Index: clang/lib/Frontend/CompilerInvocation.cpp
===================================================================
--- clang/lib/Frontend/CompilerInvocation.cpp
+++ clang/lib/Frontend/CompilerInvocation.cpp
@@ -1566,7 +1566,14 @@
     frontend::IncludeDirGroup Group = frontend::System;
     if (A->getOption().matches(OPT_internal_externc_isystem))
       Group = frontend::ExternCSystem;
-    Opts.AddPath(A->getValue(), Group, false, true);
+
+    SmallString<128> P(D.ResourceDir);
+    llvm::sys::path::append(P, "include");
+
+    if (StringRef(A->getValue()) == P)
+      Opts.AddPath(A->getValue(), Group, false, true);
+    else
+      Opts.AddPath(A->getValue(), Group, false, false);
   }
 
   // Add the path prefixes which are implicitly treated as being system headers.
@@ -2765,8 +2772,6 @@
       Diags.Report(diag::err_invalid_vfs_overlay) << File;
       return IntrusiveRefCntPtr<vfs::FileSystem>();
     }
-    Overlay->pushOverlay(FS);
-  }
   return Overlay;
 }
 } // end namespace clang