METS: Cleanup handling of parsed metadata from CSVs

Clean up data to be sane before passing to helper function. Adjust
helper function parameters and return value to work better with reingest.
Support metadata files added during Ingest

refs #6488

When writing the METS, check for a metadata.csv added to the SIP,
in addition to ones from the originating transfers.  Add conversion
of metadata.json to metadata.csv for files added during ingest.

Move metadata reminder to before processing metadata directory, so new
files are processed.