ENH: extend rmDir to handle removal of empty directories only
- recursively remove directories that only contain other directories
but no other contents. Treats dead links as non-content.
Automatic hole closure:
- introduces 'holeToFace' topoSet source
- used when detecting a 'leak-path'
- creates additional baffles to close the leak
Multi-stage layer addition:
- Can add layers in multiple passes
See issues: #2403, #2404
