Index: include/clang/Tooling/Tooling.h
===================================================================
--- include/clang/Tooling/Tooling.h
+++ include/clang/Tooling/Tooling.h
@@ -296,22 +296,24 @@
 /// arguments adjuster by calling the appendArgumentsAdjuster() method.
 class ClangTool {
 public:
-  /// \brief Constructs a clang tool to run over a list of files.
+  /// \brief Constructs a Clang tool to run over a list of files.
   ///
   /// \param Compilations The CompilationDatabase which contains the compile
   ///        command lines for the given source paths.
   /// \param SourcePaths The source files to run over. If a source files is
   ///        not found in Compilations, it is skipped.
   /// \param PCHContainerOps The PCHContainerOperations for loading and creating
-  /// clang modules.
-  /// \param BaseFS VFS used for all underlying file accesses when running the
-  /// tool.
+  ///        clang modules.
+  /// \param FileSystem The Virtual File System that is used to retrieve file
+  ///        contents by the tool.
+  /// \param AlsoUseRealFileSystem Sets the Clang tool to also use the machine's
+  ///        filesystem as the lowest layer to retrieve files from.
   ClangTool(const CompilationDatabase &Compilations,
             ArrayRef<std::string> SourcePaths,
             std::shared_ptr<PCHContainerOperations> PCHContainerOps =
                 std::make_shared<PCHContainerOperations>(),
-            IntrusiveRefCntPtr<vfs::FileSystem> BaseFS =
-                vfs::getRealFileSystem());
+            IntrusiveRefCntPtr<vfs::FileSystem> FileSystem = nullptr,
+            bool AlsoUseRealFileSystem = true);
 
   ~ClangTool();
 
Index: lib/Tooling/Tooling.cpp
===================================================================
--- lib/Tooling/Tooling.cpp
+++ lib/Tooling/Tooling.cpp
@@ -358,13 +358,22 @@
 ClangTool::ClangTool(const CompilationDatabase &Compilations,
                      ArrayRef<std::string> SourcePaths,
                      std::shared_ptr<PCHContainerOperations> PCHContainerOps,
-                     IntrusiveRefCntPtr<vfs::FileSystem> BaseFS)
+                     IntrusiveRefCntPtr<vfs::FileSystem> FileSystem,
+                     bool AlsoUseRealFileSystem)
     : Compilations(Compilations), SourcePaths(SourcePaths),
       PCHContainerOps(std::move(PCHContainerOps)),
-      OverlayFileSystem(new vfs::OverlayFileSystem(std::move(BaseFS))),
-      InMemoryFileSystem(new vfs::InMemoryFileSystem),
-      Files(new FileManager(FileSystemOptions(), OverlayFileSystem)) {
+      InMemoryFileSystem(new vfs::InMemoryFileSystem) {
+  assert(!(!AlsoUseRealFileSystem && !FileSystem) && "ClangTool initialized "
+         "without providing a FileSystem to get files from!");
+  if (AlsoUseRealFileSystem) {
+    OverlayFileSystem = new vfs::OverlayFileSystem(vfs::getRealFileSystem());
+    if (FileSystem)
+      OverlayFileSystem->pushOverlay(FileSystem);
+  }
+  else
+    OverlayFileSystem = new vfs::OverlayFileSystem(FileSystem);
   OverlayFileSystem->pushOverlay(InMemoryFileSystem);
+  Files = new FileManager(FileSystemOptions(), OverlayFileSystem);
   appendArgumentsAdjuster(getClangStripOutputAdjuster());
   appendArgumentsAdjuster(getClangSyntaxOnlyAdjuster());
   appendArgumentsAdjuster(getClangStripDependencyFileAdjuster());
Index: unittests/Tooling/ToolingTest.cpp
===================================================================
--- unittests/Tooling/ToolingTest.cpp
+++ unittests/Tooling/ToolingTest.cpp
@@ -402,24 +402,48 @@
   EXPECT_FALSE(Found);
 }
 
-TEST(ClangToolTest, BaseVirtualFileSystemUsage) {
+TEST(ClangToolVFSTest, MustGiveFileSystem) {
+  FixedCompilationDatabase Compilations("/", std::vector<std::string>());
+
+  EXPECT_DEATH(ClangTool(Compilations, std::vector<std::string>(),
+                         std::make_shared<PCHContainerOperations>(),
+                         nullptr, false),
+               "without providing a FileSystem");
+}
+
+TEST(ClangToolVFSTest, VirtualFileSystemUsage) {
   FixedCompilationDatabase Compilations("/", std::vector<std::string>());
-  llvm::IntrusiveRefCntPtr<vfs::OverlayFileSystem> OverlayFileSystem(
-      new vfs::OverlayFileSystem(vfs::getRealFileSystem()));
   llvm::IntrusiveRefCntPtr<vfs::InMemoryFileSystem> InMemoryFileSystem(
-      new vfs::InMemoryFileSystem);
-  OverlayFileSystem->pushOverlay(InMemoryFileSystem);
+    new vfs::InMemoryFileSystem);
 
   InMemoryFileSystem->addFile(
-      "a.cpp", 0, llvm::MemoryBuffer::getMemBuffer("int main() {}"));
+    "/a.cpp", 0, llvm::MemoryBuffer::getMemBuffer("int main() {}"));
 
-  ClangTool Tool(Compilations, std::vector<std::string>(1, "a.cpp"),
-                 std::make_shared<PCHContainerOperations>(), OverlayFileSystem);
+  ClangTool Tool(Compilations, std::vector<std::string>(1, "/a.cpp"),
+                 std::make_shared<PCHContainerOperations>(),
+                 InMemoryFileSystem, false);
   std::unique_ptr<FrontendActionFactory> Action(
-      newFrontendActionFactory<SyntaxOnlyAction>());
+    newFrontendActionFactory<SyntaxOnlyAction>());
   EXPECT_EQ(0, Tool.run(Action.get()));
 }
 
+TEST(ClangToolVFSTest, VFSDoesntContainEveryFile) {
+  FixedCompilationDatabase Compilations("/", std::vector<std::string>());
+  llvm::IntrusiveRefCntPtr<vfs::InMemoryFileSystem> InMemoryFileSystem(
+    new vfs::InMemoryFileSystem);
+
+  InMemoryFileSystem->addFile(
+    "/a.cpp", 0, llvm::MemoryBuffer::getMemBuffer("#include <cstdio>\n"
+                                                   "int main() {}"));
+
+  ClangTool Tool(Compilations, std::vector<std::string>(1, "/a.cpp"),
+                 std::make_shared<PCHContainerOperations>(),
+                 InMemoryFileSystem, false);
+  std::unique_ptr<FrontendActionFactory> Action(
+    newFrontendActionFactory<SyntaxOnlyAction>());
+  EXPECT_NE(0, Tool.run(Action.get()));
+}
+
 // Check getClangStripDependencyFileAdjuster doesn't strip args after -MD/-MMD.
 TEST(ClangToolTest, StripDependencyFileAdjuster) {
   FixedCompilationDatabase Compilations("/", {"-MD", "-c", "-MMD", "-w"});