CHEF-3716: Fix intermittent 404s after cookbook upload

The ultimate problem was that we were inadvertently deleting some files from S3 / Bookshelf on cookbook updates.  When a file was no longer referenced by that cookbook version, we would delete it without first checking that it wasn't being referenced by any other cookbooks.  The database was internally consistent (modulo some "garbage" checksums remaining), but it was inconsistent with S3 / Bookshelf, which resulted in the 404 errors when trying to download.