[clang] [clang][deps] Fix dependency scanning with -working-directory (PR #84525)

[Jan Svoboda via cfe-commits]

jansvoboda11 wrote:

Do you have any concerns about the consistency of `FileManager` caches?

I can see a situation where we ask `FileManager` about the same relative path _before_ and _after_ setting the parsed `FileSystemOptions`. The second call would blindly return the cached result, effectively ignoring `-working-directory` for that file.

https://github.com/llvm/llvm-project/pull/84525