Index: lib/Tooling/Tooling.cpp
===================================================================
--- lib/Tooling/Tooling.cpp
+++ lib/Tooling/Tooling.cpp
@@ -301,10 +301,18 @@
   std::string MainExecutable =
       llvm::sys::fs::getMainExecutable("clang_tool", &StaticSymbol);
 
+  llvm::SmallString<128> InitialDirectory;
+  if (std::error_code EC = llvm::sys::fs::current_path(InitialDirectory))
+    llvm::report_fatal_error("Cannot detect current path: " +
+                             Twine(EC.message()));
   bool ProcessingFailed = false;
   for (const auto &SourcePath : SourcePaths) {
     std::string File(getAbsolutePath(SourcePath));
 
+    // FIXME: getCompileCommands can change the state of the file system (e.g.
+    // prepare generated headers), so it needs to run right before we invoke the
+    // tool, as the next file may require a different (incompatible) state of
+    // the file system.
     std::vector<CompileCommand> CompileCommandsForFile =
         Compilations.getCompileCommands(File);
     if (CompileCommandsForFile.empty()) {
@@ -345,6 +353,11 @@
         llvm::errs() << "Error while processing " << File << ".\n";
         ProcessingFailed = true;
       }
+      // Return to the initial directory to correctly resolve next file by
+      // relative path.
+      if (chdir(InitialDirectory.c_str()))
+        llvm::report_fatal_error("Cannot chdir into \"" +
+                                 Twine(InitialDirectory) + "\n!");
     }
   }
   return ProcessingFailed ? 1 : 0;