BAIN: Rework uninstall empty directory processing

Logic errors caused most files in "to be empty" directories to
actually not be removed at all.
BAIN: Rework empty directory logic for Annealing
BAIN refactor common file removal code for uninstall/anneal

- has the side effect of fixing errors due to naming differences in anneal

May possibly have an effect on #93 (need to verify)
Fixes #130
Merge branch 'lojack-issue-130' into dev