Index: clang-tools-extra/trunk/clang-tidy/ClangTidyOptions.h
===================================================================
--- clang-tools-extra/trunk/clang-tidy/ClangTidyOptions.h
+++ clang-tools-extra/trunk/clang-tidy/ClangTidyOptions.h
@@ -13,7 +13,9 @@
 #include "llvm/ADT/Optional.h"
 #include "llvm/ADT/StringMap.h"
 #include "llvm/ADT/StringRef.h"
+#include "llvm/ADT/IntrusiveRefCntPtr.h"
 #include "llvm/Support/ErrorOr.h"
+#include "clang/Basic/VirtualFileSystem.h"
 #include <functional>
 #include <map>
 #include <string>
@@ -221,7 +223,8 @@
   /// whatever options are read from the configuration file.
   FileOptionsProvider(const ClangTidyGlobalOptions &GlobalOptions,
                       const ClangTidyOptions &DefaultOptions,
-                      const ClangTidyOptions &OverrideOptions);
+                      const ClangTidyOptions &OverrideOptions,
+                      llvm::IntrusiveRefCntPtr<vfs::FileSystem> FS = nullptr);
 
   /// \brief Initializes the \c FileOptionsProvider instance with a custom set
   /// of configuration file handlers.
@@ -255,6 +258,7 @@
   llvm::StringMap<OptionsSource> CachedOptions;
   ClangTidyOptions OverrideOptions;
   ConfigFileHandlers ConfigHandlers;
+  llvm::IntrusiveRefCntPtr<vfs::FileSystem> FS;
 };
 
 /// \brief Parses LineFilter from JSON and stores it to the \p Options.
Index: clang-tools-extra/trunk/clang-tidy/ClangTidyOptions.cpp
===================================================================
--- clang-tools-extra/trunk/clang-tidy/ClangTidyOptions.cpp
+++ clang-tools-extra/trunk/clang-tidy/ClangTidyOptions.cpp
@@ -204,9 +204,12 @@
 FileOptionsProvider::FileOptionsProvider(
     const ClangTidyGlobalOptions &GlobalOptions,
     const ClangTidyOptions &DefaultOptions,
-    const ClangTidyOptions &OverrideOptions)
+    const ClangTidyOptions &OverrideOptions,
+    llvm::IntrusiveRefCntPtr<vfs::FileSystem> VFS)
     : DefaultOptionsProvider(GlobalOptions, DefaultOptions),
-      OverrideOptions(OverrideOptions) {
+      OverrideOptions(OverrideOptions), FS(std::move(VFS)) {
+  if (!FS)
+    FS = vfs::getRealFileSystem();
   ConfigHandlers.emplace_back(".clang-tidy", parseConfiguration);
 }
 
@@ -224,14 +227,19 @@
 std::vector<OptionsSource>
 FileOptionsProvider::getRawOptions(StringRef FileName) {
   DEBUG(llvm::dbgs() << "Getting options for file " << FileName << "...\n");
+  assert(FS && "FS must be set.");
+
+  llvm::SmallString<128> AbsoluteFilePath(FileName);
+  if (std::error_code ec = FS->makeAbsolute(AbsoluteFilePath))
+    return {};
 
   std::vector<OptionsSource> RawOptions =
-      DefaultOptionsProvider::getRawOptions(FileName);
+      DefaultOptionsProvider::getRawOptions(AbsoluteFilePath.str());
   OptionsSource CommandLineOptions(OverrideOptions,
                                    OptionsSourceTypeCheckCommandLineOption);
   // Look for a suitable configuration file in all parent directories of the
   // file. Start with the immediate parent directory and move up.
-  StringRef Path = llvm::sys::path::parent_path(FileName);
+  StringRef Path = llvm::sys::path::parent_path(AbsoluteFilePath.str());
   for (StringRef CurrentPath = Path; !CurrentPath.empty();
        CurrentPath = llvm::sys::path::parent_path(CurrentPath)) {
     llvm::Optional<OptionsSource> Result;
Index: clang-tools-extra/trunk/clang-tidy/tool/ClangTidyMain.cpp
===================================================================
--- clang-tools-extra/trunk/clang-tidy/tool/ClangTidyMain.cpp
+++ clang-tools-extra/trunk/clang-tidy/tool/ClangTidyMain.cpp
@@ -286,7 +286,8 @@
   OS.flush();
 }
 
-static std::unique_ptr<ClangTidyOptionsProvider> createOptionsProvider() {
+static std::unique_ptr<ClangTidyOptionsProvider> createOptionsProvider(
+   llvm::IntrusiveRefCntPtr<vfs::FileSystem> FS) {
   ClangTidyGlobalOptions GlobalOptions;
   if (std::error_code Err = parseLineFilter(LineFilter, GlobalOptions)) {
     llvm::errs() << "Invalid LineFilter: " << Err.message() << "\n\nUsage:\n";
@@ -334,7 +335,7 @@
     }
   }
   return llvm::make_unique<FileOptionsProvider>(GlobalOptions, DefaultOptions,
-                                                OverrideOptions);
+                                                OverrideOptions, std::move(FS));
 }
 
 llvm::IntrusiveRefCntPtr<vfs::FileSystem>
@@ -364,8 +365,13 @@
 static int clangTidyMain(int argc, const char **argv) {
   CommonOptionsParser OptionsParser(argc, argv, ClangTidyCategory,
                                     cl::ZeroOrMore);
+  llvm::IntrusiveRefCntPtr<vfs::FileSystem> BaseFS(
+      VfsOverlay.empty() ? vfs::getRealFileSystem()
+                         : getVfsOverlayFromFile(VfsOverlay));
+  if (!BaseFS)
+    return 1;
 
-  auto OwningOptionsProvider = createOptionsProvider();
+  auto OwningOptionsProvider = createOptionsProvider(BaseFS);
   auto *OptionsProvider = OwningOptionsProvider.get();
   if (!OptionsProvider)
     return 1;
@@ -432,12 +438,6 @@
     llvm::cl::PrintHelpMessage(/*Hidden=*/false, /*Categorized=*/true);
     return 1;
   }
-  llvm::IntrusiveRefCntPtr<vfs::FileSystem> BaseFS(
-      VfsOverlay.empty() ? vfs::getRealFileSystem()
-                         : getVfsOverlayFromFile(VfsOverlay));
-  if (!BaseFS)
-    return 1;
-
   ProfileData Profile;
 
   llvm::InitializeAllTargetInfos();
Index: clang-tools-extra/trunk/test/clang-tidy/read_file_config.cpp
===================================================================
--- clang-tools-extra/trunk/test/clang-tidy/read_file_config.cpp
+++ clang-tools-extra/trunk/test/clang-tidy/read_file_config.cpp
@@ -0,0 +1,12 @@
+// RUN: mkdir -p %T/read-file-config/
+// RUN: cp %s %T/read-file-config/test.cpp
+// RUN: echo 'Checks: "-*,modernize-use-nullptr"' > %T/read-file-config/.clang-tidy
+// RUN: echo '[{"command": "cc -c -o test.o test.cpp", "directory": "%T/read-file-config", "file": "%T/read-file-config/test.cpp"}]' > %T/read-file-config/compile_commands.json
+// RUN: clang-tidy %T/read-file-config/test.cpp | not grep "warning: .*\[clang-analyzer-deadcode.DeadStores\]$"
+// RUN: clang-tidy -checks="-*,clang-analyzer-*" %T/read-file-config/test.cpp | grep "warning: .*\[clang-analyzer-deadcode.DeadStores\]$"
+
+void f() {
+  int x;
+  x = 1;
+  x = 2;
+}