Revert "Module: Use FileEntryRef and DirectoryEntryRef in Umbrella, Header, and DirectoryName, NFC"

This (mostly) reverts 32c501dd.  Hit a
case where this causes a behaviour change, perhaps the same root cause
that triggered the revert of a40db550 in
7799ef71.

(The API changes in DirectoryEntry.h have NOT been reverted as a number
of subsequent commits depend on those.)

https://reviews.llvm.org/D90497#2582166