Revert "Module: Use FileEntryRef and DirectoryEntryRef in Umbrella, Header, and Direc...

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

This (mostly) reverts 32c501dd88b62787d3a5ffda7aabcf4650dbe3cd.  Hit a
case where this causes a behaviour change, perhaps the same root cause
that triggered the revert of a40db5502b2515a6f2f1676b5d7a655ae0f41179 in
7799ef7121aa7d59f4bd95cdf70035de724ead6f.

(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