diff --git a/src/compiler/commandLineParser.ts b/src/compiler/commandLineParser.ts
index 8169421ca1763..47f0594a76e65 100644
--- a/src/compiler/commandLineParser.ts
+++ b/src/compiler/commandLineParser.ts
@@ -110,6 +110,13 @@ module ts {
             type: "boolean",
             description: Diagnostics.Do_not_emit_comments_to_output,
         },
+        {
+            name: "rootDir",
+            type: "string",
+            isFilePath: true,
+            description: Diagnostics.Specifies_the_root_directory_of_input_files_Use_to_control_the_output_directory_structure_with_outDir,
+            paramType: Diagnostics.LOCATION,
+        },
         {
             name: "separateCompilation",
             type: "boolean",
diff --git a/src/compiler/diagnosticInformationMap.generated.ts b/src/compiler/diagnosticInformationMap.generated.ts
index f3e9c325da611..90f0ed0a0dfce 100644
--- a/src/compiler/diagnosticInformationMap.generated.ts
+++ b/src/compiler/diagnosticInformationMap.generated.ts
@@ -496,6 +496,8 @@ module ts {
         Suppress_noImplicitAny_errors_for_indexing_objects_lacking_index_signatures: { code: 6055, category: DiagnosticCategory.Message, key: "Suppress noImplicitAny errors for indexing objects lacking index signatures." },
         Do_not_emit_declarations_for_code_that_has_an_internal_annotation: { code: 6056, category: DiagnosticCategory.Message, key: "Do not emit declarations for code that has an '@internal' annotation." },
         Preserve_new_lines_when_emitting_code: { code: 6057, category: DiagnosticCategory.Message, key: "Preserve new-lines when emitting code." },
+        Specifies_the_root_directory_of_input_files_Use_to_control_the_output_directory_structure_with_outDir: { code: 6058, category: DiagnosticCategory.Message, key: "Specifies the root directory of input files. Use to control the output directory structure with --outDir." },
+        File_0_is_not_under_rootDir_1_rootDir_is_expected_to_contain_all_source_files: { code: 6059, category: DiagnosticCategory.Error, key: "File '{0}' is not under 'rootDir' '{1}'. 'rootDir' is expected to contain all source files." },
         Variable_0_implicitly_has_an_1_type: { code: 7005, category: DiagnosticCategory.Error, key: "Variable '{0}' implicitly has an '{1}' type." },
         Parameter_0_implicitly_has_an_1_type: { code: 7006, category: DiagnosticCategory.Error, key: "Parameter '{0}' implicitly has an '{1}' type." },
         Member_0_implicitly_has_an_1_type: { code: 7008, category: DiagnosticCategory.Error, key: "Member '{0}' implicitly has an '{1}' type." },
diff --git a/src/compiler/diagnosticMessages.json b/src/compiler/diagnosticMessages.json
index 61ce23c316bd5..48ef245c76612 100644
--- a/src/compiler/diagnosticMessages.json
+++ b/src/compiler/diagnosticMessages.json
@@ -1972,6 +1972,15 @@
         "category": "Message",
         "code": 6057
     },
+    "Specifies the root directory of input files. Use to control the output directory structure with --outDir.": {
+        "category": "Message",
+        "code": 6058
+    },
+    "File '{0}' is not under 'rootDir' '{1}'. 'rootDir' is expected to contain all source files.": {
+        "category": "Error",
+        "code": 6059
+    },
+
 
     "Variable '{0}' implicitly has an '{1}' type.": {
         "category": "Error",
diff --git a/src/compiler/program.ts b/src/compiler/program.ts
index a27f943dc7e5f..d49e01bd45d68 100644
--- a/src/compiler/program.ts
+++ b/src/compiler/program.ts
@@ -455,6 +455,66 @@ module ts {
             }
         }
 
+        function computeCommonSourceDirectory(sourceFiles: SourceFile[]): string {
+            let commonPathComponents: string[];
+            let currentDirectory = host.getCurrentDirectory();
+            forEach(files, sourceFile => {
+                // Each file contributes into common source file path
+                if (isDeclarationFile(sourceFile)) {
+                    return;
+                }
+
+                let sourcePathComponents = getNormalizedPathComponents(sourceFile.fileName, currentDirectory);
+                sourcePathComponents.pop(); // The base file name is not part of the common directory path
+
+                if (!commonPathComponents) {
+                    // first file
+                    commonPathComponents = sourcePathComponents;
+                    return;
+                }
+
+                for (let i = 0, n = Math.min(commonPathComponents.length, sourcePathComponents.length); i < n; i++) {
+                    if (commonPathComponents[i] !== sourcePathComponents[i]) {
+                        if (i === 0) {
+                            diagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_find_the_common_subdirectory_path_for_the_input_files));
+                            return;
+                        }
+
+                        // New common path found that is 0 -> i-1
+                        commonPathComponents.length = i;
+                        break;
+                    }
+                }
+
+                // If the sourcePathComponents was shorter than the commonPathComponents, truncate to the sourcePathComponents
+                if (sourcePathComponents.length < commonPathComponents.length) {
+                    commonPathComponents.length = sourcePathComponents.length;
+                }
+            });
+
+            return getNormalizedPathFromPathComponents(commonPathComponents);
+        }
+
+        function checkSourceFilesBelongToPath(sourceFiles: SourceFile[], rootDirectory: string): boolean {
+            let allFilesBelongToPath = true;
+            if (sourceFiles) {
+                let currentDirectory = host.getCurrentDirectory();
+                let absoluteRootDirectoryPath = host.getCanonicalFileName(getNormalizedAbsolutePath(rootDirectory, currentDirectory));
+
+                for (var sourceFile of sourceFiles) {
+                    if (!isDeclarationFile(sourceFile)) {
+                        let absoluteSourceFilePath = host.getCanonicalFileName(getNormalizedAbsolutePath(sourceFile.fileName, currentDirectory));
+                        if (absoluteSourceFilePath.indexOf(absoluteRootDirectoryPath) !== 0) {
+                            diagnostics.add(createCompilerDiagnostic(Diagnostics.File_0_is_not_under_rootDir_1_rootDir_is_expected_to_contain_all_source_files, sourceFile.fileName, options.rootDir));
+                            allFilesBelongToPath = false;
+                        }
+                    }
+                }
+            }
+
+            return allFilesBelongToPath;
+        }
+
         function verifyCompilerOptions() {
             if (options.separateCompilation) {
                 if (options.sourceMap) {
@@ -517,41 +577,16 @@ module ts {
                 (options.mapRoot &&  // there is --mapRoot specified and there would be multiple js files generated
                     (!options.out || firstExternalModuleSourceFile !== undefined))) {
 
-                let commonPathComponents: string[];
-                forEach(files, sourceFile => {
-                    // Each file contributes into common source file path
-                    if (!(sourceFile.flags & NodeFlags.DeclarationFile)
-                        && !fileExtensionIs(sourceFile.fileName, ".js")) {
-                        let sourcePathComponents = getNormalizedPathComponents(sourceFile.fileName, host.getCurrentDirectory());
-                        sourcePathComponents.pop(); // FileName is not part of directory
-                        if (commonPathComponents) {
-                            for (let i = 0; i < Math.min(commonPathComponents.length, sourcePathComponents.length); i++) {
-                                if (commonPathComponents[i] !== sourcePathComponents[i]) {
-                                    if (i === 0) {
-                                        diagnostics.add(createCompilerDiagnostic(Diagnostics.Cannot_find_the_common_subdirectory_path_for_the_input_files));
-                                        return;
-                                    }
-
-                                    // New common path found that is 0 -> i-1
-                                    commonPathComponents.length = i;
-                                    break;
-                                }
-                            }
-
-                            // If the fileComponent path completely matched and less than already found update the length
-                            if (sourcePathComponents.length < commonPathComponents.length) {
-                                commonPathComponents.length = sourcePathComponents.length;
-                            }
-                        }
-                        else {
-                            // first file
-                            commonPathComponents = sourcePathComponents;
-                        }
-                    }
-                });
+                if (options.rootDir && checkSourceFilesBelongToPath(files, options.rootDir)) {
+                    // If a rootDir is specified and is valid use it as the commonSourceDirectory
+                    commonSourceDirectory = getNormalizedAbsolutePath(options.rootDir, host.getCurrentDirectory());
+                }
+                else {
+                    // Compute the commonSourceDirectory from the input files
+                    commonSourceDirectory = computeCommonSourceDirectory(files);
+                }
 
-                commonSourceDirectory = getNormalizedPathFromPathComponents(commonPathComponents);
-                if (commonSourceDirectory) {
+                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
diff --git a/src/compiler/types.ts b/src/compiler/types.ts
index 9191a6999bf50..bff15a1ab9d03 100644
--- a/src/compiler/types.ts
+++ b/src/compiler/types.ts
@@ -1654,6 +1654,7 @@ module ts {
         preserveConstEnums?: boolean;
         project?: string;
         removeComments?: boolean;
+        rootDir?: string;
         sourceMap?: boolean;
         sourceRoot?: string;
         suppressImplicitAnyIndexErrors?: boolean;
diff --git a/src/harness/projectsRunner.ts b/src/harness/projectsRunner.ts
index 3291128a7a543..6823bfafac28a 100644
--- a/src/harness/projectsRunner.ts
+++ b/src/harness/projectsRunner.ts
@@ -18,6 +18,7 @@ interface ProjectRunnerTestCase {
     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 {
@@ -160,7 +161,8 @@ class ProjectRunner extends RunnerBase {
                     mapRoot: testCase.resolveMapRoot && testCase.mapRoot ? ts.sys.resolvePath(testCase.mapRoot) : testCase.mapRoot,
                     sourceRoot: testCase.resolveSourceRoot && testCase.sourceRoot ? ts.sys.resolvePath(testCase.sourceRoot) : testCase.sourceRoot,
                     module: moduleKind,
-                    noResolve: testCase.noResolve
+                    noResolve: testCase.noResolve,
+                    rootDir: testCase.rootDir
                 };
             }
 
@@ -344,6 +346,7 @@ class ProjectRunner extends RunnerBase {
                         baselineCheck: testCase.baselineCheck,
                         runTest: testCase.runTest,
                         bug: testCase.bug,
+                        rootDir: testCase.rootDir,
                         resolvedInputFiles: ts.map(compilerResult.program.getSourceFiles(), inputFile => inputFile.fileName),
                         emittedFiles: ts.map(compilerResult.outputFiles, outputFile => outputFile.emittedFileName)
                     };
diff --git a/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.d.ts b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.d.ts
new file mode 100644
index 0000000000000..8147620b2111b
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.d.ts
@@ -0,0 +1,2 @@
+declare class C {
+}
diff --git a/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.js b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.js
new file mode 100644
index 0000000000000..8840c2117cfd2
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.js
@@ -0,0 +1,6 @@
+var C = (function () {
+    function C() {
+    }
+    return C;
+})();
+//# sourceMappingURL=fileC.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.js.map b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.js.map
new file mode 100644
index 0000000000000..de54805ee5425
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/FolderC/fileC.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"fileC.js","sourceRoot":"","sources":["../../../../FolderA/FolderB/FolderC/fileC.ts"],"names":["C","C.constructor"],"mappings":"AAAA;IAAAA;IACAC,CAACA;IAADD,QAACA;AAADA,CAACA,AADD,IACC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.d.ts b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.d.ts
new file mode 100644
index 0000000000000..4ff813c3839e8
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.d.ts
@@ -0,0 +1,4 @@
+/// <reference path="FolderC/fileC.d.ts" />
+declare class B {
+    c: C;
+}
diff --git a/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.js b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.js
new file mode 100644
index 0000000000000..84af55d2d89e1
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.js
@@ -0,0 +1,7 @@
+/// <reference path='FolderC/fileC.ts'/>
+var B = (function () {
+    function B() {
+    }
+    return B;
+})();
+//# sourceMappingURL=fileB.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.js.map b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.js.map
new file mode 100644
index 0000000000000..d1c844d32478d
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/outdir/simple/FolderB/fileB.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"fileB.js","sourceRoot":"","sources":["../../../FolderA/FolderB/fileB.ts"],"names":["B","B.constructor"],"mappings":"AACA,AADA,wCAAwC;;IACxCA;IAEAC,CAACA;IAADD,QAACA;AAADA,CAACA,AAFD,IAEC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.json b/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.json
new file mode 100644
index 0000000000000..2ec18b3ac5acf
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.json
@@ -0,0 +1,25 @@
+{
+    "scenario": "rootDirectory: specify rootDirectory",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "sourceMap": true,
+    "declaration": true,
+    "baselineCheck": true,
+    "rootDir": "FolderA",
+    "resolvedInputFiles": [
+        "lib.d.ts",
+        "FolderA/FolderB/FolderC/fileC.ts",
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "emittedFiles": [
+        "outdir/simple/FolderB/FolderC/fileC.js.map",
+        "outdir/simple/FolderB/FolderC/fileC.js",
+        "outdir/simple/FolderB/FolderC/fileC.d.ts",
+        "outdir/simple/FolderB/fileB.js.map",
+        "outdir/simple/FolderB/fileB.js",
+        "outdir/simple/FolderB/fileB.d.ts"
+    ]
+}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.sourcemap.txt b/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.sourcemap.txt
new file mode 100644
index 0000000000000..83ee3b40181b4
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.sourcemap.txt
@@ -0,0 +1,123 @@
+===================================================================
+JsFile: fileC.js
+mapUrl: fileC.js.map
+sourceRoot: 
+sources: ../../../../FolderA/FolderB/FolderC/fileC.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:outdir/simple/FolderB/FolderC/fileC.js
+sourceFile:../../../../FolderA/FolderB/FolderC/fileC.ts
+-------------------------------------------------------------------
+>>>var C = (function () {
+1 >
+2 >^^^^^^^^^^^^^^^^^^^->
+1 >
+1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
+---
+>>>    function C() {
+1->^^^^
+2 >    ^^->
+1->
+1->Emitted(2, 5) Source(1, 1) + SourceIndex(0) name (C)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^->
+1->class C {
+  >
+2 >    }
+1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (C.constructor)
+2 >Emitted(3, 6) Source(2, 2) + SourceIndex(0) name (C.constructor)
+---
+>>>    return C;
+1->^^^^
+2 >    ^^^^^^^^
+1->
+2 >    }
+1->Emitted(4, 5) Source(2, 1) + SourceIndex(0) name (C)
+2 >Emitted(4, 13) Source(2, 2) + SourceIndex(0) name (C)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class C {
+  > }
+1 >Emitted(5, 1) Source(2, 1) + SourceIndex(0) name (C)
+2 >Emitted(5, 2) Source(2, 2) + SourceIndex(0) name (C)
+3 >Emitted(5, 2) Source(1, 1) + SourceIndex(0)
+4 >Emitted(5, 6) Source(2, 2) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=fileC.js.map===================================================================
+JsFile: fileB.js
+mapUrl: fileB.js.map
+sourceRoot: 
+sources: ../../../FolderA/FolderB/fileB.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:outdir/simple/FolderB/fileB.js
+sourceFile:../../../FolderA/FolderB/fileB.ts
+-------------------------------------------------------------------
+>>>/// <reference path='FolderC/fileC.ts'/>
+1 >
+2 >
+3 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1 >/// <reference path='FolderC/fileC.ts'/>
+  >
+2 >
+3 >/// <reference path='FolderC/fileC.ts'/>
+1 >Emitted(1, 1) Source(2, 1) + SourceIndex(0)
+2 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
+3 >Emitted(1, 41) Source(1, 41) + SourceIndex(0)
+---
+>>>var B = (function () {
+>>>    function B() {
+1 >^^^^
+2 >    ^^->
+1 >
+  >
+1 >Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (B)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^->
+1->class B {
+  >    public c: C;
+  >
+2 >    }
+1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (B.constructor)
+2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (B.constructor)
+---
+>>>    return B;
+1->^^^^
+2 >    ^^^^^^^^
+1->
+2 >    }
+1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (B)
+2 >Emitted(5, 13) Source(4, 2) + SourceIndex(0) name (B)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class B {
+  >     public c: C;
+  > }
+1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (B)
+2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (B)
+3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
+4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=fileB.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.d.ts b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.d.ts
new file mode 100644
index 0000000000000..8147620b2111b
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.d.ts
@@ -0,0 +1,2 @@
+declare class C {
+}
diff --git a/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.js b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.js
new file mode 100644
index 0000000000000..8840c2117cfd2
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.js
@@ -0,0 +1,6 @@
+var C = (function () {
+    function C() {
+    }
+    return C;
+})();
+//# sourceMappingURL=fileC.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.js.map b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.js.map
new file mode 100644
index 0000000000000..de54805ee5425
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/FolderC/fileC.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"fileC.js","sourceRoot":"","sources":["../../../../FolderA/FolderB/FolderC/fileC.ts"],"names":["C","C.constructor"],"mappings":"AAAA;IAAAA;IACAC,CAACA;IAADD,QAACA;AAADA,CAACA,AADD,IACC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.d.ts b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.d.ts
new file mode 100644
index 0000000000000..4ff813c3839e8
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.d.ts
@@ -0,0 +1,4 @@
+/// <reference path="FolderC/fileC.d.ts" />
+declare class B {
+    c: C;
+}
diff --git a/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.js b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.js
new file mode 100644
index 0000000000000..84af55d2d89e1
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.js
@@ -0,0 +1,7 @@
+/// <reference path='FolderC/fileC.ts'/>
+var B = (function () {
+    function B() {
+    }
+    return B;
+})();
+//# sourceMappingURL=fileB.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.js.map b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.js.map
new file mode 100644
index 0000000000000..d1c844d32478d
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/outdir/simple/FolderB/fileB.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"fileB.js","sourceRoot":"","sources":["../../../FolderA/FolderB/fileB.ts"],"names":["B","B.constructor"],"mappings":"AACA,AADA,wCAAwC;;IACxCA;IAEAC,CAACA;IAADD,QAACA;AAADA,CAACA,AAFD,IAEC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/node/rootDirectory.json b/tests/baselines/reference/project/rootDirectory/node/rootDirectory.json
new file mode 100644
index 0000000000000..2ec18b3ac5acf
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/rootDirectory.json
@@ -0,0 +1,25 @@
+{
+    "scenario": "rootDirectory: specify rootDirectory",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "sourceMap": true,
+    "declaration": true,
+    "baselineCheck": true,
+    "rootDir": "FolderA",
+    "resolvedInputFiles": [
+        "lib.d.ts",
+        "FolderA/FolderB/FolderC/fileC.ts",
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "emittedFiles": [
+        "outdir/simple/FolderB/FolderC/fileC.js.map",
+        "outdir/simple/FolderB/FolderC/fileC.js",
+        "outdir/simple/FolderB/FolderC/fileC.d.ts",
+        "outdir/simple/FolderB/fileB.js.map",
+        "outdir/simple/FolderB/fileB.js",
+        "outdir/simple/FolderB/fileB.d.ts"
+    ]
+}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/node/rootDirectory.sourcemap.txt b/tests/baselines/reference/project/rootDirectory/node/rootDirectory.sourcemap.txt
new file mode 100644
index 0000000000000..83ee3b40181b4
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/rootDirectory.sourcemap.txt
@@ -0,0 +1,123 @@
+===================================================================
+JsFile: fileC.js
+mapUrl: fileC.js.map
+sourceRoot: 
+sources: ../../../../FolderA/FolderB/FolderC/fileC.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:outdir/simple/FolderB/FolderC/fileC.js
+sourceFile:../../../../FolderA/FolderB/FolderC/fileC.ts
+-------------------------------------------------------------------
+>>>var C = (function () {
+1 >
+2 >^^^^^^^^^^^^^^^^^^^->
+1 >
+1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
+---
+>>>    function C() {
+1->^^^^
+2 >    ^^->
+1->
+1->Emitted(2, 5) Source(1, 1) + SourceIndex(0) name (C)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^->
+1->class C {
+  >
+2 >    }
+1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (C.constructor)
+2 >Emitted(3, 6) Source(2, 2) + SourceIndex(0) name (C.constructor)
+---
+>>>    return C;
+1->^^^^
+2 >    ^^^^^^^^
+1->
+2 >    }
+1->Emitted(4, 5) Source(2, 1) + SourceIndex(0) name (C)
+2 >Emitted(4, 13) Source(2, 2) + SourceIndex(0) name (C)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class C {
+  > }
+1 >Emitted(5, 1) Source(2, 1) + SourceIndex(0) name (C)
+2 >Emitted(5, 2) Source(2, 2) + SourceIndex(0) name (C)
+3 >Emitted(5, 2) Source(1, 1) + SourceIndex(0)
+4 >Emitted(5, 6) Source(2, 2) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=fileC.js.map===================================================================
+JsFile: fileB.js
+mapUrl: fileB.js.map
+sourceRoot: 
+sources: ../../../FolderA/FolderB/fileB.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:outdir/simple/FolderB/fileB.js
+sourceFile:../../../FolderA/FolderB/fileB.ts
+-------------------------------------------------------------------
+>>>/// <reference path='FolderC/fileC.ts'/>
+1 >
+2 >
+3 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1 >/// <reference path='FolderC/fileC.ts'/>
+  >
+2 >
+3 >/// <reference path='FolderC/fileC.ts'/>
+1 >Emitted(1, 1) Source(2, 1) + SourceIndex(0)
+2 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
+3 >Emitted(1, 41) Source(1, 41) + SourceIndex(0)
+---
+>>>var B = (function () {
+>>>    function B() {
+1 >^^^^
+2 >    ^^->
+1 >
+  >
+1 >Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (B)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^->
+1->class B {
+  >    public c: C;
+  >
+2 >    }
+1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (B.constructor)
+2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (B.constructor)
+---
+>>>    return B;
+1->^^^^
+2 >    ^^^^^^^^
+1->
+2 >    }
+1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (B)
+2 >Emitted(5, 13) Source(4, 2) + SourceIndex(0) name (B)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class B {
+  >     public c: C;
+  > }
+1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (B)
+2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (B)
+3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
+4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=fileB.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/FolderC/fileC.d.ts b/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/FolderC/fileC.d.ts
new file mode 100644
index 0000000000000..8147620b2111b
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/FolderC/fileC.d.ts
@@ -0,0 +1,2 @@
+declare class C {
+}
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/FolderC/fileC.js b/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/FolderC/fileC.js
new file mode 100644
index 0000000000000..325ac60ee3288
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/FolderC/fileC.js
@@ -0,0 +1,5 @@
+var C = (function () {
+    function C() {
+    }
+    return C;
+})();
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/fileB.d.ts b/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/fileB.d.ts
new file mode 100644
index 0000000000000..4ff813c3839e8
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/fileB.d.ts
@@ -0,0 +1,4 @@
+/// <reference path="FolderC/fileC.d.ts" />
+declare class B {
+    c: C;
+}
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/fileB.js b/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/fileB.js
new file mode 100644
index 0000000000000..99199ca1742b3
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/outdir/simple/fileB.js
@@ -0,0 +1,6 @@
+/// <reference path='FolderC/fileC.ts'/>
+var B = (function () {
+    function B() {
+    }
+    return B;
+})();
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt
new file mode 100644
index 0000000000000..dfbdd67968588
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt
@@ -0,0 +1,14 @@
+error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
+
+
+!!! error TS6059: File 'fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
+==== FolderA/FolderB/FolderC/fileC.ts (0 errors) ====
+    class C {
+    }
+    
+==== FolderA/FolderB/fileB.ts (0 errors) ====
+    /// <reference path='FolderC/fileC.ts'/>
+    class B {
+        public c: C;
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.json b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.json
new file mode 100644
index 0000000000000..fdde42592ca8d
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.json
@@ -0,0 +1,22 @@
+{
+    "scenario": "rootDirectory: Files outside the rootDirectory",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "declaration": true,
+    "baselineCheck": true,
+    "rootDir": "FolderA/FolderB/FolderC",
+    "resolvedInputFiles": [
+        "lib.d.ts",
+        "FolderA/FolderB/FolderC/fileC.ts",
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "emittedFiles": [
+        "outdir/simple/FolderC/fileC.js",
+        "outdir/simple/FolderC/fileC.d.ts",
+        "outdir/simple/fileB.js",
+        "outdir/simple/fileB.d.ts"
+    ]
+}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/FolderC/fileC.d.ts b/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/FolderC/fileC.d.ts
new file mode 100644
index 0000000000000..8147620b2111b
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/FolderC/fileC.d.ts
@@ -0,0 +1,2 @@
+declare class C {
+}
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/FolderC/fileC.js b/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/FolderC/fileC.js
new file mode 100644
index 0000000000000..325ac60ee3288
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/FolderC/fileC.js
@@ -0,0 +1,5 @@
+var C = (function () {
+    function C() {
+    }
+    return C;
+})();
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/fileB.d.ts b/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/fileB.d.ts
new file mode 100644
index 0000000000000..4ff813c3839e8
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/fileB.d.ts
@@ -0,0 +1,4 @@
+/// <reference path="FolderC/fileC.d.ts" />
+declare class B {
+    c: C;
+}
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/fileB.js b/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/fileB.js
new file mode 100644
index 0000000000000..99199ca1742b3
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/outdir/simple/fileB.js
@@ -0,0 +1,6 @@
+/// <reference path='FolderC/fileC.ts'/>
+var B = (function () {
+    function B() {
+    }
+    return B;
+})();
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt
new file mode 100644
index 0000000000000..dfbdd67968588
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt
@@ -0,0 +1,14 @@
+error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
+
+
+!!! error TS6059: File 'fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
+==== FolderA/FolderB/FolderC/fileC.ts (0 errors) ====
+    class C {
+    }
+    
+==== FolderA/FolderB/fileB.ts (0 errors) ====
+    /// <reference path='FolderC/fileC.ts'/>
+    class B {
+        public c: C;
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.json b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.json
new file mode 100644
index 0000000000000..fdde42592ca8d
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.json
@@ -0,0 +1,22 @@
+{
+    "scenario": "rootDirectory: Files outside the rootDirectory",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "declaration": true,
+    "baselineCheck": true,
+    "rootDir": "FolderA/FolderB/FolderC",
+    "resolvedInputFiles": [
+        "lib.d.ts",
+        "FolderA/FolderB/FolderC/fileC.ts",
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "emittedFiles": [
+        "outdir/simple/FolderC/fileC.js",
+        "outdir/simple/FolderC/fileC.d.ts",
+        "outdir/simple/fileB.js",
+        "outdir/simple/fileB.d.ts"
+    ]
+}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/FolderC/fileC.js b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/FolderC/fileC.js
new file mode 100644
index 0000000000000..8840c2117cfd2
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/FolderC/fileC.js
@@ -0,0 +1,6 @@
+var C = (function () {
+    function C() {
+    }
+    return C;
+})();
+//# sourceMappingURL=fileC.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/FolderC/fileC.js.map b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/FolderC/fileC.js.map
new file mode 100644
index 0000000000000..9a35f3fbc3ecc
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/FolderC/fileC.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"fileC.js","sourceRoot":"SourceRootPath/","sources":["FolderB/FolderC/fileC.ts"],"names":["C","C.constructor"],"mappings":"AAAA;IAAAA;IACAC,CAACA;IAADD,QAACA;AAADA,CAACA,AADD,IACC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/fileB.js b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/fileB.js
new file mode 100644
index 0000000000000..84af55d2d89e1
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/fileB.js
@@ -0,0 +1,7 @@
+/// <reference path='FolderC/fileC.ts'/>
+var B = (function () {
+    function B() {
+    }
+    return B;
+})();
+//# sourceMappingURL=fileB.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/fileB.js.map b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/fileB.js.map
new file mode 100644
index 0000000000000..16a4538542059
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/outdir/simple/FolderB/fileB.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"fileB.js","sourceRoot":"SourceRootPath/","sources":["FolderB/fileB.ts"],"names":["B","B.constructor"],"mappings":"AACA,AADA,wCAAwC;;IACxCA;IAEAC,CAACA;IAADD,QAACA;AAADA,CAACA,AAFD,IAEC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/rootDirectoryWithSourceRoot.json b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/rootDirectoryWithSourceRoot.json
new file mode 100644
index 0000000000000..deb12150736aa
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/rootDirectoryWithSourceRoot.json
@@ -0,0 +1,23 @@
+{
+    "scenario": "rootDirectory: specify rootDirectory with sourceRoot",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "sourceMap": true,
+    "sourceRoot": "SourceRootPath",
+    "baselineCheck": true,
+    "rootDir": "FolderA",
+    "resolvedInputFiles": [
+        "lib.d.ts",
+        "FolderA/FolderB/FolderC/fileC.ts",
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "emittedFiles": [
+        "outdir/simple/FolderB/FolderC/fileC.js.map",
+        "outdir/simple/FolderB/FolderC/fileC.js",
+        "outdir/simple/FolderB/fileB.js.map",
+        "outdir/simple/FolderB/fileB.js"
+    ]
+}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/rootDirectoryWithSourceRoot.sourcemap.txt b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/rootDirectoryWithSourceRoot.sourcemap.txt
new file mode 100644
index 0000000000000..7c5843bdd3433
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/amd/rootDirectoryWithSourceRoot.sourcemap.txt
@@ -0,0 +1,123 @@
+===================================================================
+JsFile: fileC.js
+mapUrl: fileC.js.map
+sourceRoot: SourceRootPath/
+sources: FolderB/FolderC/fileC.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:outdir/simple/FolderB/FolderC/fileC.js
+sourceFile:FolderB/FolderC/fileC.ts
+-------------------------------------------------------------------
+>>>var C = (function () {
+1 >
+2 >^^^^^^^^^^^^^^^^^^^->
+1 >
+1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
+---
+>>>    function C() {
+1->^^^^
+2 >    ^^->
+1->
+1->Emitted(2, 5) Source(1, 1) + SourceIndex(0) name (C)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^->
+1->class C {
+  >
+2 >    }
+1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (C.constructor)
+2 >Emitted(3, 6) Source(2, 2) + SourceIndex(0) name (C.constructor)
+---
+>>>    return C;
+1->^^^^
+2 >    ^^^^^^^^
+1->
+2 >    }
+1->Emitted(4, 5) Source(2, 1) + SourceIndex(0) name (C)
+2 >Emitted(4, 13) Source(2, 2) + SourceIndex(0) name (C)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class C {
+  > }
+1 >Emitted(5, 1) Source(2, 1) + SourceIndex(0) name (C)
+2 >Emitted(5, 2) Source(2, 2) + SourceIndex(0) name (C)
+3 >Emitted(5, 2) Source(1, 1) + SourceIndex(0)
+4 >Emitted(5, 6) Source(2, 2) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=fileC.js.map===================================================================
+JsFile: fileB.js
+mapUrl: fileB.js.map
+sourceRoot: SourceRootPath/
+sources: FolderB/fileB.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:outdir/simple/FolderB/fileB.js
+sourceFile:FolderB/fileB.ts
+-------------------------------------------------------------------
+>>>/// <reference path='FolderC/fileC.ts'/>
+1 >
+2 >
+3 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1 >/// <reference path='FolderC/fileC.ts'/>
+  >
+2 >
+3 >/// <reference path='FolderC/fileC.ts'/>
+1 >Emitted(1, 1) Source(2, 1) + SourceIndex(0)
+2 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
+3 >Emitted(1, 41) Source(1, 41) + SourceIndex(0)
+---
+>>>var B = (function () {
+>>>    function B() {
+1 >^^^^
+2 >    ^^->
+1 >
+  >
+1 >Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (B)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^->
+1->class B {
+  >    public c: C;
+  >
+2 >    }
+1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (B.constructor)
+2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (B.constructor)
+---
+>>>    return B;
+1->^^^^
+2 >    ^^^^^^^^
+1->
+2 >    }
+1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (B)
+2 >Emitted(5, 13) Source(4, 2) + SourceIndex(0) name (B)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class B {
+  >     public c: C;
+  > }
+1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (B)
+2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (B)
+3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
+4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=fileB.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/FolderC/fileC.js b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/FolderC/fileC.js
new file mode 100644
index 0000000000000..8840c2117cfd2
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/FolderC/fileC.js
@@ -0,0 +1,6 @@
+var C = (function () {
+    function C() {
+    }
+    return C;
+})();
+//# sourceMappingURL=fileC.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/FolderC/fileC.js.map b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/FolderC/fileC.js.map
new file mode 100644
index 0000000000000..9a35f3fbc3ecc
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/FolderC/fileC.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"fileC.js","sourceRoot":"SourceRootPath/","sources":["FolderB/FolderC/fileC.ts"],"names":["C","C.constructor"],"mappings":"AAAA;IAAAA;IACAC,CAACA;IAADD,QAACA;AAADA,CAACA,AADD,IACC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/fileB.js b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/fileB.js
new file mode 100644
index 0000000000000..84af55d2d89e1
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/fileB.js
@@ -0,0 +1,7 @@
+/// <reference path='FolderC/fileC.ts'/>
+var B = (function () {
+    function B() {
+    }
+    return B;
+})();
+//# sourceMappingURL=fileB.js.map
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/fileB.js.map b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/fileB.js.map
new file mode 100644
index 0000000000000..16a4538542059
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/outdir/simple/FolderB/fileB.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"fileB.js","sourceRoot":"SourceRootPath/","sources":["FolderB/fileB.ts"],"names":["B","B.constructor"],"mappings":"AACA,AADA,wCAAwC;;IACxCA;IAEAC,CAACA;IAADD,QAACA;AAADA,CAACA,AAFD,IAEC"}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/rootDirectoryWithSourceRoot.json b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/rootDirectoryWithSourceRoot.json
new file mode 100644
index 0000000000000..deb12150736aa
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/rootDirectoryWithSourceRoot.json
@@ -0,0 +1,23 @@
+{
+    "scenario": "rootDirectory: specify rootDirectory with sourceRoot",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "sourceMap": true,
+    "sourceRoot": "SourceRootPath",
+    "baselineCheck": true,
+    "rootDir": "FolderA",
+    "resolvedInputFiles": [
+        "lib.d.ts",
+        "FolderA/FolderB/FolderC/fileC.ts",
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "emittedFiles": [
+        "outdir/simple/FolderB/FolderC/fileC.js.map",
+        "outdir/simple/FolderB/FolderC/fileC.js",
+        "outdir/simple/FolderB/fileB.js.map",
+        "outdir/simple/FolderB/fileB.js"
+    ]
+}
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/rootDirectoryWithSourceRoot.sourcemap.txt b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/rootDirectoryWithSourceRoot.sourcemap.txt
new file mode 100644
index 0000000000000..7c5843bdd3433
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectoryWithSourceRoot/node/rootDirectoryWithSourceRoot.sourcemap.txt
@@ -0,0 +1,123 @@
+===================================================================
+JsFile: fileC.js
+mapUrl: fileC.js.map
+sourceRoot: SourceRootPath/
+sources: FolderB/FolderC/fileC.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:outdir/simple/FolderB/FolderC/fileC.js
+sourceFile:FolderB/FolderC/fileC.ts
+-------------------------------------------------------------------
+>>>var C = (function () {
+1 >
+2 >^^^^^^^^^^^^^^^^^^^->
+1 >
+1 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
+---
+>>>    function C() {
+1->^^^^
+2 >    ^^->
+1->
+1->Emitted(2, 5) Source(1, 1) + SourceIndex(0) name (C)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^->
+1->class C {
+  >
+2 >    }
+1->Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (C.constructor)
+2 >Emitted(3, 6) Source(2, 2) + SourceIndex(0) name (C.constructor)
+---
+>>>    return C;
+1->^^^^
+2 >    ^^^^^^^^
+1->
+2 >    }
+1->Emitted(4, 5) Source(2, 1) + SourceIndex(0) name (C)
+2 >Emitted(4, 13) Source(2, 2) + SourceIndex(0) name (C)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class C {
+  > }
+1 >Emitted(5, 1) Source(2, 1) + SourceIndex(0) name (C)
+2 >Emitted(5, 2) Source(2, 2) + SourceIndex(0) name (C)
+3 >Emitted(5, 2) Source(1, 1) + SourceIndex(0)
+4 >Emitted(5, 6) Source(2, 2) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=fileC.js.map===================================================================
+JsFile: fileB.js
+mapUrl: fileB.js.map
+sourceRoot: SourceRootPath/
+sources: FolderB/fileB.ts
+===================================================================
+-------------------------------------------------------------------
+emittedFile:outdir/simple/FolderB/fileB.js
+sourceFile:FolderB/fileB.ts
+-------------------------------------------------------------------
+>>>/// <reference path='FolderC/fileC.ts'/>
+1 >
+2 >
+3 >^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1 >/// <reference path='FolderC/fileC.ts'/>
+  >
+2 >
+3 >/// <reference path='FolderC/fileC.ts'/>
+1 >Emitted(1, 1) Source(2, 1) + SourceIndex(0)
+2 >Emitted(1, 1) Source(1, 1) + SourceIndex(0)
+3 >Emitted(1, 41) Source(1, 41) + SourceIndex(0)
+---
+>>>var B = (function () {
+>>>    function B() {
+1 >^^^^
+2 >    ^^->
+1 >
+  >
+1 >Emitted(3, 5) Source(2, 1) + SourceIndex(0) name (B)
+---
+>>>    }
+1->^^^^
+2 >    ^
+3 >     ^^^^^^^^^->
+1->class B {
+  >    public c: C;
+  >
+2 >    }
+1->Emitted(4, 5) Source(4, 1) + SourceIndex(0) name (B.constructor)
+2 >Emitted(4, 6) Source(4, 2) + SourceIndex(0) name (B.constructor)
+---
+>>>    return B;
+1->^^^^
+2 >    ^^^^^^^^
+1->
+2 >    }
+1->Emitted(5, 5) Source(4, 1) + SourceIndex(0) name (B)
+2 >Emitted(5, 13) Source(4, 2) + SourceIndex(0) name (B)
+---
+>>>})();
+1 >
+2 >^
+3 > 
+4 > ^^^^
+5 >     ^^^^^^^^^^^^^^^^^^^^^^^^^^^->
+1 >
+2 >}
+3 > 
+4 > class B {
+  >     public c: C;
+  > }
+1 >Emitted(6, 1) Source(4, 1) + SourceIndex(0) name (B)
+2 >Emitted(6, 2) Source(4, 2) + SourceIndex(0) name (B)
+3 >Emitted(6, 2) Source(2, 1) + SourceIndex(0)
+4 >Emitted(6, 6) Source(4, 2) + SourceIndex(0)
+---
+>>>//# sourceMappingURL=fileB.js.map
\ No newline at end of file
diff --git a/tests/cases/project/rootDirectory.json b/tests/cases/project/rootDirectory.json
new file mode 100644
index 0000000000000..6dad3982f93ad
--- /dev/null
+++ b/tests/cases/project/rootDirectory.json
@@ -0,0 +1,12 @@
+{
+    "scenario": "rootDirectory: specify rootDirectory",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "rootDir": "FolderA",
+    "sourceMap":  true,
+    "declaration": true,
+    "baselineCheck": true
+}
\ No newline at end of file
diff --git a/tests/cases/project/rootDirectoryErrors.json b/tests/cases/project/rootDirectoryErrors.json
new file mode 100644
index 0000000000000..18a256486d026
--- /dev/null
+++ b/tests/cases/project/rootDirectoryErrors.json
@@ -0,0 +1,11 @@
+{
+    "scenario": "rootDirectory: Files outside the rootDirectory",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "rootDir": "FolderA/FolderB/FolderC",
+    "declaration": true,
+    "baselineCheck": true
+}
\ No newline at end of file
diff --git a/tests/cases/project/rootDirectoryWithSourceRoot.json b/tests/cases/project/rootDirectoryWithSourceRoot.json
new file mode 100644
index 0000000000000..227b55c13fd9d
--- /dev/null
+++ b/tests/cases/project/rootDirectoryWithSourceRoot.json
@@ -0,0 +1,12 @@
+{
+    "scenario": "rootDirectory: specify rootDirectory with sourceRoot",
+    "projectRoot": "tests/cases/projects/rootDirectory",
+    "inputFiles": [
+        "FolderA/FolderB/fileB.ts"
+    ],
+    "outDir": "outdir/simple",
+    "rootDir": "FolderA",
+    "sourceMap": true,
+    "sourceRoot":  "SourceRootPath",
+    "baselineCheck": true
+}
\ No newline at end of file
diff --git a/tests/cases/projects/rootDirectory/FolderA/FolderB/FolderC/fileC.ts b/tests/cases/projects/rootDirectory/FolderA/FolderB/FolderC/fileC.ts
new file mode 100644
index 0000000000000..f4885b3ca74d4
--- /dev/null
+++ b/tests/cases/projects/rootDirectory/FolderA/FolderB/FolderC/fileC.ts
@@ -0,0 +1,2 @@
+class C {
+}
diff --git a/tests/cases/projects/rootDirectory/FolderA/FolderB/fileB.ts b/tests/cases/projects/rootDirectory/FolderA/FolderB/fileB.ts
new file mode 100644
index 0000000000000..03e0f4ad3327d
--- /dev/null
+++ b/tests/cases/projects/rootDirectory/FolderA/FolderB/fileB.ts
@@ -0,0 +1,4 @@
+/// <reference path='FolderC/fileC.ts'/>
+class B {
+    public c: C;
+}