Index: clang-tidy/ClangTidy.h
===================================================================
--- clang-tidy/ClangTidy.h
+++ clang-tidy/ClangTidy.h
@@ -227,6 +227,7 @@
 void runClangTidy(clang::tidy::ClangTidyContext &Context,
                   const tooling::CompilationDatabase &Compilations,
                   ArrayRef<std::string> InputFiles,
+                  llvm::IntrusiveRefCntPtr<vfs::FileSystem> BaseFS,
                   ProfileData *Profile = nullptr);
 
 // FIXME: This interface will need to be significantly extended to be useful.
@@ -236,7 +237,8 @@
 /// Errors containing fixes are automatically applied and reformatted. If no
 /// clang-format configuration file is found, the given \P FormatStyle is used.
 void handleErrors(ClangTidyContext &Context, bool Fix,
-                  unsigned &WarningsAsErrorsCount);
+                  unsigned &WarningsAsErrorsCount,
+                  llvm::IntrusiveRefCntPtr<vfs::FileSystem> BaseFS);
 
 /// \brief Serializes replacements into YAML and writes them to the specified
 /// output stream.
Index: clang-tidy/ClangTidy.cpp
===================================================================
--- clang-tidy/ClangTidy.cpp
+++ clang-tidy/ClangTidy.cpp
@@ -89,8 +89,9 @@
 
 class ErrorReporter {
 public:
-  ErrorReporter(ClangTidyContext &Context, bool ApplyFixes)
-      : Files(FileSystemOptions()), DiagOpts(new DiagnosticOptions()),
+  ErrorReporter(ClangTidyContext &Context, bool ApplyFixes,
+                llvm::IntrusiveRefCntPtr<vfs::FileSystem> BaseFS)
+      : Files(FileSystemOptions(), BaseFS), DiagOpts(new DiagnosticOptions()),
         DiagPrinter(new TextDiagnosticPrinter(llvm::outs(), &*DiagOpts)),
         Diags(IntrusiveRefCntPtr<DiagnosticIDs>(new DiagnosticIDs), &*DiagOpts,
               DiagPrinter),
@@ -474,8 +475,11 @@
 
 void runClangTidy(clang::tidy::ClangTidyContext &Context,
                   const CompilationDatabase &Compilations,
-                  ArrayRef<std::string> InputFiles, ProfileData *Profile) {
-  ClangTool Tool(Compilations, InputFiles);
+                  ArrayRef<std::string> InputFiles,
+                  llvm::IntrusiveRefCntPtr<vfs::FileSystem> BaseFS,
+                  ProfileData *Profile) {
+  ClangTool Tool(Compilations, InputFiles,
+                 std::make_shared<PCHContainerOperations>(), BaseFS);
 
   // Add extra arguments passed by the clang-tidy command-line.
   ArgumentsAdjuster PerFileExtraArgumentsInserter =
@@ -546,8 +550,9 @@
 }
 
 void handleErrors(ClangTidyContext &Context, bool Fix,
-                  unsigned &WarningsAsErrorsCount) {
-  ErrorReporter Reporter(Context, Fix);
+                  unsigned &WarningsAsErrorsCount,
+                  llvm::IntrusiveRefCntPtr<vfs::FileSystem> BaseFS) {
+  ErrorReporter Reporter(Context, Fix, BaseFS);
   vfs::FileSystem &FileSystem =
       *Reporter.getSourceManager().getFileManager().getVirtualFileSystem();
   auto InitialWorkingDir = FileSystem.getCurrentWorkingDirectory();
Index: clang-tidy/tool/ClangTidyMain.cpp
===================================================================
--- clang-tidy/tool/ClangTidyMain.cpp
+++ clang-tidy/tool/ClangTidyMain.cpp
@@ -209,6 +209,13 @@
                            cl::init(false),
                            cl::cat(ClangTidyCategory));
 
+static cl::opt<std::string> VfsOverlay("vfsoverlay", cl::desc(R"(
+Overlay the virtual filesystem described by file
+over the real file system.
+)"),
+                                       cl::value_desc("filename"),
+                                       cl::cat(ClangTidyCategory));
+
 namespace clang {
 namespace tidy {
 
@@ -330,6 +337,30 @@
                                                 OverrideOptions);
 }
 
+llvm::IntrusiveRefCntPtr<vfs::FileSystem>
+getVfsOverlayFromFile(const std::string &OverlayFile) {
+  llvm::IntrusiveRefCntPtr<vfs::OverlayFileSystem> OverlayFS(
+      new vfs::OverlayFileSystem(vfs::getRealFileSystem()));
+  llvm::ErrorOr<std::unique_ptr<llvm::MemoryBuffer>> Buffer =
+      OverlayFS->getBufferForFile(OverlayFile);
+  if (!Buffer) {
+    llvm::errs() << "Can't load virtual filesystem overlay file '"
+                 << OverlayFile << "': " << Buffer.getError().message()
+                 << ".\n";
+    return nullptr;
+  }
+
+  IntrusiveRefCntPtr<vfs::FileSystem> FS = vfs::getVFSFromYAML(
+      std::move(Buffer.get()), /*DiagHandler*/ nullptr, OverlayFile);
+  if (!FS) {
+    llvm::errs() << "Error: invalid virtual filesystem overlay file '"
+                 << OverlayFile << "'.\n";
+    return nullptr;
+  }
+  OverlayFS->pushOverlay(FS);
+  return OverlayFS;
+}
+
 static int clangTidyMain(int argc, const char **argv) {
   CommonOptionsParser OptionsParser(argc, argv, ClangTidyCategory,
                                     cl::ZeroOrMore);
@@ -401,6 +432,11 @@
     llvm::cl::PrintHelpMessage(/*Hidden=*/false, /*Categorized=*/true);
     return 0;
   }
+  llvm::IntrusiveRefCntPtr<vfs::FileSystem> BaseFS(
+      VfsOverlay.empty() ? vfs::getRealFileSystem()
+                         : getVfsOverlayFromFile(VfsOverlay));
+  if (!BaseFS)
+    return 1;
 
   ProfileData Profile;
 
@@ -409,7 +445,7 @@
   llvm::InitializeAllAsmParsers();
 
   ClangTidyContext Context(std::move(OwningOptionsProvider));
-  runClangTidy(Context, OptionsParser.getCompilations(), PathList,
+  runClangTidy(Context, OptionsParser.getCompilations(), PathList, BaseFS,
                EnableCheckProfile ? &Profile : nullptr);
   ArrayRef<ClangTidyError> Errors = Context.getErrors();
   bool FoundErrors =
@@ -422,7 +458,8 @@
   unsigned WErrorCount = 0;
 
   // -fix-errors implies -fix.
-  handleErrors(Context, (FixErrors || Fix) && !DisableFixes, WErrorCount);
+  handleErrors(Context, (FixErrors || Fix) && !DisableFixes, WErrorCount,
+               BaseFS);
 
   if (!ExportFixes.empty() && !Errors.empty()) {
     std::error_code EC;
Index: test/clang-tidy/Inputs/vfsoverlay/actual_header.h
===================================================================
--- test/clang-tidy/Inputs/vfsoverlay/actual_header.h
+++ test/clang-tidy/Inputs/vfsoverlay/actual_header.h
@@ -0,0 +1 @@
+struct X {};
Index: test/clang-tidy/Inputs/vfsoverlay/vfsoverlay.yaml
===================================================================
--- test/clang-tidy/Inputs/vfsoverlay/vfsoverlay.yaml
+++ test/clang-tidy/Inputs/vfsoverlay/vfsoverlay.yaml
@@ -0,0 +1,12 @@
+{
+  'version': 0,
+  'roots': [
+    { 'name': 'OUT_DIR', 'type': 'directory',
+      'contents': [
+        { 'name': 'not_real.h', 'type': 'file',
+          'external-contents': 'INPUT_DIR/actual_header.h'
+        }
+      ]
+    }
+  ]
+}
Index: test/clang-tidy/vfsoverlay.cpp
===================================================================
--- test/clang-tidy/vfsoverlay.cpp
+++ test/clang-tidy/vfsoverlay.cpp
@@ -0,0 +1,8 @@
+// RUN: sed -e "s:INPUT_DIR:%S/Inputs/vfsoverlay:g" -e "s:OUT_DIR:%t:g" %S/Inputs/vfsoverlay/vfsoverlay.yaml > %t.yaml
+// RUN: clang-tidy %s -checks='-*,modernize-use-nullptr' -vfsoverlay %t.yaml -- -I %t | FileCheck %s
+// REQUIRES: shell
+
+#include "not_real.h"
+
+X *ptr = 0;
+// CHECK: warning: use nullptr [modernize-use-nullptr]