Fix a bug in the MODULE_DIRECTORY serialization logic
that would cause MODULE_DIRECTORY to be serialized when
-fmodule-file-home-is-cwd is specified.
This matches the original logic added in:
https://github.com/apple/llvm-project/commit/f7b41371d9ede1aecf0930e5bd4a463519264633
Instead of doing 2 invocations you can do --check-prefixes=CHECK,INPUT