Index: include/clang/Tooling/Core/Replacement.h
===================================================================
--- include/clang/Tooling/Core/Replacement.h
+++ include/clang/Tooling/Core/Replacement.h
@@ -19,6 +19,7 @@
 #ifndef LLVM_CLANG_TOOLING_CORE_REPLACEMENT_H
 #define LLVM_CLANG_TOOLING_CORE_REPLACEMENT_H
 
+#include "clang/Basic/FileManager.h"
 #include "clang/Basic/LangOptions.h"
 #include "clang/Basic/SourceLocation.h"
 #include "llvm/ADT/StringRef.h"
@@ -293,9 +294,9 @@
                                  const std::vector<Range> &Ranges);
 
 /// \brief If there are multiple <File, Replacements> pairs with the same file
-/// path after removing dots, we only keep one pair (with path after dots being
-/// removed) and discard the rest.
+/// entry, we only keep one pair and discard the rest.
 std::map<std::string, Replacements> groupReplacementsByFile(
+    FileManager &FileMgr,
     const std::map<std::string, Replacements> &FileToReplaces);
 
 template <typename Node>
Index: lib/Tooling/Core/Replacement.cpp
===================================================================
--- lib/Tooling/Core/Replacement.cpp
+++ lib/Tooling/Core/Replacement.cpp
@@ -20,6 +20,7 @@
 #include "clang/Basic/SourceManager.h"
 #include "clang/Lex/Lexer.h"
 #include "clang/Rewrite/Core/Rewriter.h"
+#include "llvm/ADT/SmallPtrSet.h"
 #include "llvm/Support/FileSystem.h"
 #include "llvm/Support/Path.h"
 #include "llvm/Support/raw_os_ostream.h"
@@ -566,12 +567,16 @@
 }
 
 std::map<std::string, Replacements> groupReplacementsByFile(
+    FileManager &FileMgr,
     const std::map<std::string, Replacements> &FileToReplaces) {
   std::map<std::string, Replacements> Result;
+  llvm::SmallPtrSet<const FileEntry *, 16> ProcessedFileEntries;
   for (const auto &Entry : FileToReplaces) {
-    llvm::SmallString<256> CleanPath(Entry.first.data());
-    llvm::sys::path::remove_dots(CleanPath, /*remove_dot_dot=*/true);
-    Result[CleanPath.str()] = std::move(Entry.second);
+    const FileEntry *FE = FileMgr.getFile(Entry.first);
+    if (!FE)
+      llvm::errs() << "File path " << Entry.first << " is invalid.\n";
+    else if (ProcessedFileEntries.insert(FE).second)
+      Result[Entry.first] = std::move(Entry.second);
   }
   return Result;
 }
Index: lib/Tooling/Refactoring.cpp
===================================================================
--- lib/Tooling/Refactoring.cpp
+++ lib/Tooling/Refactoring.cpp
@@ -57,7 +57,8 @@
 
 bool RefactoringTool::applyAllReplacements(Rewriter &Rewrite) {
   bool Result = true;
-  for (const auto &Entry : groupReplacementsByFile(FileToReplaces))
+  for (const auto &Entry : groupReplacementsByFile(
+           Rewrite.getSourceMgr().getFileManager(), FileToReplaces))
     Result = tooling::applyAllReplacements(Entry.second, Rewrite) && Result;
   return Result;
 }
@@ -73,7 +74,8 @@
   FileManager &Files = SM.getFileManager();
 
   bool Result = true;
-  for (const auto &FileAndReplaces : groupReplacementsByFile(FileToReplaces)) {
+  for (const auto &FileAndReplaces : groupReplacementsByFile(
+           Rewrite.getSourceMgr().getFileManager(), FileToReplaces)) {
     const std::string &FilePath = FileAndReplaces.first;
     auto &CurReplaces = FileAndReplaces.second;
 
Index: unittests/Tooling/RefactoringTest.cpp
===================================================================
--- unittests/Tooling/RefactoringTest.cpp
+++ unittests/Tooling/RefactoringTest.cpp
@@ -19,6 +19,7 @@
 #include "clang/Basic/FileManager.h"
 #include "clang/Basic/LangOptions.h"
 #include "clang/Basic/SourceManager.h"
+#include "clang/Basic/VirtualFileSystem.h"
 #include "clang/Format/Format.h"
 #include "clang/Frontend/CompilerInstance.h"
 #include "clang/Frontend/FrontendAction.h"
@@ -972,40 +973,64 @@
       toReplacements({{"", 0, 3, "cc"}, {"", 3, 3, "dd"}}));
 }
 
-TEST(DeduplicateByFileTest, LeaveLeadingDotDot) {
+TEST(DeduplicateByFileTest, PathsWithDots) {
   std::map<std::string, Replacements> FileToReplaces;
+  llvm::IntrusiveRefCntPtr<vfs::InMemoryFileSystem> VFS(
+      new vfs::InMemoryFileSystem());
+  FileManager *FileMgr = new FileManager(FileSystemOptions(), VFS);
 #if !defined(LLVM_ON_WIN32)
-  FileToReplaces["../../a/b/.././c.h"] = Replacements();
-  FileToReplaces["../../a/c.h"] = Replacements();
+  StringRef Path1 = "a/b/.././c.h";
+  StringRef Path2 = "a/c.h";
 #else
-  FileToReplaces["..\\..\\a\\b\\..\\.\\c.h"] = Replacements();
-  FileToReplaces["..\\..\\a\\c.h"] = Replacements();
+  StringRef Path1 = "a\\b\\..\\.\\c.h";
+  StringRef Path2 = "a\\c.h";
 #endif
-  FileToReplaces = groupReplacementsByFile(FileToReplaces);
+  EXPECT_TRUE(VFS->addFile(Path1, 0, llvm::MemoryBuffer::getMemBuffer("")));
+  EXPECT_TRUE(VFS->addFile(Path2, 0, llvm::MemoryBuffer::getMemBuffer("")));
+  FileToReplaces[Path1] = Replacements();
+  FileToReplaces[Path2] = Replacements();
+  FileToReplaces = groupReplacementsByFile(*FileMgr, FileToReplaces);
   EXPECT_EQ(1u, FileToReplaces.size());
-#if !defined(LLVM_ON_WIN32)
-  EXPECT_EQ("../../a/c.h", FileToReplaces.begin()->first);
-#else
-  EXPECT_EQ("..\\..\\a\\c.h", FileToReplaces.begin()->first);
-#endif
+  EXPECT_EQ(Path1, FileToReplaces.begin()->first);
 }
 
-TEST(DeduplicateByFileTest, RemoveDotSlash) {
+TEST(DeduplicateByFileTest, PathWithDotSlash) {
   std::map<std::string, Replacements> FileToReplaces;
+  llvm::IntrusiveRefCntPtr<vfs::InMemoryFileSystem> VFS(
+      new vfs::InMemoryFileSystem());
+  FileManager *FileMgr = new FileManager(FileSystemOptions(), VFS);
 #if !defined(LLVM_ON_WIN32)
-  FileToReplaces["./a/b/.././c.h"] = Replacements();
-  FileToReplaces["a/c.h"] = Replacements();
+  StringRef Path1 = "./a/b/c.h";
+  StringRef Path2 = "a/b/c.h";
 #else
-  FileToReplaces[".\\a\\b\\..\\.\\c.h"] = Replacements();
-  FileToReplaces["a\\c.h"] = Replacements();
+  StringRef Path1 = ".\\a\\b\\c.h";
+  StringRef Path2 = "a\\b\\c.h";
 #endif
-  FileToReplaces = groupReplacementsByFile(FileToReplaces);
+  EXPECT_TRUE(VFS->addFile(Path1, 0, llvm::MemoryBuffer::getMemBuffer("")));
+  EXPECT_TRUE(VFS->addFile(Path2, 0, llvm::MemoryBuffer::getMemBuffer("")));
+  FileToReplaces[Path1] = Replacements();
+  FileToReplaces[Path2] = Replacements();
+  FileToReplaces = groupReplacementsByFile(*FileMgr, FileToReplaces);
   EXPECT_EQ(1u, FileToReplaces.size());
+  EXPECT_EQ(Path1, FileToReplaces.begin()->first);
+}
+
+TEST(DeduplicateByFileTest, NonExistingFilePath) {
+  std::map<std::string, Replacements> FileToReplaces;
+  llvm::IntrusiveRefCntPtr<vfs::InMemoryFileSystem> VFS(
+      new vfs::InMemoryFileSystem());
+  FileManager *FileMgr = new FileManager(FileSystemOptions(), VFS);
 #if !defined(LLVM_ON_WIN32)
-  EXPECT_EQ("a/c.h", FileToReplaces.begin()->first);
+  StringRef Path1 = "./a/b/c.h";
+  StringRef Path2 = "a/b/c.h";
 #else
-  EXPECT_EQ("a\\c.h", FileToReplaces.begin()->first);
+  StringRef Path1 = ".\\a\\b\\c.h";
+  StringRef Path2 = "a\\b\\c.h";
 #endif
+  FileToReplaces[Path1] = Replacements();
+  FileToReplaces[Path2] = Replacements();
+  FileToReplaces = groupReplacementsByFile(*FileMgr, FileToReplaces);
+  EXPECT_TRUE(FileToReplaces.empty());
 }
 
 } // end namespace tooling