Fix remaining tests:

- track which files have been renamed by appendSuffixTo and exclude them from needing to be in rootFileNames
- check for project references before rootFileNames
- fix up remaining test tsconfigs

src/index.ts

@@ -23,6 +23,7 @@ import {
   formatErrors,
   getAndCacheOutputJSFileName,
   getAndCacheProjectReference,
+  isRootFileOrExempt,
   validateSourceMapOncePerProject
 } from './utils';
 
@@ -75,22 +76,11 @@ function successLoader(
 
   const { version: fileVersion, changedFilesList } = updateFileInCache(
     filePath,
+    loaderContext.resourcePath,
     contents,
     instance
   );
 
-  if (changedFilesList && !instance.rootFileNames.has(filePath)) {
-    reloadRootFileNamesFromConfig(loaderContext, instance);
-    if (
-      !instance.rootFileNames.has(filePath) &&
-      !options.onlyCompileBundledFiles
-    ) {
-      throw new Error(
-        `The file ${filePath} is not part of the project specified in tsconfig.json. Make sure it is covered by the fields 'include', 'exclude' and 'files'.`
-      );
-    }
-  }
-
   const referencedProject = getAndCacheProjectReference(filePath, instance);
   if (referencedProject !== undefined) {
     const [relativeProjectConfigPath, relativeFilePath] = [
@@ -155,6 +145,18 @@ function successLoader(
       callback
     );
   } else {
+    if (changedFilesList && !isRootFileOrExempt(filePath, instance)) {
+      reloadRootFileNamesFromConfig(loaderContext, instance);
+      if (
+        !instance.rootFileNames.has(filePath) &&
+        !options.onlyCompileBundledFiles
+      ) {
+        throw new Error(
+          `The file ${filePath} is not part of the project specified in tsconfig.json. Make sure it is covered by the fields 'include', 'exclude' and 'files'.`
+        );
+      }
+    }
+
     const { outputText, sourceMapText } = options.transpileOnly
       ? getTranspilationEmit(filePath, contents, instance, loaderContext)
       : getEmit(rawFilePath, filePath, instance, loaderContext);
@@ -396,28 +398,32 @@ function makeLoaderOptions(instanceName: string, loaderOptions: LoaderOptions) {
 /**
  * Either add file to the overall files cache or update it in the cache when the file contents have changed
  * Also add the file to the modified files
+ * @param internalFilePath The path ts-loader uses to track files and register them with the TypeScript compiler. Usually the same as `realFilePath`, but can be different if `loaderOptions.appendTsSuffixTo` or `loaderOptions.appendTsxSuffixTo` are set.
+ * @param realFilePath The absolute path of the input file on disk.
+ * @param contents The file contents as a string.
  */
 function updateFileInCache(
-  filePath: string,
+  internalFilePath: string,
+  realFilePath: string,
   contents: string,
   instance: TSInstance
 ) {
   let fileWatcherEventKind: typescript.FileWatcherEventKind | undefined;
   let changedFilesList = false;
 
   // Update file contents
-  let file = instance.files.get(filePath);
+  let file = instance.files.get(internalFilePath);
   if (file === undefined) {
-    file = instance.otherFiles.get(filePath);
+    file = instance.otherFiles.get(internalFilePath);
     if (file !== undefined) {
-      instance.otherFiles.delete(filePath);
-      instance.files.set(filePath, file);
+      instance.otherFiles.delete(internalFilePath);
+      instance.files.set(internalFilePath, file);
     } else {
       if (instance.watchHost !== undefined) {
         fileWatcherEventKind = instance.compiler.FileWatcherEventKind.Created;
       }
       file = { version: 0 };
-      instance.files.set(filePath, file);
+      instance.files.set(internalFilePath, file);
     }
     changedFilesList = true;
     instance.changedFilesList = true;
@@ -430,7 +436,7 @@ function updateFileInCache(
   //
   // See https://github.com/TypeStrong/ts-loader/issues/943
   //
-  if (!instance.rootFileNames.has(filePath)) {
+  if (!instance.rootFileNames.has(internalFilePath)) {
     instance.version!++;
   }
 
@@ -450,17 +456,27 @@ function updateFileInCache(
     }
   }
 
+  // Set the real file path if it’s different than the one ts-loader generally uses
+  file.realFileName =
+    internalFilePath === realFilePath ? undefined : realFilePath;
+
   if (instance.watchHost !== undefined && fileWatcherEventKind !== undefined) {
     instance.hasUnaccountedModifiedFiles = true;
-    instance.watchHost.invokeFileWatcher(filePath, fileWatcherEventKind);
-    instance.watchHost.invokeDirectoryWatcher(path.dirname(filePath), filePath);
+    instance.watchHost.invokeFileWatcher(
+      internalFilePath,
+      fileWatcherEventKind
+    );
+    instance.watchHost.invokeDirectoryWatcher(
+      path.dirname(internalFilePath),
+      internalFilePath
+    );
   }
 
   // push this file to modified files hash.
   if (instance.modifiedFiles === null || instance.modifiedFiles === undefined) {
     instance.modifiedFiles = new Map<string, TSFile>();
   }
-  instance.modifiedFiles.set(filePath, file);
+  instance.modifiedFiles.set(internalFilePath, file);
   return {
     version: file.version,
     changedFilesList

src/interfaces.ts

@@ -179,6 +179,8 @@ export interface LoaderOptions {
 export interface TSFile {
   text?: string;
   version: number;
+  /** Only defined when ts-loader has renamed the file internally */
+  realFileName?: string;
   projectReference?: {
     /**
      * Undefined here means we’ve already checked and confirmed there is no

src/utils.ts

@@ -255,6 +255,24 @@ export function ensureProgram(instance: TSInstance) {
   return instance.program;
 }
 
+export function isRootFileOrExempt(
+  fileName: string,
+  instance: TSInstance
+): boolean {
+  if (instance.rootFileNames.has(fileName)) {
+    return true;
+  }
+
+  const file = instance.files.get(fileName);
+  // Indicates that ts-loader is tracking this file by a different path,
+  // so should be exempt from being in tsconfig’s root files.
+  if (file && file.realFileName) {
+    return true;
+  }
+
+  return false;
+}
+
 export function supportsProjectReferences(instance: TSInstance) {
   const program = ensureProgram(instance);
   return program && !!program.getProjectReferences;

test/execution-tests/3.0.1_projectReferences/tsconfig.json

@@ -1,6 +1,7 @@
 {
   "files": [
-    "./src/app.ts"
+    "./src/app.ts",
+    "./test/app.tests.ts"
   ],
   "references": [
     { "path": "./lib" }

test/execution-tests/3.0.1_projectReferences/yarn.lock

@@ -5,7 +5,9 @@
 "@types/jasmine@^2.5.35":
   version "2.8.5"
   resolved "https://registry.yarnpkg.com/@types/jasmine/-/jasmine-2.8.5.tgz#96e58872583fa80c7ea0dd29024b180d5e133678"
+  integrity sha512-mkrHFZTgOXkZhau36K628iKFkjbp11t/bHCkY4Mefu4R6McMg2FD9P3naBv/0Ygyn4sz8baColJp2gdmSekgiw==
 
 jasmine-core@^2.3.4:
   version "2.9.1"
   resolved "https://registry.yarnpkg.com/jasmine-core/-/jasmine-core-2.9.1.tgz#b6bbc1d8e65250d56f5888461705ebeeeb88f22f"
+  integrity sha1-trvB2OZSUNVvWIhGFwXr7uuI8i8=

test/execution-tests/allowTsInNodeModules/tsconfig.json

@@ -3,9 +3,8 @@
     "noEmitOnError": true
   },
   "include": [
-    "./node_modules/whitelistedModule"
-  ],
-  "files": [
-    "./node_modules/whitelistedFiles/file.ts"
+    "./node_modules/whitelistedModule",
+    "./src",
+    "./test"
   ]
 }

test/execution-tests/allowTsInNodeModules/yarn.lock

@@ -5,10 +5,12 @@
 "@types/jasmine@^2.5.35":
   version "2.8.6"
   resolved "https://registry.yarnpkg.com/@types/jasmine/-/jasmine-2.8.6.tgz#14445b6a1613cf4e05dd61c3c3256d0e95c0421e"
+  integrity sha512-clg9raJTY0EOo5pVZKX3ZlMjlYzVU73L71q5OV1jhE2Uezb7oF94jh4CvwrW6wInquQAdhOxJz5VDF2TLUGmmA==
 
 jasmine-core@^2.3.4:
   version "2.99.1"
   resolved "https://registry.yarnpkg.com/jasmine-core/-/jasmine-core-2.99.1.tgz#e6400df1e6b56e130b61c4bcd093daa7f6e8ca15"
+  integrity sha1-5kAN8ea1bhMLYcS80JPap/boyhU=
 
 "whitelistedFiles@file:../../testPackages/whitelistedFiles":
   version "1.0.0"

test/execution-tests/optionsCaching/tsconfig.json

@@ -3,5 +3,8 @@
     "target": "esnext",
     "jsx": "react",
     "noEmitOnError": true
-  }
+  },
+  "include": [
+    "*"
+  ]
 }

test/execution-tests/run-tests.js

@@ -140,7 +140,7 @@ function runTests(testName) {
             console.log('running webpack compilation');
             var webpackPath = path.resolve(__dirname, '../../node_modules/webpack/bin/webpack.js');
             var program = debug ? 'node --inspect-brk=5858 ' + webpackPath : 'webpack';
-            execSync(webpackPath + ' --bail', { cwd: testPath, stdio: 'inherit' });
+            execSync(program + ' --bail', { cwd: testPath, stdio: 'inherit' });
             passingTests.push(testName);
         }
     }