Isn't

find ~/ -mtime 180 -type d -empty

equivalent to

find $HOME/ -mtime 180 -type d -empty  ??

I don't see any files below a user's $HOME belonging to any packages....  So, I 
don't really understand the objective.

I missed that he was only looking under home. There wouldn't be anything there owned by packages. Some directories would be created from /etc/skel when the account is created. (I think stuff from something under /usr/local/ is also picked up if it exists.) Any directories there should probably be kept even if they are empty.

Most programs that need config directories will create their own. However if some subdirectories are deleted, I am not sure those would be relibably recreated when needed if the top level config directory is present.

I guess it might be best to manually look at the list of empty directories to see which ones are being created that can be removed. If there is a pattern to the names of ones that can be safely deleted and that seem to be regularly being created, then perhaps the script could just automatically delete those directories instead of any empty directory.
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