Publish sometimes leaves stale files

[marta-lokhova]

Observed while running simulations which utilize publish command. The two problems are:

• publish does not forget unreferenced buckets. Typically, this is done when closing ledgers, but since the command just runs publishing in a loop, cleanup never happens
• Some stale zipped files are left in the buckets directory. This is probably related to one of the underlying works not cleaning up zipped files