+    },
+
     "Variable '{0}' implicitly has an '{1}' type.": {
         "category": "Error",
         "code": 7005

src/compiler/emitter.ts

@@ -3,10 +3,6 @@
 
 /* @internal */
 namespace ts {
-    export function isExternalModuleOrDeclarationFile(sourceFile: SourceFile) {
-        return isExternalModule(sourceFile) || isDeclarationFile(sourceFile);
-    }
-
     export function getResolvedExternalModuleName(host: EmitHost, file: SourceFile): string {
         return file.moduleName || getExternalModuleNameFromPath(host, file.fileName);
     }
@@ -337,47 +333,19 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
 };`;
 
         const compilerOptions = host.getCompilerOptions();
-        const languageVersion = compilerOptions.target || ScriptTarget.ES3;
-        const modulekind = compilerOptions.module ? compilerOptions.module : languageVersion === ScriptTarget.ES6 ? ModuleKind.ES6 : ModuleKind.None;
+        const languageVersion = getEmitScriptTarget(compilerOptions);
+        const modulekind = getEmitModuleKind(compilerOptions);
         const sourceMapDataList: SourceMapData[] = compilerOptions.sourceMap || compilerOptions.inlineSourceMap ? [] : undefined;
-        let diagnostics: Diagnostic[] = [];
+        const emitterDiagnostics = createDiagnosticCollection();
+        let emitSkipped = false;
         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) {
-            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 {
-            // targetSourceFile is specified (e.g calling emitter from language service or calling getSemanticDiagnostic from language service)
-            if (shouldEmitToOwnFile(targetSourceFile, compilerOptions)) {
-                const jsFilePath = getOwnEmitOutputFilePath(targetSourceFile, host, shouldEmitJsx(targetSourceFile) ? ".jsx" : ".js");
-                emitFile(jsFilePath, targetSourceFile);
-            }
-            else if (!isDeclarationFile(targetSourceFile) && outFile) {
-                emitFile(outFile);
-            }
-        }
-
-        // Sort and make the unique list of diagnostics
-        diagnostics = sortAndDeduplicateDiagnostics(diagnostics);
+        forEachExpectedEmitFile(host, emitFile, targetSourceFile);
 
         return {
-            emitSkipped: false,
-            diagnostics,
+            emitSkipped,
+            diagnostics: emitterDiagnostics.getDiagnostics(),
             sourceMaps: sourceMapDataList
         };
 
@@ -486,8 +454,8 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
         }
 
-        function createFileEmitter(): (jsFilePath: string, root?: SourceFile) => void {
-            const writer: EmitTextWriter = createTextWriter(newLine);
+        function createFileEmitter(): (jsFilePath: string, sourceMapFilePath: string, sourceFiles: SourceFile[], isBundledEmit: boolean) => void {
+            const writer = createTextWriter(newLine);
             const { write, writeTextOfNode, writeLine, increaseIndent, decreaseIndent } = writer;
 
             let currentSourceFile: SourceFile;
@@ -559,8 +527,8 @@ 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;
+            /** Is the file being emitted into its own file */
+            let isOwnFileEmit: boolean;
 
             /** If removeComments is true, no leading-comments needed to be emitted **/
             const emitLeadingCommentsOfPosition = compilerOptions.removeComments ? function (pos: number) { } : emitLeadingCommentsOfPositionWorker;
@@ -581,32 +549,26 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 [ModuleKind.CommonJS]() {},
             };
 
+
             return doEmit;
 
-            function doEmit(jsFilePath: string, rootFile?: SourceFile) {
+            function doEmit(jsFilePath: string, sourceMapFilePath: string, sourceFiles: SourceFile[], isBundledEmit: boolean) {
                 generatedNameSet = {};
                 nodeToGeneratedName = [];
-                root = rootFile;
+                isOwnFileEmit = !isBundledEmit;
 
                 if (compilerOptions.sourceMap || compilerOptions.inlineSourceMap) {
-                    initializeEmitterWithSourceMaps(jsFilePath, root);
+                    initializeEmitterWithSourceMaps(jsFilePath, sourceMapFilePath, sourceFiles, isBundledEmit);
                 }
 
-                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);
-                        }
-                    });
+                // Emit helpers from all the files
+                if (isBundledEmit && modulekind) {
+                    forEach(sourceFiles, emitEmitHelpers);
                 }
 
+                // Do not call emit directly. It does not set the currentSourceFile.
+                forEach(sourceFiles, emitSourceFile);
+
                 writeLine();
                 writeEmittedFiles(writer.getText(), jsFilePath, /*writeByteOrderMark*/ compilerOptions.emitBOM);
 
@@ -636,7 +598,6 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 isEs6Module = false;
                 renamedDependencies = undefined;
                 isCurrentFileExternalModule = false;
-                root = undefined;
             }
 
             function emitSourceFile(sourceFile: SourceFile): void {
@@ -747,7 +708,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 return nodeToGeneratedName[id] || (nodeToGeneratedName[id] = unescapeIdentifier(generateNameForNode(node)));
             }
 
-            function initializeEmitterWithSourceMaps(jsFilePath: string, root?: SourceFile) {
+            function initializeEmitterWithSourceMaps(jsFilePath: string, sourceMapFilePath: string, sourceFiles: SourceFile[], isBundledEmit: boolean) {
                 let sourceMapDir: string; // The directory in which sourcemap will be
 
                 // Current source map file and its index in the sources list
@@ -1048,24 +1009,23 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                     if (compilerOptions.inlineSourceMap) {
                         // Encode the sourceMap into the sourceMap url
                         const base64SourceMapText = convertToBase64(sourceMapText);
-                        sourceMapUrl = `//# sourceMappingURL=data:application/json;base64,${base64SourceMapText}`;
+                        sourceMapData.jsSourceMappingURL = `data:application/json;base64,${base64SourceMapText}`;
                     }
                     else {
                         // Write source map file
-                        writeFile(host, diagnostics, sourceMapData.sourceMapFilePath, sourceMapText, /*writeByteOrderMark*/ false);
-                        sourceMapUrl = `//# sourceMappingURL=${sourceMapData.jsSourceMappingURL}`;
+                        writeFile(host, emitterDiagnostics, sourceMapData.sourceMapFilePath, sourceMapText, /*writeByteOrderMark*/ false);
                     }
+                    sourceMapUrl = `//# sourceMappingURL=${sourceMapData.jsSourceMappingURL}`;
 
                     // Write sourcemap url to the js file and write the js file
                     writeJavaScriptFile(emitOutput + sourceMapUrl, jsFilePath, writeByteOrderMark);
                 }
 
                 // Initialize source map data
-                const sourceMapJsFile = getBaseFileName(normalizeSlashes(jsFilePath));
                 sourceMapData = {
-                    sourceMapFilePath: jsFilePath + ".map",
-                    jsSourceMappingURL: sourceMapJsFile + ".map",
-                    sourceMapFile: sourceMapJsFile,
+                    sourceMapFilePath: sourceMapFilePath,
+                    jsSourceMappingURL: !compilerOptions.inlineSourceMap ? getBaseFileName(normalizeSlashes(sourceMapFilePath)) : undefined,
+                    sourceMapFile: getBaseFileName(normalizeSlashes(jsFilePath)),
                     sourceMapSourceRoot: compilerOptions.sourceRoot || "",
                     sourceMapSources: [],
                     inputSourceFileNames: [],
@@ -1084,10 +1044,11 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
 
                 if (compilerOptions.mapRoot) {
                     sourceMapDir = normalizeSlashes(compilerOptions.mapRoot);
-                    if (root) { // emitting single module file
+                    if (!isBundledEmit) { // emitting single module file
+                        Debug.assert(sourceFiles.length === 1);
                         // For modules or multiple emit files the mapRoot will have directory structure like the sources
                         // So if src\a.ts and src\lib\b.ts are compiled together user would be moving the maps into mapRoot\a.js.map and mapRoot\lib\b.js.map
-                        sourceMapDir = getDirectoryPath(getSourceFilePathInNewDir(root, host, sourceMapDir));
+                        sourceMapDir = getDirectoryPath(getSourceFilePathInNewDir(sourceFiles[0], host, sourceMapDir));
                     }
 
                     if (!isRootedDiskPath(sourceMapDir) && !isUrl(sourceMapDir)) {
@@ -1140,7 +1101,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
 
             function writeJavaScriptFile(emitOutput: string, jsFilePath: string, writeByteOrderMark: boolean) {
-                writeFile(host, diagnostics, jsFilePath, emitOutput, writeByteOrderMark);
+                writeFile(host, emitterDiagnostics, jsFilePath, emitOutput, writeByteOrderMark);
             }
 
             // Create a temporary variable with a unique unused name.
@@ -7752,7 +7713,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
                 emitDetachedCommentsAndUpdateCommentsInfo(node);
 
                 if (isExternalModule(node) || compilerOptions.isolatedModules) {
-                    if (root || (!isExternalModule(node) && compilerOptions.isolatedModules)) {
+                    if (isOwnFileEmit || (!isExternalModule(node) && compilerOptions.isolatedModules)) {
                         const emitModule = moduleEmitDelegates[modulekind] || moduleEmitDelegates[ModuleKind.CommonJS];
                         emitModule(node);
                     }
@@ -8204,11 +8165,18 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, Promi
             }
         }
 
-        function emitFile(jsFilePath: string, sourceFile?: SourceFile) {
-            emitJavaScript(jsFilePath, sourceFile);
+        function emitFile({ jsFilePath, sourceMapFilePath, declarationFilePath}: { jsFilePath: string, sourceMapFilePath: string, declarationFilePath: string },
+            sourceFiles: SourceFile[], isBundledEmit: boolean) {
+            // Make sure not to write js File and source map file if any of them cannot be written
+            if (!host.isEmitBlocked(jsFilePath)) {
+                emitJavaScript(jsFilePath, sourceMapFilePath, sourceFiles, isBundledEmit);
+            }
+            else {
+                emitSkipped = true;
+            }
 
-            if (compilerOptions.declaration) {
-                writeDeclarationFile(jsFilePath, sourceFile, host, resolver, diagnostics);
+            if (declarationFilePath) {
+                emitSkipped = writeDeclarationFile(declarationFilePath, sourceFiles, isBundledEmit, host, resolver, emitterDiagnostics) || emitSkipped;
             }
         }
     }

src/compiler/parser.ts

@@ -544,6 +544,11 @@ namespace ts {
             return result;
         }
 
+        function getLanguageVariant(fileName: string) {
+            // .tsx and .jsx files are treated as jsx language variant.
+            return fileExtensionIs(fileName, ".tsx") || fileExtensionIs(fileName, ".jsx") ?  LanguageVariant.JSX  : LanguageVariant.Standard;
+        }
+
         function initializeState(fileName: string, _sourceText: string, languageVersion: ScriptTarget, isJavaScriptFile: boolean, _syntaxCursor: IncrementalParser.SyntaxCursor) {
             NodeConstructor = objectAllocator.getNodeConstructor();
             SourceFileConstructor = objectAllocator.getSourceFileConstructor();
@@ -564,7 +569,7 @@ namespace ts {
             scanner.setText(sourceText);
             scanner.setOnError(scanError);
             scanner.setScriptTarget(languageVersion);
-            scanner.setLanguageVariant(allowsJsxExpressions(fileName) ? LanguageVariant.JSX : LanguageVariant.Standard);
+            scanner.setLanguageVariant(getLanguageVariant(fileName));
         }
 
         function clearState() {
@@ -682,7 +687,7 @@ namespace ts {
             sourceFile.languageVersion = languageVersion;
             sourceFile.fileName = normalizePath(fileName);
             sourceFile.flags = fileExtensionIs(sourceFile.fileName, ".d.ts") ? NodeFlags.DeclarationFile : 0;
-            sourceFile.languageVariant = allowsJsxExpressions(sourceFile.fileName) ? LanguageVariant.JSX : LanguageVariant.Standard;
+            sourceFile.languageVariant = getLanguageVariant(sourceFile.fileName);
 
             return sourceFile;
         }

src/compiler/program.ts

@@ -14,10 +14,10 @@ namespace ts {
 
     export const version = "1.8.0";
 
-    export function findConfigFile(searchPath: string): string {
+    export function findConfigFile(searchPath: string, fileExists: (fileName: string) => boolean): string {
         let fileName = "tsconfig.json";
         while (true) {
-            if (sys.fileExists(fileName)) {
+            if (fileExists(fileName)) {
                 return fileName;
             }
             const parentPath = getDirectoryPath(searchPath);
@@ -42,24 +42,24 @@ namespace ts {
             : compilerOptions.module === ModuleKind.CommonJS ? ModuleResolutionKind.NodeJs : ModuleResolutionKind.Classic;
 
         switch (moduleResolution) {
-            case ModuleResolutionKind.NodeJs: return nodeModuleNameResolver(moduleName, containingFile, host);
+            case ModuleResolutionKind.NodeJs: return nodeModuleNameResolver(moduleName, containingFile, compilerOptions, host);
             case ModuleResolutionKind.Classic: return classicNameResolver(moduleName, containingFile, compilerOptions, host);
         }
     }
 
-    export function nodeModuleNameResolver(moduleName: string, containingFile: string, host: ModuleResolutionHost): ResolvedModuleWithFailedLookupLocations {
+    export function nodeModuleNameResolver(moduleName: string, containingFile: string, compilerOptions: CompilerOptions, host: ModuleResolutionHost): ResolvedModuleWithFailedLookupLocations {
         const containingDirectory = getDirectoryPath(containingFile);
-
+        const supportedExtensions = getSupportedExtensions(compilerOptions);
         if (getRootLength(moduleName) !== 0 || nameStartsWithDotSlashOrDotDotSlash(moduleName)) {
             const failedLookupLocations: string[] = [];
             const candidate = normalizePath(combinePaths(containingDirectory, moduleName));
-            let resolvedFileName = loadNodeModuleFromFile(supportedJsExtensions, candidate, failedLookupLocations, host);
+            let resolvedFileName = loadNodeModuleFromFile(supportedExtensions, candidate, failedLookupLocations, host);
 
             if (resolvedFileName) {
                 return { resolvedModule: { resolvedFileName }, failedLookupLocations };
             }
 
-            resolvedFileName = loadNodeModuleFromDirectory(supportedJsExtensions, candidate, failedLookupLocations, host);
+            resolvedFileName = loadNodeModuleFromDirectory(supportedExtensions, candidate, failedLookupLocations, host);
             return resolvedFileName
                 ? { resolvedModule: { resolvedFileName }, failedLookupLocations }
                 : { resolvedModule: undefined, failedLookupLocations };
@@ -122,12 +122,13 @@ namespace ts {
             if (baseName !== "node_modules") {
                 const nodeModulesFolder = combinePaths(directory, "node_modules");
                 const candidate = normalizePath(combinePaths(nodeModulesFolder, moduleName));
-                let result = loadNodeModuleFromFile(supportedExtensions, candidate, failedLookupLocations, host);
+                // Load only typescript files irrespective of allowJs option if loading from node modules
+                let result = loadNodeModuleFromFile(supportedTypeScriptExtensions, candidate, failedLookupLocations, host);
                 if (result) {
                     return { resolvedModule: { resolvedFileName: result, isExternalLibraryImport: true }, failedLookupLocations };
                 }
 
-                result = loadNodeModuleFromDirectory(supportedExtensions, candidate, failedLookupLocations, host);
+                result = loadNodeModuleFromDirectory(supportedTypeScriptExtensions, candidate, failedLookupLocations, host);
                 if (result) {
                     return { resolvedModule: { resolvedFileName: result, isExternalLibraryImport: true }, failedLookupLocations };
                 }
@@ -162,10 +163,10 @@ namespace ts {
         const failedLookupLocations: string[] = [];
 
         let referencedSourceFile: string;
-        const extensions = compilerOptions.allowNonTsExtensions ? supportedJsExtensions : supportedExtensions;
+        const supportedExtensions = getSupportedExtensions(compilerOptions);
         while (true) {
             searchName = normalizePath(combinePaths(searchPath, moduleName));
-            referencedSourceFile = forEach(extensions, extension => {
+            referencedSourceFile = forEach(supportedExtensions, extension => {
                 if (extension === ".tsx" && !compilerOptions.jsx) {
                     // resolve .tsx files only if jsx support is enabled 
                     // 'logical not' handles both undefined and None cases
@@ -285,13 +286,13 @@ namespace ts {
     }
 
     export function getPreEmitDiagnostics(program: Program, sourceFile?: SourceFile, cancellationToken?: CancellationToken): Diagnostic[] {
-        const diagnostics = program.getOptionsDiagnostics(cancellationToken).concat(
+        let diagnostics = program.getOptionsDiagnostics(cancellationToken).concat(
                           program.getSyntacticDiagnostics(sourceFile, cancellationToken),
                           program.getGlobalDiagnostics(cancellationToken),
                           program.getSemanticDiagnostics(sourceFile, cancellationToken));
 
         if (program.getCompilerOptions().declaration) {
-            diagnostics.concat(program.getDeclarationDiagnostics(sourceFile, cancellationToken));
+            diagnostics = diagnostics.concat(program.getDeclarationDiagnostics(sourceFile, cancellationToken));
         }
 
         return sortAndDeduplicateDiagnostics(diagnostics);
@@ -335,10 +336,13 @@ namespace ts {
         let classifiableNames: Map<string>;
 
         let skipDefaultLib = options.noLib;
+        const supportedExtensions = getSupportedExtensions(options);
 
         const start = new Date().getTime();
 
         host = host || createCompilerHost(options);
+        // Map storing if there is emit blocking diagnostics for given input
+        const hasEmitBlockingDiagnostics = createFileMap<boolean>(getCanonicalFileName);
 
         const currentDirectory = host.getCurrentDirectory();
         const resolveModuleNamesWorker = host.resolveModuleNames
@@ -358,7 +362,8 @@ namespace ts {
                 (oldOptions.noResolve !== options.noResolve) ||
                 (oldOptions.target !== options.target) ||
                 (oldOptions.noLib !== options.noLib) ||
-                (oldOptions.jsx !== options.jsx)) {
+                (oldOptions.jsx !== options.jsx) ||
+                (oldOptions.allowJs !== options.allowJs)) {
                 oldProgram = undefined;
             }
         }
@@ -374,13 +379,9 @@ namespace ts {
             }
         }
 
-        verifyCompilerOptions();
-
         // unconditionally set oldProgram to undefined to prevent it from being captured in closure
         oldProgram = undefined;
 
-        programTime += new Date().getTime() - start;
-
         program = {
             getRootFileNames: () => rootNames,
             getSourceFile,
@@ -403,6 +404,11 @@ namespace ts {
             getTypeCount: () => getDiagnosticsProducingTypeChecker().getTypeCount(),
             getFileProcessingDiagnostics: () => fileProcessingDiagnostics
         };
+
+        verifyCompilerOptions();
+
+        programTime += new Date().getTime() - start;
+
         return program;
 
         function getClassifiableNames() {
@@ -524,6 +530,7 @@ namespace ts {
                 getSourceFiles: program.getSourceFiles,
                 writeFile: writeFileCallback || (
                     (fileName, data, writeByteOrderMark, onError) => host.writeFile(fileName, data, writeByteOrderMark, onError)),
+                isEmitBlocked,
             };
         }
 
@@ -539,6 +546,10 @@ namespace ts {
             return runWithCancellationToken(() => emitWorker(this, sourceFile, writeFileCallback, cancellationToken));
         }
 
+        function isEmitBlocked(emitFileName: string): boolean {
+            return hasEmitBlockingDiagnostics.contains(toPath(emitFileName, currentDirectory, getCanonicalFileName));
+        }
+
         function emitWorker(program: Program, sourceFile: SourceFile, writeFileCallback: WriteFileCallback, cancellationToken: CancellationToken): EmitResult {
             // If the noEmitOnError flag is set, then check if we have any errors so far.  If so,
             // immediately bail out.  Note that we pass 'undefined' for 'sourceFile' so that we
@@ -631,6 +642,13 @@ namespace ts {
         }
 
         function getSemanticDiagnosticsForFile(sourceFile: SourceFile, cancellationToken: CancellationToken): Diagnostic[] {
+            // For JavaScript files, we don't want to report the normal typescript semantic errors.
+            // Instead, we just report errors for using TypeScript-only constructs from within a
+            // JavaScript file.
+            if (isSourceFileJavaScript(sourceFile)) {
+                return getJavaScriptSemanticDiagnosticsForFile(sourceFile, cancellationToken);
+            }
+
             return runWithCancellationToken(() => {
                 const typeChecker = getDiagnosticsProducingTypeChecker();
 
@@ -644,6 +662,165 @@ namespace ts {
             });
         }
 
+        function getJavaScriptSemanticDiagnosticsForFile(sourceFile: SourceFile, cancellationToken: CancellationToken): Diagnostic[] {
+            return runWithCancellationToken(() => {
+                const diagnostics: Diagnostic[] = [];
+                walk(sourceFile);
+
+                return diagnostics;
+
+                function walk(node: Node): boolean {
+                    if (!node) {
+                        return false;
+                    }
+
+                    switch (node.kind) {
+                        case SyntaxKind.ImportEqualsDeclaration:
+                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.import_can_only_be_used_in_a_ts_file));
+                            return true;
+                        case SyntaxKind.ExportAssignment:
+                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.export_can_only_be_used_in_a_ts_file));
+                            return true;
+                        case SyntaxKind.ClassDeclaration:
+                            let classDeclaration = <ClassDeclaration>node;
+                            if (checkModifiers(classDeclaration.modifiers) ||
+                                checkTypeParameters(classDeclaration.typeParameters)) {
+                                return true;
+                            }
+                            break;
+                        case SyntaxKind.HeritageClause:
+                            let heritageClause = <HeritageClause>node;
+                            if (heritageClause.token === SyntaxKind.ImplementsKeyword) {
+                                diagnostics.push(createDiagnosticForNode(node, Diagnostics.implements_clauses_can_only_be_used_in_a_ts_file));
+                                return true;
+                            }
+                            break;
+                        case SyntaxKind.InterfaceDeclaration:
+                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.interface_declarations_can_only_be_used_in_a_ts_file));
+                            return true;
+                        case SyntaxKind.ModuleDeclaration:
+                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.module_declarations_can_only_be_used_in_a_ts_file));
+                            return true;
+                        case SyntaxKind.TypeAliasDeclaration:
+                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.type_aliases_can_only_be_used_in_a_ts_file));
+                            return true;
+                        case SyntaxKind.MethodDeclaration:
+                        case SyntaxKind.MethodSignature:
+                        case SyntaxKind.Constructor:
+                        case SyntaxKind.GetAccessor:
+                        case SyntaxKind.SetAccessor:
+                        case SyntaxKind.FunctionExpression:
+                        case SyntaxKind.FunctionDeclaration:
+                        case SyntaxKind.ArrowFunction:
+                        case SyntaxKind.FunctionDeclaration:
+                            const functionDeclaration = <FunctionLikeDeclaration>node;
+                            if (checkModifiers(functionDeclaration.modifiers) ||
+                                checkTypeParameters(functionDeclaration.typeParameters) ||
+                                checkTypeAnnotation(functionDeclaration.type)) {
+                                return true;
+                            }
+                            break;
+                        case SyntaxKind.VariableStatement:
+                            const variableStatement = <VariableStatement>node;
+                            if (checkModifiers(variableStatement.modifiers)) {
+                                return true;
+                            }
+                            break;
+                        case SyntaxKind.VariableDeclaration:
+                            const variableDeclaration = <VariableDeclaration>node;
+                            if (checkTypeAnnotation(variableDeclaration.type)) {
+                                return true;
+                            }
+                            break;
+                        case SyntaxKind.CallExpression:
+                        case SyntaxKind.NewExpression:
+                            const expression = <CallExpression>node;
+                            if (expression.typeArguments && expression.typeArguments.length > 0) {
+                                const start = expression.typeArguments.pos;
+                                diagnostics.push(createFileDiagnostic(sourceFile, start, expression.typeArguments.end - start,
+                                    Diagnostics.type_arguments_can_only_be_used_in_a_ts_file));
+                                return true;
+                            }
+                            break;
+                        case SyntaxKind.Parameter:
+                            const parameter = <ParameterDeclaration>node;
+                            if (parameter.modifiers) {
+                                const start = parameter.modifiers.pos;
+                                diagnostics.push(createFileDiagnostic(sourceFile, start, parameter.modifiers.end - start,
+                                    Diagnostics.parameter_modifiers_can_only_be_used_in_a_ts_file));
+                                return true;
+                            }
+                            if (parameter.questionToken) {
+                                diagnostics.push(createDiagnosticForNode(parameter.questionToken, Diagnostics._0_can_only_be_used_in_a_ts_file, "?"));
+                                return true;
+                            }
+                            if (parameter.type) {
+                                diagnostics.push(createDiagnosticForNode(parameter.type, Diagnostics.types_can_only_be_used_in_a_ts_file));
+                                return true;
+                            }
+                            break;
+                        case SyntaxKind.PropertyDeclaration:
+                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.property_declarations_can_only_be_used_in_a_ts_file));
+                            return true;
+                        case SyntaxKind.EnumDeclaration:
+                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.enum_declarations_can_only_be_used_in_a_ts_file));
+                            return true;
+                        case SyntaxKind.TypeAssertionExpression:
+                            let typeAssertionExpression = <TypeAssertion>node;
+                            diagnostics.push(createDiagnosticForNode(typeAssertionExpression.type, Diagnostics.type_assertion_expressions_can_only_be_used_in_a_ts_file));
+                            return true;
+                        case SyntaxKind.Decorator:
+                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.decorators_can_only_be_used_in_a_ts_file));
+                            return true;
+                    }
+
+                    return forEachChild(node, walk);
+                }
+
+                function checkTypeParameters(typeParameters: NodeArray<TypeParameterDeclaration>): boolean {
+                    if (typeParameters) {
+                        const start = typeParameters.pos;
+                        diagnostics.push(createFileDiagnostic(sourceFile, start, typeParameters.end - start, Diagnostics.type_parameter_declarations_can_only_be_used_in_a_ts_file));
+                        return true;
+                    }
+                    return false;
+                }
+
+                function checkTypeAnnotation(type: TypeNode): boolean {
+                    if (type) {
+                        diagnostics.push(createDiagnosticForNode(type, Diagnostics.types_can_only_be_used_in_a_ts_file));
+                        return true;
+                    }
+
+                    return false;
+                }
+
+                function checkModifiers(modifiers: ModifiersArray): boolean {
+                    if (modifiers) {
+                        for (const modifier of modifiers) {
+                            switch (modifier.kind) {
+                                case SyntaxKind.PublicKeyword:
+                                case SyntaxKind.PrivateKeyword:
+                                case SyntaxKind.ProtectedKeyword:
+                                case SyntaxKind.DeclareKeyword:
+                                    diagnostics.push(createDiagnosticForNode(modifier, Diagnostics._0_can_only_be_used_in_a_ts_file, tokenToString(modifier.kind)));
+                                    return true;
+
+                                // These are all legal modifiers.
+                                case SyntaxKind.StaticKeyword:
+                                case SyntaxKind.ExportKeyword:
+                                case SyntaxKind.ConstKeyword:
+                                case SyntaxKind.DefaultKeyword:
+                                case SyntaxKind.AbstractKeyword:
+                            }
+                        }
+                    }
+
+                    return false;
+                }
+            });
+        }
+
         function getDeclarationDiagnosticsForFile(sourceFile: SourceFile, cancellationToken: CancellationToken): Diagnostic[] {
             return runWithCancellationToken(() => {
                 if (!isDeclarationFile(sourceFile)) {
@@ -1095,11 +1272,49 @@ namespace ts {
                     programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "noEmit", "declaration"));
                 }
             }
+            else if (options.allowJs && options.declaration) {
+                programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_with_option_1, "allowJs", "declaration"));
+            }
 
             if (options.emitDecoratorMetadata &&
                 !options.experimentalDecorators) {
                 programDiagnostics.add(createCompilerDiagnostic(Diagnostics.Option_0_cannot_be_specified_without_specifying_option_1, "emitDecoratorMetadata", "experimentalDecorators"));
             }
+
+            // If the emit is enabled make sure that every output file is unique and not overwriting any of the input files
+            if (!options.noEmit) {
+                const emitHost = getEmitHost();
+                const emitFilesSeen = createFileMap<boolean>(!host.useCaseSensitiveFileNames() ? key => key.toLocaleLowerCase() : undefined);
+                forEachExpectedEmitFile(emitHost, (emitFileNames, sourceFiles, isBundledEmit) => {
+                    verifyEmitFilePath(emitFileNames.jsFilePath, emitFilesSeen);
+                    verifyEmitFilePath(emitFileNames.declarationFilePath, emitFilesSeen);
+                });
+            }
+
+            // Verify that all the emit files are unique and don't overwrite input files
+            function verifyEmitFilePath(emitFileName: string, emitFilesSeen: FileMap<boolean>) {
+                if (emitFileName) {
+                    const emitFilePath = toPath(emitFileName, currentDirectory, getCanonicalFileName);
+                    // Report error if the output overwrites input file
+                    if (filesByName.contains(emitFilePath)) {
+                        createEmitBlockingDiagnostics(emitFileName, emitFilePath, Diagnostics.Cannot_write_file_0_because_it_would_overwrite_input_file);
+                    }
+
+                    // Report error if multiple files write into same file
+                    if (emitFilesSeen.contains(emitFilePath)) {
+                        // Already seen the same emit file - report error
+                        createEmitBlockingDiagnostics(emitFileName, emitFilePath, Diagnostics.Cannot_write_file_0_because_it_would_be_overwritten_by_multiple_input_files);
+                    }
+                    else {
+                        emitFilesSeen.set(emitFilePath, true);
+                    }
+                }
+            }
+        }
+
+        function createEmitBlockingDiagnostics(emitFileName: string, emitFilePath: Path, message: DiagnosticMessage) {
+            hasEmitBlockingDiagnostics.set(toPath(emitFileName, currentDirectory, getCanonicalFileName), true);
+            programDiagnostics.add(createCompilerDiagnostic(message, emitFileName));
         }
     }
 }

src/compiler/tsc.ts

@@ -303,7 +303,7 @@ namespace ts {
         }
         else if (commandLine.fileNames.length === 0 && isJSONSupported()) {
             const searchPath = normalizePath(sys.getCurrentDirectory());
-            configFileName = findConfigFile(searchPath);
+            configFileName = findConfigFile(searchPath, sys.fileExists);
         }
 
         if (commandLine.fileNames.length === 0 && !configFileName) {
@@ -360,7 +360,7 @@ namespace ts {
                 sys.exit(ExitStatus.DiagnosticsPresent_OutputsSkipped);
                 return;
             }
-            const configParseResult = parseJsonConfigFileContent(configObject, sys, getDirectoryPath(configFileName));
+            const configParseResult = parseJsonConfigFileContent(configObject, sys, getDirectoryPath(configFileName), commandLine.options);
             if (configParseResult.errors.length > 0) {
                 reportDiagnostics(configParseResult.errors, /* compilerHost */ undefined);
                 sys.exit(ExitStatus.DiagnosticsPresent_OutputsSkipped);
@@ -376,7 +376,7 @@ namespace ts {
                 if (configFileName) {
                     const configParseResult = parseConfigFile();
                     rootFileNames = configParseResult.fileNames;
-                    compilerOptions = extend(commandLine.options, configParseResult.options);
+                    compilerOptions = configParseResult.options;
                 }
                 else {
                     rootFileNames = commandLine.fileNames;
@@ -469,7 +469,7 @@ namespace ts {
         }
 
         function watchedDirectoryChanged(fileName: string) {
-            if (fileName && !ts.isSupportedSourceFileName(fileName)) {
+            if (fileName && !ts.isSupportedSourceFileName(fileName, commandLine.options)) {
                 return;
             }
 

src/compiler/types.ts

@@ -2360,6 +2360,7 @@ namespace ts {
         noImplicitReturns?: boolean;
         noFallthroughCasesInSwitch?: boolean;
         forceConsistentCasingInFileNames?: boolean;
+        allowJs?: boolean;
         /* @internal */ stripInternal?: boolean;
 
         // Skip checking lib.d.ts to help speed up tests.

src/compiler/utilities.ts

@@ -38,6 +38,8 @@ namespace ts {
         getCanonicalFileName(fileName: string): string;
         getNewLine(): string;
 
+        isEmitBlocked(emitFileName: string): boolean;
+
         writeFile: WriteFileCallback;
     }
 
@@ -1885,15 +1887,85 @@ namespace ts {
         return emitOutputFilePathWithoutExtension + extension;
     }
 
+    export function getEmitScriptTarget(compilerOptions: CompilerOptions) {
+        return compilerOptions.target || ScriptTarget.ES3;
+    }
+
+    export function getEmitModuleKind(compilerOptions: CompilerOptions) {
+        return compilerOptions.module ?
+            compilerOptions.module :
+            getEmitScriptTarget(compilerOptions) === ScriptTarget.ES6 ? ModuleKind.ES6 : ModuleKind.None;
+    }
+
+    export interface EmitFileNames {
+        jsFilePath: string;
+        sourceMapFilePath: string;
+        declarationFilePath: string;
+    }
+
+    export function forEachExpectedEmitFile(host: EmitHost,
+        action: (emitFileNames: EmitFileNames, sourceFiles: SourceFile[], isBundledEmit: boolean) => void,
+        targetSourceFile?: SourceFile) {
+        const options = host.getCompilerOptions();
+        // Emit on each source file
+        if (options.outFile || options.out) {
+            onBundledEmit(host);
+        }
+        else {
+            const sourceFiles = targetSourceFile === undefined ? host.getSourceFiles() : [targetSourceFile];
+            for (const sourceFile of sourceFiles) {
+                if (!isDeclarationFile(sourceFile)) {
+                    onSingleFileEmit(host, sourceFile);
+                }
+            }
+        }
+
+        function onSingleFileEmit(host: EmitHost, sourceFile: SourceFile) {
+            const jsFilePath = getOwnEmitOutputFilePath(sourceFile, host,
+                sourceFile.languageVariant === LanguageVariant.JSX && options.jsx === JsxEmit.Preserve ? ".jsx" : ".js");
+            const emitFileNames: EmitFileNames = {
+                jsFilePath,
+                sourceMapFilePath: getSourceMapFilePath(jsFilePath, options),
+                declarationFilePath: !isSourceFileJavaScript(sourceFile) ? getDeclarationEmitFilePath(jsFilePath, options) : undefined
+            };
+            action(emitFileNames, [sourceFile], /*isBundledEmit*/false);
+        }
+
+        function onBundledEmit(host: EmitHost) {
+            // Can emit only sources that are not declaration file and are either non module code or module with --module or --target es6 specified
+            const bundledSources = filter(host.getSourceFiles(),
+                sourceFile => !isDeclarationFile(sourceFile) && // Not a declaration file
+                    (!isExternalModule(sourceFile) || // non module file
+                        (getEmitModuleKind(options) && isExternalModule(sourceFile)))); // module that can emit - note falsy value from getEmitModuleKind means the module kind that shouldn't be emitted 
+            if (bundledSources.length) {
+                const jsFilePath = options.outFile || options.out;
+                const emitFileNames: EmitFileNames = {
+                    jsFilePath,
+                    sourceMapFilePath: getSourceMapFilePath(jsFilePath, options),
+                    declarationFilePath: getDeclarationEmitFilePath(jsFilePath, options)
+                };
+                action(emitFileNames, bundledSources, /*isBundledEmit*/true);
+            }
+        }
+
+        function getSourceMapFilePath(jsFilePath: string, options: CompilerOptions) {
+            return options.sourceMap ? jsFilePath + ".map" : undefined;
+        }
+
+        function getDeclarationEmitFilePath(jsFilePath: string, options: CompilerOptions) {
+            return options.declaration ? removeFileExtension(jsFilePath) + ".d.ts" : undefined;
+        }
+    }
+
     export function getSourceFilePathInNewDir(sourceFile: SourceFile, host: EmitHost, newDirPath: string) {
         let sourceFilePath = getNormalizedAbsolutePath(sourceFile.fileName, host.getCurrentDirectory());
         sourceFilePath = sourceFilePath.replace(host.getCommonSourceDirectory(), "");
         return combinePaths(newDirPath, sourceFilePath);
     }
 
-    export function writeFile(host: EmitHost, diagnostics: Diagnostic[], fileName: string, data: string, writeByteOrderMark: boolean) {
+    export function writeFile(host: EmitHost, diagnostics: DiagnosticCollection, fileName: string, data: string, writeByteOrderMark: boolean) {
         host.writeFile(fileName, data, writeByteOrderMark, hostErrorMessage => {
-            diagnostics.push(createCompilerDiagnostic(Diagnostics.Could_not_write_file_0_Colon_1, fileName, hostErrorMessage));
+            diagnostics.add(createCompilerDiagnostic(Diagnostics.Could_not_write_file_0_Colon_1, fileName, hostErrorMessage));
         });
     }
 
@@ -1917,18 +1989,6 @@ namespace ts {
         return accessor && accessor.parameters.length > 0 && accessor.parameters[0].type;
     }
 
-    export function shouldEmitToOwnFile(sourceFile: SourceFile, compilerOptions: CompilerOptions): boolean {
-        if (!isDeclarationFile(sourceFile)) {
-            if ((isExternalModule(sourceFile) || !(compilerOptions.outFile || compilerOptions.out))) {
-                // 1. in-browser single file compilation scenario
-                // 2. non .js file
-                return compilerOptions.isolatedModules || !fileExtensionIs(sourceFile.fileName, ".js");
-            }
-            return false;
-        }
-        return false;
-    }
-
     export function getAllAccessorDeclarations(declarations: NodeArray<Declaration>, accessor: AccessorDeclaration) {
         let firstAccessor: AccessorDeclaration;
         let secondAccessor: AccessorDeclaration;
@@ -2273,11 +2333,7 @@ namespace ts {
     }
 
     export function hasJavaScriptFileExtension(fileName: string) {
-        return fileExtensionIs(fileName, ".js") || fileExtensionIs(fileName, ".jsx");
-    }
-
-    export function allowsJsxExpressions(fileName: string) {
-        return fileExtensionIs(fileName, ".tsx") || fileExtensionIs(fileName, ".jsx");
+        return forEach(supportedJavascriptExtensions, extension => fileExtensionIs(fileName, extension));
     }
 
     /**

src/harness/compilerRunner.ts

@@ -52,6 +52,7 @@ class CompilerBaselineRunner extends RunnerBase {
 
             let lastUnit: Harness.TestCaseParser.TestUnitData;
             let harnessSettings: Harness.TestCaseParser.CompilerSettings;
+            let hasNonDtsFiles: boolean;
 
             let result: Harness.Compiler.CompilerResult;
             let options: ts.CompilerOptions;
@@ -67,6 +68,7 @@ class CompilerBaselineRunner extends RunnerBase {
                 const units = testCaseContent.testUnitData;
                 harnessSettings = testCaseContent.settings;
                 lastUnit = units[units.length - 1];
+                hasNonDtsFiles = ts.forEach(units, unit => !ts.fileExtensionIs(unit.name, ".d.ts"));
                 const rootDir = lastUnit.originalFilePath.indexOf("conformance") === -1 ? "tests/cases/compiler/" : lastUnit.originalFilePath.substring(0, lastUnit.originalFilePath.lastIndexOf("/")) + "/";
                 // We need to assemble the list of input files for the compiler and other related files on the 'filesystem' (ie in a multi-file test)
                 // If the last file in a test uses require or a triple slash reference we'll assume all other files will be brought in via references,
@@ -99,6 +101,7 @@ class CompilerBaselineRunner extends RunnerBase {
                 // Therefore we have to clean out large objects after the test is done.
                 justName = undefined;
                 lastUnit = undefined;
+                hasNonDtsFiles = undefined;
                 result = undefined;
                 options = undefined;
                 toBeCompiled = undefined;
@@ -138,7 +141,7 @@ class CompilerBaselineRunner extends RunnerBase {
             });
 
             it("Correct JS output for " + fileName, () => {
-                if (!ts.fileExtensionIs(lastUnit.name, ".d.ts") && this.emit) {
+                if (hasNonDtsFiles && this.emit) {
                     if (result.files.length === 0 && result.errors.length === 0) {
                         throw new Error("Expected at least one js file to be emitted or at least one error to be created.");
                     }

src/harness/fourslash.ts

@@ -286,7 +286,7 @@ namespace FourSlash {
                     // Fourslash insert tests/cases/fourslash into inputFile.unitName and import statement doesn't require ".ts"
                     // so convert them before making appropriate comparison
                     const importedFilePath = this.basePath + "/" + importedFile.fileName;
-                    this.addMatchedInputFile(importedFilePath, compilationOptions.allowNonTsExtensions ? ts.supportedJsExtensions : ts.supportedExtensions);
+                    this.addMatchedInputFile(importedFilePath, ts.getSupportedExtensions(compilationOptions));
                 });
 
                 // Check if no-default-lib flag is false and if so add default library
@@ -514,6 +514,15 @@ namespace FourSlash {
             }
         }
 
+        public verifyGetEmitOutputContentsForCurrentFile(expected: ts.OutputFile[]): void {
+            const emit = this.languageService.getEmitOutput(this.activeFile.fileName);
+            assert.equal(emit.outputFiles.length, expected.length, "Number of emit output files");
+            for (let i = 0; i < emit.outputFiles.length; i++) {
+                assert.equal(emit.outputFiles[i].name, expected[i].name, "FileName");
+                assert.equal(emit.outputFiles[i].text, expected[i].text, "Content");
+            }
+        }
+
         public verifyMemberListContains(symbol: string, text?: string, documentation?: string, kind?: string) {
             const members = this.getMemberListAtCaret();
             if (members) {
@@ -2862,6 +2871,10 @@ namespace FourSlashInterface {
             this.state.verifyGetEmitOutputForCurrentFile(expected);
         }
 
+        public verifyGetEmitOutputContentsForCurrentFile(expected: ts.OutputFile[]): void {
+            this.state.verifyGetEmitOutputContentsForCurrentFile(expected);
+        }
+
         public currentParameterHelpArgumentNameIs(name: string) {
             this.state.verifyCurrentParameterHelpName(name);
         }
@@ -3274,4 +3287,4 @@ namespace FourSlashInterface {
             };
         }
     }
-}
+}

src/harness/harness.ts

@@ -176,7 +176,9 @@ namespace Utils {
             ts.forEachChild(node, child => { childNodesAndArrays.push(child); }, array => { childNodesAndArrays.push(array); });
 
             for (const childName in node) {
-                if (childName === "parent" || childName === "nextContainer" || childName === "modifiers" || childName === "externalModuleIndicator") {
+                if (childName === "parent" || childName === "nextContainer" || childName === "modifiers" || childName === "externalModuleIndicator" ||
+                    // for now ignore jsdoc comments
+                    childName === "jsDocComment") {
                     continue;
                 }
                 const child = (<any>node)[childName];
@@ -1028,7 +1030,7 @@ namespace Harness {
 
             const emitResult = program.emit();
 
-            const errors = ts.getPreEmitDiagnostics(program).concat(emitResult.diagnostics);
+            const errors = ts.getPreEmitDiagnostics(program);
 
             const result = new CompilerResult(fileOutputs, errors, program, Harness.IO.getCurrentDirectory(), emitResult.sourceMaps);
             return { result, options };
@@ -1053,7 +1055,6 @@ namespace Harness {
                 ts.forEach(inputFiles, file => addDtsFile(file, declInputFiles));
                 ts.forEach(otherFiles, file => addDtsFile(file, declOtherFiles));
                 const output = compileFiles(declInputFiles, declOtherFiles, harnessSettings, options, currentDirectory);
-
                 return { declInputFiles, declOtherFiles, declResult: output.result };
             }
 
@@ -1075,7 +1076,7 @@ namespace Harness {
                 // Is this file going to be emitted separately
                 let sourceFileName: string;
                 const outFile = options.outFile || options.out;
-                if (ts.isExternalModule(sourceFile) || !outFile) {
+                if (!outFile) {
                     if (options.outDir) {
                         let sourceFilePath = ts.getNormalizedAbsolutePath(sourceFile.fileName, result.currentDirectoryForProgram);
                         sourceFilePath = sourceFilePath.replace(result.program.getCommonSourceDirectory(), "");
@@ -1438,7 +1439,7 @@ namespace Harness {
             }
 
             // normalize the fileName for the single file case
-            currentFileName = testUnitData.length > 0 ? currentFileName : Path.getFileName(fileName);
+            currentFileName = testUnitData.length > 0 || currentFileName ? currentFileName : Path.getFileName(fileName);
 
             // EOF, push whatever remains
             const newTestFile2 = {
@@ -1557,7 +1558,7 @@ namespace Harness {
             const encoded_actual =  Utils.encodeString(actual);
             if (expected != encoded_actual) {
                 // Overwrite & issue error
-                const errMsg = "The baseline file " + relativeFileName + " has changed";
+                const errMsg = "The baseline file " + relativeFileName + " has changed.";
                 throw new Error(errMsg);
             }
         }

src/harness/projectsRunner.ts

@@ -7,19 +7,11 @@ interface ProjectRunnerTestCase {
     scenario: string;
     projectRoot: string; // project where it lives - this also is the current directory when compiling
     inputFiles: string[]; // list of input files to be given to program
-    out?: string; // --out
-    outDir?: string; // --outDir
-    sourceMap?: boolean; // --map
-    mapRoot?: string; // --mapRoot
     resolveMapRoot?: boolean; // should we resolve this map root and give compiler the absolute disk path as map root?
-    sourceRoot?: string; // --sourceRoot
     resolveSourceRoot?: boolean; // should we resolve this source root and give compiler the absolute disk path as map root?
-    declaration?: boolean; // --d
     baselineCheck?: boolean; // Verify the baselines of output files, if this is false, we will write to output to the disk but there is no verification of baselines
     runTest?: boolean; // Run the resulting test
     bug?: string; // If there is any bug associated with this test case
-    noResolve?: boolean;
-    rootDir?: string; // --rootDir
 }
 
 interface ProjectRunnerTestCaseResolutionInfo extends ProjectRunnerTestCase {
@@ -34,14 +26,14 @@ interface BatchCompileProjectTestCaseEmittedFile extends Harness.Compiler.Genera
 
 interface CompileProjectFilesResult {
     moduleKind: ts.ModuleKind;
-    program: ts.Program;
+    program?: ts.Program;
+    compilerOptions?: ts.CompilerOptions;
     errors: ts.Diagnostic[];
-    sourceMapData: ts.SourceMapData[];
+    sourceMapData?: ts.SourceMapData[];
 }
 
 interface BatchCompileProjectTestCaseResult extends CompileProjectFilesResult {
-    outputFiles: BatchCompileProjectTestCaseEmittedFile[];
-    nonSubfolderDiskFiles: number;
+    outputFiles?: BatchCompileProjectTestCaseEmittedFile[];
 }
 
 class ProjectRunner extends RunnerBase {
@@ -59,7 +51,7 @@ class ProjectRunner extends RunnerBase {
     }
 
     private runProjectTestCase(testCaseFileName: string) {
-        let testCase: ProjectRunnerTestCase;
+        let testCase: ProjectRunnerTestCase & ts.CompilerOptions;
 
         let testFileText: string = null;
         try {
@@ -70,7 +62,7 @@ class ProjectRunner extends RunnerBase {
         }
 
         try {
-            testCase = <ProjectRunnerTestCase>JSON.parse(testFileText);
+            testCase = <ProjectRunnerTestCase & ts.CompilerOptions>JSON.parse(testFileText);
         }
         catch (e) {
             assert(false, "Testcase: " + testCaseFileName + " does not contain valid json format: " + e.message);
@@ -128,9 +120,10 @@ class ProjectRunner extends RunnerBase {
 
         function compileProjectFiles(moduleKind: ts.ModuleKind, getInputFiles: () => string[],
             getSourceFileTextImpl: (fileName: string) => string,
-            writeFile: (fileName: string, data: string, writeByteOrderMark: boolean) => void): CompileProjectFilesResult {
+            writeFile: (fileName: string, data: string, writeByteOrderMark: boolean) => void,
+            compilerOptions: ts.CompilerOptions): CompileProjectFilesResult {
 
-            const program = ts.createProgram(getInputFiles(), createCompilerOptions(), createCompilerHost());
+            const program = ts.createProgram(getInputFiles(), compilerOptions, createCompilerHost());
             let errors = ts.getPreEmitDiagnostics(program);
 
             const emitResult = program.emit();
@@ -155,21 +148,6 @@ class ProjectRunner extends RunnerBase {
                 sourceMapData
             };
 
-            function createCompilerOptions(): ts.CompilerOptions {
-                return {
-                    declaration: !!testCase.declaration,
-                    sourceMap: !!testCase.sourceMap,
-                    outFile: testCase.out,
-                    outDir: testCase.outDir,
-                    mapRoot: testCase.resolveMapRoot && testCase.mapRoot ? Harness.IO.resolvePath(testCase.mapRoot) : testCase.mapRoot,
-                    sourceRoot: testCase.resolveSourceRoot && testCase.sourceRoot ? Harness.IO.resolvePath(testCase.sourceRoot) : testCase.sourceRoot,
-                    module: moduleKind,
-                    moduleResolution: ts.ModuleResolutionKind.Classic, // currently all tests use classic module resolution kind, this will change in the future 
-                    noResolve: testCase.noResolve,
-                    rootDir: testCase.rootDir
-                };
-            }
-
             function getSourceFileText(fileName: string): string {
                 const text = getSourceFileTextImpl(fileName);
                 return text !== undefined ? text : getSourceFileTextImpl(ts.getNormalizedAbsolutePath(fileName, getCurrentDirectory()));
@@ -209,23 +187,105 @@ class ProjectRunner extends RunnerBase {
             let nonSubfolderDiskFiles = 0;
 
             const outputFiles: BatchCompileProjectTestCaseEmittedFile[] = [];
+            let inputFiles = testCase.inputFiles;
+            let compilerOptions = createCompilerOptions();
 
-            const projectCompilerResult = compileProjectFiles(moduleKind, () => testCase.inputFiles, getSourceFileText, writeFile);
+            let configFileName: string;
+            if (compilerOptions.project) {
+                // Parse project
+                configFileName = ts.normalizePath(ts.combinePaths(compilerOptions.project, "tsconfig.json"));
+                assert(!inputFiles || inputFiles.length === 0, "cannot specify input files and project option together");
+            }
+            else if (!inputFiles || inputFiles.length === 0) {
+                configFileName = ts.findConfigFile("", fileExists);
+            }
+
+            if (configFileName) {
+                const result = ts.readConfigFile(configFileName, getSourceFileText);
+                if (result.error) {
+                    return {
+                        moduleKind,
+                        errors: [result.error]
+                    };
+                }
+
+                const configObject = result.config;
+                const configParseResult = ts.parseJsonConfigFileContent(configObject, { readDirectory }, ts.getDirectoryPath(configFileName), compilerOptions);
+                if (configParseResult.errors.length > 0) {
+                    return {
+                        moduleKind,
+                        errors: configParseResult.errors
+                    };
+                }
+                inputFiles = configParseResult.fileNames;
+                compilerOptions = configParseResult.options;
+            }
+
+            const projectCompilerResult = compileProjectFiles(moduleKind, () => inputFiles, getSourceFileText, writeFile, compilerOptions);
             return {
                 moduleKind,
                 program: projectCompilerResult.program,
+                compilerOptions,
                 sourceMapData: projectCompilerResult.sourceMapData,
                 outputFiles,
                 errors: projectCompilerResult.errors,
-                nonSubfolderDiskFiles,
             };
 
+            function createCompilerOptions() {
+                // Set the special options that depend on other testcase options
+                const compilerOptions: ts.CompilerOptions = {
+                    mapRoot: testCase.resolveMapRoot && testCase.mapRoot ? Harness.IO.resolvePath(testCase.mapRoot) : testCase.mapRoot,
+                    sourceRoot: testCase.resolveSourceRoot && testCase.sourceRoot ? Harness.IO.resolvePath(testCase.sourceRoot) : testCase.sourceRoot,
+                    module: moduleKind,
+                    moduleResolution: ts.ModuleResolutionKind.Classic, // currently all tests use classic module resolution kind, this will change in the future 
+                };
+                // Set the values specified using json
+                const optionNameMap: ts.Map<ts.CommandLineOption> = {};
+                ts.forEach(ts.optionDeclarations, option => {
+                    optionNameMap[option.name] = option;
+                });
+                for (const name in testCase) {
+                    if (name !== "mapRoot" && name !== "sourceRoot" && ts.hasProperty(optionNameMap, name)) {
+                        const option = optionNameMap[name];
+                        const optType = option.type;
+                        let value = <any>testCase[name];
+                        if (typeof optType !== "string") {
+                            const key = value.toLowerCase();
+                            if (ts.hasProperty(optType, key)) {
+                                value = optType[key];
+                            }
+                        }
+                        compilerOptions[option.name] = value;
+                    }
+                }
+
+                return compilerOptions;
+            }
+
+            function getFileNameInTheProjectTest(fileName: string): string {
+                return ts.isRootedDiskPath(fileName)
+                    ? fileName
+                    : ts.normalizeSlashes(testCase.projectRoot) + "/" + ts.normalizeSlashes(fileName);
+            }
+
+            function readDirectory(rootDir: string, extension: string, exclude: string[]): string[] {
+                const harnessReadDirectoryResult = Harness.IO.readDirectory(getFileNameInTheProjectTest(rootDir), extension, exclude);
+                const result: string[] = [];
+                for (let i = 0; i < harnessReadDirectoryResult.length; i++) {
+                    result[i] = ts.getRelativePathToDirectoryOrUrl(testCase.projectRoot, harnessReadDirectoryResult[i],
+                        getCurrentDirectory(), Harness.Compiler.getCanonicalFileName, /*isAbsolutePathAnUrl*/ false);
+                }
+                return result;
+            }
+
+            function fileExists(fileName: string): boolean {
+                return Harness.IO.fileExists(getFileNameInTheProjectTest(fileName));
+            }
+
             function getSourceFileText(fileName: string): string {
                 let text: string = undefined;
                 try {
-                    text = Harness.IO.readFile(ts.isRootedDiskPath(fileName)
-                        ? fileName
-                        : ts.normalizeSlashes(testCase.projectRoot) + "/" + ts.normalizeSlashes(fileName));
+                    text = Harness.IO.readFile(getFileNameInTheProjectTest(fileName));
                 }
                 catch (e) {
                     // text doesn't get defined.
@@ -288,13 +348,16 @@ class ProjectRunner extends RunnerBase {
 
         function compileCompileDTsFiles(compilerResult: BatchCompileProjectTestCaseResult) {
             const allInputFiles: { emittedFileName: string; code: string; }[] = [];
+            if (!compilerResult.program) {
+                return;
+            }
             const compilerOptions = compilerResult.program.getCompilerOptions();
 
             ts.forEach(compilerResult.program.getSourceFiles(), sourceFile => {
-                if (Harness.Compiler.isDTS(sourceFile.fileName)) {
+                if (ts.isDeclarationFile(sourceFile)) {
                     allInputFiles.unshift({ emittedFileName: sourceFile.fileName, code: sourceFile.text });
                 }
-                else if (ts.shouldEmitToOwnFile(sourceFile, compilerResult.program.getCompilerOptions())) {
+                else if (!(compilerOptions.outFile || compilerOptions.out)) {
                     let emitOutputFilePathWithoutExtension: string = undefined;
                     if (compilerOptions.outDir) {
                         let sourceFilePath = ts.getNormalizedAbsolutePath(sourceFile.fileName, compilerResult.program.getCurrentDirectory());
@@ -320,7 +383,8 @@ class ProjectRunner extends RunnerBase {
                 }
             });
 
-            return compileProjectFiles(compilerResult.moduleKind, getInputFiles, getSourceFileText, writeFile);
+            // Dont allow config files since we are compiling existing source options
+            return compileProjectFiles(compilerResult.moduleKind, getInputFiles, getSourceFileText, writeFile, compilerResult.compilerOptions);
 
             function findOutpuDtsFile(fileName: string) {
                 return ts.forEach(compilerResult.outputFiles, outputFile => outputFile.emittedFileName === fileName ? outputFile : undefined);
@@ -346,11 +410,16 @@ class ProjectRunner extends RunnerBase {
         }
 
         function getErrorsBaseline(compilerResult: CompileProjectFilesResult) {
-            const inputFiles = ts.map(ts.filter(compilerResult.program.getSourceFiles(),
+            const inputFiles = compilerResult.program ? ts.map(ts.filter(compilerResult.program.getSourceFiles(),
                 sourceFile => sourceFile.fileName !== "lib.d.ts"),
                 sourceFile => {
-                    return { unitName: RunnerBase.removeFullPaths(sourceFile.fileName), content: sourceFile.text, };
-                });
+                    return {
+                        unitName: ts.isRootedDiskPath(sourceFile.fileName) ?
+                            RunnerBase.removeFullPaths(sourceFile.fileName) :
+                            sourceFile.fileName,
+                        content: sourceFile.text
+                    };
+                }) : [];
 
             return Harness.Compiler.getErrorBaseline(inputFiles, compilerResult.errors);
         }
@@ -363,30 +432,13 @@ class ProjectRunner extends RunnerBase {
                     let compilerResult: BatchCompileProjectTestCaseResult;
 
                     function getCompilerResolutionInfo() {
-                        const resolutionInfo: ProjectRunnerTestCaseResolutionInfo = {
-                            scenario: testCase.scenario,
-                            projectRoot: testCase.projectRoot,
-                            inputFiles: testCase.inputFiles,
-                            out: testCase.out,
-                            outDir: testCase.outDir,
-                            sourceMap: testCase.sourceMap,
-                            mapRoot: testCase.mapRoot,
-                            resolveMapRoot: testCase.resolveMapRoot,
-                            sourceRoot: testCase.sourceRoot,
-                            resolveSourceRoot: testCase.resolveSourceRoot,
-                            declaration: testCase.declaration,
-                            baselineCheck: testCase.baselineCheck,
-                            runTest: testCase.runTest,
-                            bug: testCase.bug,
-                            rootDir: testCase.rootDir,
-                            resolvedInputFiles: ts.map(compilerResult.program.getSourceFiles(), inputFile => {
-                                return ts.convertToRelativePath(inputFile.fileName, getCurrentDirectory(), path => Harness.Compiler.getCanonicalFileName(path));
-                            }),
-                            emittedFiles: ts.map(compilerResult.outputFiles, outputFile => {
-                                return ts.convertToRelativePath(outputFile.emittedFileName, getCurrentDirectory(), path => Harness.Compiler.getCanonicalFileName(path));
-                            })
-                        };
-
+                        const resolutionInfo: ProjectRunnerTestCaseResolutionInfo & ts.CompilerOptions = JSON.parse(JSON.stringify(testCase));
+                        resolutionInfo.resolvedInputFiles = ts.map(compilerResult.program.getSourceFiles(), inputFile => {
+                            return ts.convertToRelativePath(inputFile.fileName, getCurrentDirectory(), path => Harness.Compiler.getCanonicalFileName(path));
+                        });
+                        resolutionInfo.emittedFiles = ts.map(compilerResult.outputFiles, outputFile => {
+                            return ts.convertToRelativePath(outputFile.emittedFileName, getCurrentDirectory(), path => Harness.Compiler.getCanonicalFileName(path));
+                        });
                         return resolutionInfo;
                     }
 
@@ -442,7 +494,7 @@ class ProjectRunner extends RunnerBase {
                     it("Errors in generated Dts files for (" + moduleNameToString(moduleKind) + "): " + testCaseFileName, () => {
                         if (!compilerResult.errors.length && testCase.declaration) {
                             const dTsCompileResult = compileCompileDTsFiles(compilerResult);
-                            if (dTsCompileResult.errors.length) {
+                            if (dTsCompileResult && dTsCompileResult.errors.length) {
                                 Harness.Baseline.runBaseline("Errors in generated Dts files for (" + moduleNameToString(compilerResult.moduleKind) + "): " + testCaseFileName, getBaselineFolder(compilerResult.moduleKind) + testCaseJustName + ".dts.errors.txt", () => {
                                     return getErrorsBaseline(dTsCompileResult);
                                 });

src/server/editorServices.ts

@@ -564,7 +564,7 @@ namespace ts.server {
             // If a change was made inside "folder/file", node will trigger the callback twice:
             // one with the fileName being "folder/file", and the other one with "folder".
             // We don't respond to the second one.
-            if (fileName && !ts.isSupportedSourceFileName(fileName)) {
+            if (fileName && !ts.isSupportedSourceFileName(fileName, project.projectOptions ? project.projectOptions.compilerOptions : undefined)) {
                 return;
             }
 

src/services/navigationBar.ts

@@ -2,7 +2,7 @@
 
 /* @internal */
 namespace ts.NavigationBar {
-    export function getNavigationBarItems(sourceFile: SourceFile): ts.NavigationBarItem[]  {
+    export function getNavigationBarItems(sourceFile: SourceFile, compilerOptions: CompilerOptions): ts.NavigationBarItem[]  {
         // If the source file has any child items, then it included in the tree
         // and takes lexical ownership of all other top-level items.
         let hasGlobalNode = false;

src/services/services.ts

@@ -2023,7 +2023,7 @@ namespace ts {
         let getCanonicalFileName = createGetCanonicalFileName(!!useCaseSensitiveFileNames);
 
         function getKeyFromCompilationSettings(settings: CompilerOptions): string {
-            return "_" + settings.target + "|" + settings.module + "|" + settings.noResolve + "|" + settings.jsx;
+            return "_" + settings.target + "|" + settings.module + "|" + settings.noResolve + "|" + settings.jsx + +"|" + settings.allowJs;
         }
 
         function getBucketForCompilationSettings(settings: CompilerOptions, createIfMissing: boolean): FileMap<DocumentRegistryEntry> {
@@ -2746,7 +2746,8 @@ namespace ts {
                 (oldSettings.target !== newSettings.target ||
                  oldSettings.module !== newSettings.module ||
                  oldSettings.noResolve !== newSettings.noResolve ||
-                 oldSettings.jsx !== newSettings.jsx);
+                 oldSettings.jsx !== newSettings.jsx || 
+                 oldSettings.allowJs !== newSettings.allowJs);
 
             // Now create a new compiler
             let compilerHost: CompilerHost = {
@@ -2911,13 +2912,6 @@ namespace ts {
 
             let targetSourceFile = getValidSourceFile(fileName);
 
-            // For JavaScript files, we don't want to report the normal typescript semantic errors.
-            // Instead, we just report errors for using TypeScript-only constructs from within a
-            // JavaScript file.
-            if (isSourceFileJavaScript(targetSourceFile)) {
-                return getJavaScriptSemanticDiagnostics(targetSourceFile);
-            }
-
             // Only perform the action per file regardless of '-out' flag as LanguageServiceHost is expected to call this function per file.
             // Therefore only get diagnostics for given file.
 
@@ -2931,163 +2925,6 @@ namespace ts {
             return concatenate(semanticDiagnostics, declarationDiagnostics);
         }
 
-        function getJavaScriptSemanticDiagnostics(sourceFile: SourceFile): Diagnostic[] {
-            let diagnostics: Diagnostic[] = [];
-            walk(sourceFile);
-
-            return diagnostics;
-
-            function walk(node: Node): boolean {
-                if (!node) {
-                    return false;
-                }
-
-                switch (node.kind) {
-                    case SyntaxKind.ImportEqualsDeclaration:
-                        diagnostics.push(createDiagnosticForNode(node, Diagnostics.import_can_only_be_used_in_a_ts_file));
-                        return true;
-                    case SyntaxKind.ExportAssignment:
-                        diagnostics.push(createDiagnosticForNode(node, Diagnostics.export_can_only_be_used_in_a_ts_file));
-                        return true;
-                    case SyntaxKind.ClassDeclaration:
-                        let classDeclaration = <ClassDeclaration>node;
-                        if (checkModifiers(classDeclaration.modifiers) ||
-                            checkTypeParameters(classDeclaration.typeParameters)) {
-                            return true;
-                        }
-                        break;
-                    case SyntaxKind.HeritageClause:
-                        let heritageClause = <HeritageClause>node;
-                        if (heritageClause.token === SyntaxKind.ImplementsKeyword) {
-                            diagnostics.push(createDiagnosticForNode(node, Diagnostics.implements_clauses_can_only_be_used_in_a_ts_file));
-                            return true;
-                        }
-                        break;
-                    case SyntaxKind.InterfaceDeclaration:
-                        diagnostics.push(createDiagnosticForNode(node, Diagnostics.interface_declarations_can_only_be_used_in_a_ts_file));
-                        return true;
-                    case SyntaxKind.ModuleDeclaration:
-                        diagnostics.push(createDiagnosticForNode(node, Diagnostics.module_declarations_can_only_be_used_in_a_ts_file));
-                        return true;
-                    case SyntaxKind.TypeAliasDeclaration:
-                        diagnostics.push(createDiagnosticForNode(node, Diagnostics.type_aliases_can_only_be_used_in_a_ts_file));
-                        return true;
-                    case SyntaxKind.MethodDeclaration:
-                    case SyntaxKind.MethodSignature:
-                    case SyntaxKind.Constructor:
-                    case SyntaxKind.GetAccessor:
-                    case SyntaxKind.SetAccessor:
-                    case SyntaxKind.FunctionExpression:
-                    case SyntaxKind.FunctionDeclaration:
-                    case SyntaxKind.ArrowFunction:
-                    case SyntaxKind.FunctionDeclaration:
-                        let functionDeclaration = <FunctionLikeDeclaration>node;
-                        if (checkModifiers(functionDeclaration.modifiers) ||
-                            checkTypeParameters(functionDeclaration.typeParameters) ||
-                            checkTypeAnnotation(functionDeclaration.type)) {
-                            return true;
-                        }
-                        break;
-                    case SyntaxKind.VariableStatement:
-                        let variableStatement = <VariableStatement>node;
-                        if (checkModifiers(variableStatement.modifiers)) {
-                            return true;
-                        }
-                        break;
-                    case SyntaxKind.VariableDeclaration:
-                        let variableDeclaration = <VariableDeclaration>node;
-                        if (checkTypeAnnotation(variableDeclaration.type)) {
-                            return true;
-                        }
-                        break;
-                    case SyntaxKind.CallExpression:
-                    case SyntaxKind.NewExpression:
-                        let expression = <CallExpression>node;
-                        if (expression.typeArguments && expression.typeArguments.length > 0) {
-                            let start = expression.typeArguments.pos;
-                            diagnostics.push(createFileDiagnostic(sourceFile, start, expression.typeArguments.end - start,
-                                Diagnostics.type_arguments_can_only_be_used_in_a_ts_file));
-                            return true;
-                        }
-                        break;
-                    case SyntaxKind.Parameter:
-                        let parameter = <ParameterDeclaration>node;
-                        if (parameter.modifiers) {
-                            let start = parameter.modifiers.pos;
-                            diagnostics.push(createFileDiagnostic(sourceFile, start, parameter.modifiers.end - start,
-                                Diagnostics.parameter_modifiers_can_only_be_used_in_a_ts_file));
-                            return true;
-                        }
-                        if (parameter.questionToken) {
-                            diagnostics.push(createDiagnosticForNode(parameter.questionToken, Diagnostics._0_can_only_be_used_in_a_ts_file, '?'));
-                            return true;
-                        }
-                        if (parameter.type) {
-                            diagnostics.push(createDiagnosticForNode(parameter.type, Diagnostics.types_can_only_be_used_in_a_ts_file));
-                            return true;
-                        }
-                        break;
-                    case SyntaxKind.PropertyDeclaration:
-                        diagnostics.push(createDiagnosticForNode(node, Diagnostics.property_declarations_can_only_be_used_in_a_ts_file));
-                        return true;
-                    case SyntaxKind.EnumDeclaration:
-                        diagnostics.push(createDiagnosticForNode(node, Diagnostics.enum_declarations_can_only_be_used_in_a_ts_file));
-                        return true;
-                    case SyntaxKind.TypeAssertionExpression:
-                        let typeAssertionExpression = <TypeAssertion>node;
-                        diagnostics.push(createDiagnosticForNode(typeAssertionExpression.type, Diagnostics.type_assertion_expressions_can_only_be_used_in_a_ts_file));
-                        return true;
-                    case SyntaxKind.Decorator:
-                        diagnostics.push(createDiagnosticForNode(node, Diagnostics.decorators_can_only_be_used_in_a_ts_file));
-                        return true;
-                }
-
-                return forEachChild(node, walk);
-            }
-
-            function checkTypeParameters(typeParameters: NodeArray<TypeParameterDeclaration>): boolean {
-                if (typeParameters) {
-                    let start = typeParameters.pos;
-                    diagnostics.push(createFileDiagnostic(sourceFile, start, typeParameters.end - start, Diagnostics.type_parameter_declarations_can_only_be_used_in_a_ts_file));
-                    return true;
-                }
-                return false;
-            }
-
-            function checkTypeAnnotation(type: TypeNode): boolean {
-                if (type) {
-                    diagnostics.push(createDiagnosticForNode(type, Diagnostics.types_can_only_be_used_in_a_ts_file));
-                    return true;
-                }
-
-                return false;
-            }
-
-            function checkModifiers(modifiers: ModifiersArray): boolean {
-                if (modifiers) {
-                    for (let modifier of modifiers) {
-                        switch (modifier.kind) {
-                            case SyntaxKind.PublicKeyword:
-                            case SyntaxKind.PrivateKeyword:
-                            case SyntaxKind.ProtectedKeyword:
-                            case SyntaxKind.DeclareKeyword:
-                                diagnostics.push(createDiagnosticForNode(modifier, Diagnostics._0_can_only_be_used_in_a_ts_file, tokenToString(modifier.kind)));
-                                return true;
-
-                            // These are all legal modifiers.
-                            case SyntaxKind.StaticKeyword:
-                            case SyntaxKind.ExportKeyword:
-                            case SyntaxKind.ConstKeyword:
-                            case SyntaxKind.DefaultKeyword:
-                            case SyntaxKind.AbstractKeyword:
-                        }
-                    }
-                }
-
-                return false;
-            }
-        }
-
         function getCompilerOptionsDiagnostics() {
             synchronizeHostData();
             return program.getOptionsDiagnostics(cancellationToken).concat(
@@ -6585,7 +6422,7 @@ namespace ts {
         function getNavigationBarItems(fileName: string): NavigationBarItem[] {
             let sourceFile = syntaxTreeCache.getCurrentSourceFile(fileName);
 
-            return NavigationBar.getNavigationBarItems(sourceFile);
+            return NavigationBar.getNavigationBarItems(sourceFile, host.getCompilationSettings());
         }
 
         function getSemanticClassifications(fileName: string, span: TextSpan): ClassifiedSpan[] {