Further debug missing cache files

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• Toil now correctly accesses the database when complaining that files have gone missing from its cache.
• Toil no longer deletes files uploaded with writeGlobalFile when a job finishes with the caching file store.

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[adamnovak]

This will fix #5562 by no longer deleting files that have been uploaded to a CachingFileStore from wherever they were uploaded from when the job finishes. If the files were in the temp directory for the job, they'll get deleted when we clean that up, and if they weren't, they aren't our responsibility.

[adamnovak]

I'm not sure this will actually do anything about #5084. I don't see how the delete-all-the-ref-files step I am removing could have resulted in files missing from the actual cache (except maybe by broken symlink?).