[clang] NFCI: Use `FileEntryRef` for `FileID` creation (#67838)

This patch removes the `SourceManager` APIs that create `FileID` from a
`const FileEntry *` in favor of APIs that take `FileEntryRef`. This also
removes a misleading documentation that claims `nullptr` file entry
represents stdin. I don't think that's right, since we just try to
dereference that pointer anyways.