housekeeping: Prune empty directories

Housekeeping with transactions removes loose reference directories as part of repacking. However, it only removes the directories that had loose references in them during the reference packing run. Empty directories that didn't contain any loose references to pack are not removed. This leads to empty directories from other processes never being pruned.

With this change we will walk the entire ref folder and delete any remaining empty directories. Walk works in post order to delete in cascading effect. If a parent directory becomes empty due to child being removed, parent will also get removed.

Closes #6553 (closed)