[clang] don't serialize MODULE_DIRECTORY with ModuleFileHomeIsCwd

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

Reviewed By: keith

Differential Revision: https://reviews.llvm.org/D147561