Assume rootDir is the current configuration directory

src/compiler/diagnosticMessages.json

@@ -4469,6 +4469,10 @@
         "category": "Error",
         "code": 5010
     },
+    "Inferred common source directory differs from tsconfig directory, output layout will be changed.": {
+        "category": "Error",
+        "code": 5011
+    },
     "Cannot read file '{0}': {1}.": {
         "category": "Error",
         "code": 5012

src/compiler/emitter.ts

@@ -646,7 +646,7 @@ export function getCommonSourceDirectory(
         commonSourceDirectory = getNormalizedAbsolutePath(options.rootDir, currentDirectory);
         checkSourceFilesBelongToPath?.(options.rootDir);
     }
-    else if (options.composite && options.configFilePath) {
+    else if (options.configFilePath) {
         // Project compilations never infer their root from the input source paths
         commonSourceDirectory = getDirectoryPath(normalizeSlashes(options.configFilePath));
         checkSourceFilesBelongToPath?.(commonSourceDirectory);
@@ -664,6 +664,23 @@ export function getCommonSourceDirectory(
     return commonSourceDirectory;
 }
 
+/** @internal */
+export function getComputedCommonSourceDirectory(
+    emittedFiles: readonly string[],
+    currentDirectory: string,
+    getCanonicalFileName: GetCanonicalFileName,
+): string {
+    let commonSourceDirectory = computeCommonSourceDirectoryOfFilenames(emittedFiles, currentDirectory, getCanonicalFileName);
+
+    if (commonSourceDirectory && commonSourceDirectory[commonSourceDirectory.length - 1] !== directorySeparator) {
+        // Make sure directory path ends with directory separator so this string can directly
+        // used to replace with "" to get the relative path of the source file and the relative path doesn't
+        // start with / making it rooted path
+        commonSourceDirectory += directorySeparator;
+    }
+    return commonSourceDirectory;
+}
+
 /** @internal */
 export function getCommonSourceDirectoryOfConfig({ options, fileNames }: ParsedCommandLine, ignoreCase: boolean): string {
     return getCommonSourceDirectory(

src/compiler/moduleNameResolver.ts

@@ -2886,7 +2886,7 @@ function getLoadModuleFromTargetExportOrImport(extensions: Extensions, state: Mo
                 const commonSourceDirGuesses: string[] = [];
                 // A `rootDir` compiler option strongly indicates the root location
                 // A `composite` project is using project references and has it's common src dir set to `.`, so it shouldn't need to check any other locations
-                if (state.compilerOptions.rootDir || (state.compilerOptions.composite && state.compilerOptions.configFilePath)) {
+                if (state.compilerOptions.rootDir || state.compilerOptions.configFilePath) {
                     const commonDir = toAbsolutePath(getCommonSourceDirectory(state.compilerOptions, () => [], state.host.getCurrentDirectory?.() || "", getCanonicalFileName));
                     commonSourceDirGuesses.push(commonDir);
                 }

src/compiler/program.ts

@@ -109,6 +109,7 @@ import {
     GetCanonicalFileName,
     getCommonSourceDirectory as ts_getCommonSourceDirectory,
     getCommonSourceDirectoryOfConfig,
+    getComputedCommonSourceDirectory,
     getDeclarationDiagnostics as ts_getDeclarationDiagnostics,
     getDefaultLibFileName,
     getDirectoryPath,
@@ -4254,6 +4255,32 @@ export function createProgram(_rootNamesOrOptions: readonly string[] | CreatePro
             }
         }
 
+        if (
+            !options.noEmit &&
+            !options.composite &&
+            !options.rootDir &&
+            options.configFilePath &&
+            (options.outDir || // there is --outDir specified
+                (getEmitDeclarations(options) && options.declarationDir)) // there is --declarationDir specified
+        ) {
+            // Check if rootDir inferred changed and issue diagnostic
+            const dir = getCommonSourceDirectory();
+            const emittedFiles = mapDefined(files, file => !file.isDeclarationFile && sourceFileMayBeEmitted(file, program) ? file.fileName : undefined);
+            const dir59 = getComputedCommonSourceDirectory(emittedFiles, currentDirectory, getCanonicalFileName);
+            if (dir59 !== "" && getCanonicalFileName(dir) !== getCanonicalFileName(dir59)) {
+                // change in layout
+                createDiagnosticForOption(
+                    /*onKey*/ true,
+                    options.outDir ? "outDir" : "declarationDir",
+                    options.outDir ? "declarationDir" : undefined,
+                    chainDiagnosticMessages(
+                        chainDiagnosticMessages(/*details*/ undefined, Diagnostics.Visit_https_Colon_Slash_Slashaka_ms_Slashts6_for_migration_information),
+                        Diagnostics.Inferred_common_source_directory_differs_from_tsconfig_directory_output_layout_will_be_changed,
+                    ),
+                );
+            }
+        }
+
         if (options.checkJs && !getAllowJSCompilerOption(options)) {
             createDiagnosticForOptionName(Diagnostics.Option_0_cannot_be_specified_without_specifying_option_1, "checkJs", "allowJs");
         }

src/compiler/utilities.ts

@@ -6622,7 +6622,7 @@ export function sourceFileMayBeEmitted(sourceFile: SourceFile, host: SourceFileM
     // Json file is not emitted if outDir is not specified
     if (!options.outDir) return false;
     // Otherwise if rootDir or composite config file, we know common sourceDir and can check if file would be emitted in same location
-    if (options.rootDir || (options.composite && options.configFilePath)) {
+    if (options.rootDir || options.configFilePath) {
         const commonDir = getNormalizedAbsolutePath(getCommonSourceDirectory(options, () => [], host.getCurrentDirectory(), host.getCanonicalFileName), host.getCurrentDirectory());
         const outputPath = getSourceFilePathInNewDirWorker(sourceFile.fileName, options.outDir, host.getCurrentDirectory(), commonDir, host.getCanonicalFileName);
         if (comparePaths(sourceFile.fileName, outputPath, host.getCurrentDirectory(), !host.useCaseSensitiveFileNames()) === Comparison.EqualTo) return false;

src/testRunner/unittests/helpers/monorepoSymlinkedSiblingPackages.ts

@@ -151,6 +151,7 @@ function getMonorepoSymlinkedSiblingPackagesSysWithUnRelatedFolders(
             compilerOptions: {
                 outDir: "lib",
                 declaration: true,
+                rootDir: "src",
             },
             include: ["src/**/*.ts"],
         }),
@@ -169,6 +170,7 @@ function getMonorepoSymlinkedSiblingPackagesSysWithUnRelatedFolders(
             compilerOptions: {
                 outDir: "lib",
                 declaration: true,
+                rootDir: "src",
             },
             include: ["src/**/*.ts"],
         }),
@@ -183,6 +185,7 @@ function getMonorepoSymlinkedSiblingPackagesSysWithUnRelatedFolders(
         "/home/src/projects/b/2/b-impl/b/tsconfig.json": jsonToReadableText({
             compilerOptions: {
                 outDir: "lib",
+                rootDir: "src",
             },
             include: ["src/**/*.ts"],
         }),

src/testRunner/unittests/tsbuild/outputPaths.ts

@@ -26,7 +26,7 @@ describe("unittests:: tsbuild:: outputPaths::", () => {
             ...input,
         });
 
-        it("verify getOutputFileNames", () => {
+        it("verify getOutputFileNames " + input.subScenario, () => {
             const sys = input.sys();
             assert.deepEqual(
                 ts.getOutputFileNames(
@@ -58,7 +58,7 @@ describe("unittests:: tsbuild:: outputPaths::", () => {
                 }),
             }),
         edits,
-    }, ["/home/src/workspaces/project/dist/index.js"]);
+    }, ["/home/src/workspaces/project/dist/src/index.js"]);
 
     verify({
         subScenario: "when rootDir is not specified and is composite",

tests/baselines/reference/commonSourceDirectory.js

@@ -27,3 +27,36 @@ foo_1.x + bar_1.y;
 //// [/app/bin/index.d.ts]
 /// <reference path="../../types/bar.d.ts" preserve="true" />
 export {};
+
+
+//// [DtsFileErrors]
+
+
+/app/tsconfig.json(3,9): error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+  Visit https://aka.ms/ts6 for migration information.
+
+
+==== /app/tsconfig.json (1 errors) ====
+    {
+        "compilerOptions": {
+            "outDir": "bin",
+            ~~~~~~~~
+!!! error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+!!! error TS5011:   Visit https://aka.ms/ts6 for migration information.
+            "typeRoots": ["../types"],
+            "sourceMap": true,
+            "mapRoot": "myMapRoot",
+            "sourceRoot": "mySourceRoot",
+            "declaration": true
+        }
+    }
+
+==== /app/bin/index.d.ts (0 errors) ====
+    /// <reference path="../../types/bar.d.ts" preserve="true" />
+    export {};
+
+==== /types/bar.d.ts (0 errors) ====
+    declare module "bar" {
+        export const y = 0;
+    }
+

tests/baselines/reference/commonSourceDirectory_dts.errors.txt

@@ -0,0 +1,25 @@
+/app/tsconfig.json(3,9): error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+  Visit https://aka.ms/ts6 for migration information.
+
+
+==== /app/tsconfig.json (1 errors) ====
+    {
+        "compilerOptions": {
+            "outDir": "bin",
+            ~~~~~~~~
+!!! error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+!!! error TS5011:   Visit https://aka.ms/ts6 for migration information.
+            "sourceMap": true,
+            "mapRoot": "myMapRoot",
+            "sourceRoot": "mySourceRoot",
+            "declaration": true
+        }
+    }
+
+==== /app/lib/bar.d.ts (0 errors) ====
+    declare const y: number;
+
+==== /app/src/index.ts (0 errors) ====
+    /// <reference path="../lib/bar.d.ts" preserve="true" />
+    export const x = y;
+

tests/baselines/reference/commonSourceDirectory_dts.js

@@ -8,14 +8,14 @@ declare const y: number;
 export const x = y;
 
 
-//// [/app/bin/index.js]
+//// [/app/bin/src/index.js]
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.x = void 0;
 /// <reference path="../lib/bar.d.ts" preserve="true" />
 exports.x = y;
-//# sourceMappingURL=../src/myMapRoot/index.js.map
+//# sourceMappingURL=../../myMapRoot/src/index.js.map
 
-//// [/app/bin/index.d.ts]
-/// <reference path="../lib/bar.d.ts" preserve="true" />
+//// [/app/bin/src/index.d.ts]
+/// <reference path="../../lib/bar.d.ts" preserve="true" />
 export declare const x: number;

tests/baselines/reference/commonSourceDirectory_dts.sourcemap.txt

@@ -1,12 +1,12 @@
 ===================================================================
 JsFile: index.js
-mapUrl: ../src/myMapRoot/index.js.map
+mapUrl: ../../myMapRoot/src/index.js.map
 sourceRoot: mySourceRoot/
-sources: index.ts
+sources: src/index.ts
 ===================================================================
 -------------------------------------------------------------------
-emittedFile:/app/bin/index.js
-sourceFile:index.ts
+emittedFile:/app/bin/src/index.js
+sourceFile:src/index.ts
 -------------------------------------------------------------------
 >>>"use strict";
 >>>Object.defineProperty(exports, "__esModule", { value: true });
@@ -26,7 +26,7 @@ sourceFile:index.ts
 4 >         ^^^
 5 >            ^
 6 >             ^
-7 >              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+7 >              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^->
 1 >
   >export const 
 2 >
@@ -41,4 +41,4 @@ sourceFile:index.ts
 5 >Emitted(5, 14) Source(2, 19) + SourceIndex(0)
 6 >Emitted(5, 15) Source(2, 20) + SourceIndex(0)
 ---
->>>//# sourceMappingURL=../src/myMapRoot/index.js.map
+>>>//# sourceMappingURL=../../myMapRoot/src/index.js.map

tests/baselines/reference/declarationEmitMonorepoBaseUrl.errors.txt

@@ -1,13 +1,18 @@
+/tsconfig.json(5,5): error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+  Visit https://aka.ms/ts6 for migration information.
 /tsconfig.json(6,5): error TS5101: Option 'baseUrl' is deprecated and will stop functioning in TypeScript 7.0. Specify compilerOption '"ignoreDeprecations": "6.0"' to silence this error.
   Visit https://aka.ms/ts6 for migration information.
 
 
-==== /tsconfig.json (1 errors) ====
+==== /tsconfig.json (2 errors) ====
     {
       "compilerOptions": {
         "module": "nodenext",
         "declaration": true,
         "outDir": "temp",
+        ~~~~~~~~
+!!! error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+!!! error TS5011:   Visit https://aka.ms/ts6 for migration information.
         "baseUrl": "."
         ~~~~~~~~~
 !!! error TS5101: Option 'baseUrl' is deprecated and will stop functioning in TypeScript 7.0. Specify compilerOption '"ignoreDeprecations": "6.0"' to silence this error.

tests/baselines/reference/declarationEmitPathMappingMonorepo.errors.txt

@@ -1,11 +1,16 @@
+packages/b/tsconfig.json(3,9): error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+  Visit https://aka.ms/ts6 for migration information.
 packages/b/tsconfig.json(5,9): error TS5101: Option 'baseUrl' is deprecated and will stop functioning in TypeScript 7.0. Specify compilerOption '"ignoreDeprecations": "6.0"' to silence this error.
   Visit https://aka.ms/ts6 for migration information.
 
 
-==== packages/b/tsconfig.json (1 errors) ====
+==== packages/b/tsconfig.json (2 errors) ====
     {
         "compilerOptions": {
             "outDir": "dist",
+            ~~~~~~~~
+!!! error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+!!! error TS5011:   Visit https://aka.ms/ts6 for migration information.
             "declaration": true,
             "baseUrl": ".",
             ~~~~~~~~~

tests/baselines/reference/declarationEmitPathMappingMonorepo2.errors.txt

@@ -1,11 +1,16 @@
+packages/lab/tsconfig.json(3,9): error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+  Visit https://aka.ms/ts6 for migration information.
 packages/lab/tsconfig.json(5,9): error TS5101: Option 'baseUrl' is deprecated and will stop functioning in TypeScript 7.0. Specify compilerOption '"ignoreDeprecations": "6.0"' to silence this error.
   Visit https://aka.ms/ts6 for migration information.
 
 
-==== packages/lab/tsconfig.json (1 errors) ====
+==== packages/lab/tsconfig.json (2 errors) ====
     {
         "compilerOptions": {
             "outDir": "dist",
+            ~~~~~~~~
+!!! error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+!!! error TS5011:   Visit https://aka.ms/ts6 for migration information.
             "declaration": true,
             "baseUrl": "../",
             ~~~~~~~~~

tests/baselines/reference/declarationEmitToDeclarationDirWithDeclarationOption.js

@@ -17,3 +17,20 @@ interface Foo {
     x: number;
 }
 export default Foo;
+
+
+//// [DtsFileErrors]
+
+
+/foo/tsconfig.json(2,47): error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+  Visit https://aka.ms/ts6 for migration information.
+
+
+==== /foo/tsconfig.json (1 errors) ====
+    {
+        "compilerOptions": { "declaration": true, "declarationDir": "out" }
+                                                  ~~~~~~~~~~~~~~~~
+!!! error TS5011: Inferred common source directory differs from tsconfig directory, output layout will be changed.
+!!! error TS5011:   Visit https://aka.ms/ts6 for migration information.
+    }
+