Refactor FileManager::GetUniqueIDMapping to populate an array of
OptionalFileEntryRefDegradesToFileEntryPtr instead of UID to
FileEntry *. This should allow the path serialization of input files
to use the paths used when looking up a file entry, instead of the
Per the FileManager documentation, VirtualFileEntries is a subset of
SeenFileEntries. This means we only have to iterate over the latter
to create a complete UID mapping.