Housekeeping doesn't remove all empty loose ref directories with transactions

Housekeeping with transactions removes loose reference directories as a part of repacking. However, it only removes 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 never being pruned.

To fix this, all empty directories that existed in the refs directory before the reference packing run should be pruned.