Serialization: Change InputFile to use FileEntryRef and add getVirtualFileRef, NFC

Serialization: Change InputFile to use FileEntryRef and add getVirtualFileRef, NFC

Change the `InputFile` class to store `Optional<FileEntryRef>` instead
of `FileEntry*`. This paged in a few API changes:

- Added `FileManager::getVirtualFileRef`, and converted `getVirtualFile`
  to a wrapper of it.
- Updated `SourceManager::bypassFileContentsOverride` to take
  `FileEntryRef` and return `Optional<FileEntryRef>`
  (`ASTReader::getInputFile` is the only caller).

Differential Revision: https://reviews.llvm.org/D90053