Refactor the `Module::Header` class to use an `OptionalFileEntryRef`
instead of a `FileEntry*`. This is preparation for refactoring the
`TopHeaderNames` to use `FileEntryRef` so that we preserve the
lookup path of the headers when serializing.
This is mostly based on https://reviews.llvm.org/D90497
Reviewed By: jansvoboda11
Differential Revision: https://reviews.llvm.org/D142113