Reapply fixed "Honour 'use-external-names' in FileManager"

Was r202442

There were two issues with the original patch that have now been fixed.
1. We were memset'ing over a FileEntry in a test case. After adding a
   std::string to FileEntry, this still happened to not break for me.
2. I didn't pass the FileManager into the new compiler instance in
   compileModule. This was hidden in some cases by the fact I didn't
   clear the module cache in the test.

Also, I changed the copy constructor for FileEntry, which was memcpy'ing
in a (now) unsafe way.