diff --git a/clang-tools-extra/clang-apply-replacements/lib/Tooling/ApplyReplacements.cpp b/clang-tools-extra/clang-apply-replacements/lib/Tooling/ApplyReplacements.cpp
--- a/clang-tools-extra/clang-apply-replacements/lib/Tooling/ApplyReplacements.cpp
+++ b/clang-tools-extra/clang-apply-replacements/lib/Tooling/ApplyReplacements.cpp
@@ -156,11 +156,15 @@
                         const tooling::TranslationUnitDiagnostics *SourceTU,
                         const llvm::Optional<std::string> BuildDir) {
     // Use the file manager to deduplicate paths. FileEntries are
-    // automatically canonicalized.
-    auto PrevWorkingDir = SM.getFileManager().getFileSystemOpts().WorkingDir;
+    // automatically canonicalized. Since relative paths can come from different
+    // build directories, make them absolute immediately.
+    SmallString<128> Path = R.getFilePath();
     if (BuildDir)
-      SM.getFileManager().getFileSystemOpts().WorkingDir = std::move(*BuildDir);
-    if (auto Entry = SM.getFileManager().getFile(R.getFilePath())) {
+      llvm::sys::fs::make_absolute(*BuildDir, Path);
+    else
+      SM.getFileManager().makeAbsolutePath(Path);
+
+    if (auto Entry = SM.getFileManager().getFile(Path)) {
       if (SourceTU) {
         auto &Replaces = DiagReplacements[*Entry];
         auto It = Replaces.find(R);
@@ -171,11 +175,10 @@
           return;
       }
       GroupedReplacements[*Entry].push_back(R);
-    } else if (Warned.insert(R.getFilePath()).second) {
+    } else if (Warned.insert(Path).second) {
       errs() << "Described file '" << R.getFilePath()
              << "' doesn't exist. Ignoring...\n";
     }
-    SM.getFileManager().getFileSystemOpts().WorkingDir = PrevWorkingDir;
   };
 
   for (const auto &TU : TUs)
diff --git a/clang/include/clang/Tooling/DependencyScanning/ModuleDepCollector.h b/clang/include/clang/Tooling/DependencyScanning/ModuleDepCollector.h
--- a/clang/include/clang/Tooling/DependencyScanning/ModuleDepCollector.h
+++ b/clang/include/clang/Tooling/DependencyScanning/ModuleDepCollector.h
@@ -233,6 +233,11 @@
   /// Checks whether the module is known as being prebuilt.
   bool isPrebuiltModule(const Module *M);
 
+  /// Adds \p Path to \c FileDeps, making it absolute if necessary.
+  void addFileDep(StringRef Path);
+  /// Adds \p Path to \c MD.FileDeps, making it absolute if necessary.
+  void addFileDep(ModuleDeps &MD, StringRef Path);
+
   /// Constructs a CompilerInvocation that can be used to build the given
   /// module, excluding paths to discovered modular dependencies that are yet to
   /// be built.
diff --git a/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp b/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
--- a/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
+++ b/clang/lib/Tooling/DependencyScanning/DependencyScanningWorker.cpp
@@ -28,8 +28,9 @@
 class DependencyConsumerForwarder : public DependencyFileGenerator {
 public:
   DependencyConsumerForwarder(std::unique_ptr<DependencyOutputOptions> Opts,
-                              DependencyConsumer &C)
-      : DependencyFileGenerator(*Opts), Opts(std::move(Opts)), C(C) {}
+                              StringRef WorkingDirectory, DependencyConsumer &C)
+      : DependencyFileGenerator(*Opts), WorkingDirectory(WorkingDirectory),
+        Opts(std::move(Opts)), C(C) {}
 
   void finishedMainFile(DiagnosticsEngine &Diags) override {
     C.handleDependencyOutputOpts(*Opts);
@@ -37,11 +38,13 @@
     for (const auto &File : getDependencies()) {
       CanonPath = File;
       llvm::sys::path::remove_dots(CanonPath, /*remove_dot_dot=*/true);
+      llvm::sys::fs::make_absolute(WorkingDirectory, CanonPath);
       C.handleFileDependency(CanonPath);
     }
   }
 
 private:
+  StringRef WorkingDirectory;
   std::unique_ptr<DependencyOutputOptions> Opts;
   DependencyConsumer &C;
 };
@@ -221,8 +224,8 @@
     switch (Format) {
     case ScanningOutputFormat::Make:
       ScanInstance.addDependencyCollector(
-          std::make_shared<DependencyConsumerForwarder>(std::move(Opts),
-                                                        Consumer));
+          std::make_shared<DependencyConsumerForwarder>(
+              std::move(Opts), WorkingDirectory, Consumer));
       break;
     case ScanningOutputFormat::Full:
       ScanInstance.addDependencyCollector(std::make_shared<ModuleDepCollector>(
diff --git a/clang/lib/Tooling/DependencyScanning/ModuleDepCollector.cpp b/clang/lib/Tooling/DependencyScanning/ModuleDepCollector.cpp
--- a/clang/lib/Tooling/DependencyScanning/ModuleDepCollector.cpp
+++ b/clang/lib/Tooling/DependencyScanning/ModuleDepCollector.cpp
@@ -240,8 +240,7 @@
   // We do not want #line markers to affect dependency generation!
   if (Optional<StringRef> Filename =
           SM.getNonBuiltinFilenameForID(SM.getFileID(SM.getExpansionLoc(Loc))))
-    MDC.FileDeps.push_back(
-        std::string(llvm::sys::path::remove_leading_dotslash(*Filename)));
+    MDC.addFileDep(llvm::sys::path::remove_leading_dotslash(*Filename));
 }
 
 void ModuleDepCollectorPP::InclusionDirective(
@@ -252,7 +251,7 @@
   if (!File && !Imported) {
     // This is a non-modular include that HeaderSearch failed to find. Add it
     // here as `FileChanged` will never see it.
-    MDC.FileDeps.push_back(std::string(FileName));
+    MDC.addFileDep(FileName);
   }
   handleImport(Imported);
 }
@@ -282,8 +281,7 @@
                                  ->getName());
 
   if (!MDC.ScanInstance.getPreprocessorOpts().ImplicitPCHInclude.empty())
-    MDC.FileDeps.push_back(
-        MDC.ScanInstance.getPreprocessorOpts().ImplicitPCHInclude);
+    MDC.addFileDep(MDC.ScanInstance.getPreprocessorOpts().ImplicitPCHInclude);
 
   for (const Module *M : DirectModularDeps) {
     // A top-level module might not be actually imported as a module when
@@ -346,10 +344,10 @@
         // handle it like normal. With explicitly built modules we don't need
         // to play VFS tricks, so replace it with the correct module map.
         if (IF.getFile()->getName().endswith("__inferred_module.map")) {
-          MD.FileDeps.insert(ModuleMap->getName());
+          MDC.addFileDep(MD, ModuleMap->getName());
           return;
         }
-        MD.FileDeps.insert(IF.getFile()->getName());
+        MDC.addFileDep(MD, IF.getFile()->getName());
       });
 
   // We usually don't need to list the module map files of our dependencies when
@@ -494,3 +492,24 @@
          PrebuiltModuleFileIt->second == M->getASTFile()->getName());
   return true;
 }
+
+static StringRef makeAbsolute(CompilerInstance &CI, StringRef Path,
+                              SmallVectorImpl<char> &Storage) {
+  if (llvm::sys::path::is_absolute(Path))
+    return Path;
+  Storage.assign(Path.begin(), Path.end());
+  CI.getFileManager().makeAbsolutePath(Storage);
+  return StringRef(Storage.data(), Storage.size());
+}
+
+void ModuleDepCollector::addFileDep(StringRef Path) {
+  llvm::SmallString<256> Storage;
+  Path = makeAbsolute(ScanInstance, Path, Storage);
+  FileDeps.push_back(std::string(Path));
+}
+
+void ModuleDepCollector::addFileDep(ModuleDeps &MD, StringRef Path) {
+  llvm::SmallString<256> Storage;
+  Path = makeAbsolute(ScanInstance, Path, Storage);
+  MD.FileDeps.insert(Path);
+}