Using verify_replica instead of make_local_copy in atom_ingest's make_local_copy.
- Populate directory field for dataset records created in process_enclosure.
- Some code which was checking to see if a datafile found in an enclosure
  already exists in the database, and if so, check whether it has a timestamp
  has been updated, so now it checks the directory field to remove ambiguity
  when the same filename appears in multiple subdirectories within the same
  dataset.