Index: include/clang/Tooling/Tooling.h
===================================================================
--- include/clang/Tooling/Tooling.h
+++ include/clang/Tooling/Tooling.h
@@ -202,12 +202,16 @@
 /// \param PCHContainerOps The PCHContainerOperations for loading and creating
 /// clang modules.
 ///
+/// \param HonorDependencyOutputOptions generate dependency files if -M or
+/// a related option appears on the command line.
+///
 /// \return The resulting AST or null if an error occurred.
 std::unique_ptr<ASTUnit> buildASTFromCodeWithArgs(
     const Twine &Code, const std::vector<std::string> &Args,
     const Twine &FileName = "input.cc", const Twine &ToolName = "clang-tool",
     std::shared_ptr<PCHContainerOperations> PCHContainerOps =
-        std::make_shared<PCHContainerOperations>());
+      std::make_shared<PCHContainerOperations>(),
+    bool HonorDependencyOutputOptions = false);
 
 /// \brief Utility to run a FrontendAction in a single clang invocation.
 class ToolInvocation {
@@ -241,6 +245,9 @@
 
   ~ToolInvocation();
 
+  /// \brief Remove -M, -MD, -MF, -MM from the CommandLine.
+  void RemoveDependencyFileArgs();
+
   /// \brief Set a \c DiagnosticConsumer to use during parsing.
   void setDiagnosticConsumer(DiagnosticConsumer *DiagConsumer) {
     this->DiagConsumer = DiagConsumer;
@@ -255,8 +262,11 @@
 
   /// \brief Run the clang invocation.
   ///
+  /// \param HonorDependencyOutputOptions generate a .d file if
+  /// -M or a related option appears on the command line.
+  ///
   /// \returns True if there were no errors during execution.
-  bool run();
+  bool run(bool HonorDependencyOutputOptions = false);
 
  private:
   void addFileMappingsTo(SourceManager &SourceManager);
@@ -451,9 +461,14 @@
                                     StringRef InvokedAs);
 
 /// \brief Creates a \c CompilerInvocation.
+/// \param Diagnostics where and how to report diagnostics.
+/// \param CC1Args arguments to the compiler.
+/// \param HonorDependencyOutputOptions generate dependency files if -M or
+/// a related option appears on the command line.
 clang::CompilerInvocation *newInvocation(
     clang::DiagnosticsEngine *Diagnostics,
-    const llvm::opt::ArgStringList &CC1Args);
+    const llvm::opt::ArgStringList &CC1Args,
+    bool HonorDependencyOutputOptions = false);
 
 } // end namespace tooling
 } // end namespace clang
Index: lib/Tooling/Tooling.cpp
===================================================================
--- lib/Tooling/Tooling.cpp
+++ lib/Tooling/Tooling.cpp
@@ -92,7 +92,8 @@
 /// \brief Returns a clang build invocation initialized from the CC1 flags.
 clang::CompilerInvocation *newInvocation(
     clang::DiagnosticsEngine *Diagnostics,
-    const llvm::opt::ArgStringList &CC1Args) {
+    const llvm::opt::ArgStringList &CC1Args,
+    bool HonorDependencyOutputOptions) {
   assert(!CC1Args.empty() && "Must at least contain the program name!");
   clang::CompilerInvocation *Invocation = new clang::CompilerInvocation;
   clang::CompilerInvocation::CreateFromArgs(
@@ -100,7 +101,8 @@
       *Diagnostics);
   Invocation->getFrontendOpts().DisableFree = false;
   Invocation->getCodeGenOpts().DisableFree = false;
-  Invocation->getDependencyOutputOpts() = DependencyOutputOptions();
+  if (!HonorDependencyOutputOptions)
+    Invocation->getDependencyOutputOpts() = DependencyOutputOptions();
   return Invocation;
 }
 
@@ -237,7 +239,7 @@
   MappedFileContents[PathStorage] = Content;
 }
 
-bool ToolInvocation::run() {
+bool ToolInvocation::run(bool HonorDependencyOutputOptions) {
   std::vector<const char*> Argv;
   for (const std::string &Str : CommandLine)
     Argv.push_back(Str.c_str());
@@ -268,7 +270,7 @@
     return false;
   }
   std::unique_ptr<clang::CompilerInvocation> Invocation(
-      newInvocation(&Diagnostics, *CC1Args));
+      newInvocation(&Diagnostics, *CC1Args, HonorDependencyOutputOptions));
   // FIXME: remove this when all users have migrated!
   for (const auto &It : MappedFileContents) {
     // Inject the code as the given file name into the preprocessor options.
@@ -510,7 +512,8 @@
 std::unique_ptr<ASTUnit> buildASTFromCodeWithArgs(
     const Twine &Code, const std::vector<std::string> &Args,
     const Twine &FileName, const Twine &ToolName,
-    std::shared_ptr<PCHContainerOperations> PCHContainerOps) {
+    std::shared_ptr<PCHContainerOperations> PCHContainerOps,
+    bool HonorDependencyOutputOptions) {
   SmallString<16> FileNameStorage;
   StringRef FileNameRef = FileName.toNullTerminatedStringRef(FileNameStorage);
 
@@ -530,7 +533,7 @@
   InMemoryFileSystem->addFile(FileNameRef, 0,
                               llvm::MemoryBuffer::getMemBuffer(
                                   Code.toNullTerminatedStringRef(CodeStorage)));
-  if (!Invocation.run())
+  if (!Invocation.run(HonorDependencyOutputOptions))
     return nullptr;
 
   assert(ASTs.size() == 1);