I too am wondering about this. Is there a way to purge the empty folders? Also is there a way to move the other files in the directory to the new directory? I think MediaMonkey does this quite well if I recall.
This is contradictory. If there are other files in the directory, then it is not empty and MC is right not to delete it.
If you store other related files in the same directory as the media files themselves, MC won't know, therefore, when you ask MC to move the media files, it does just that, leaving the other related files behind. What to do?
There are a couple of options:
If the move is not a complicated tag bound move, you could use MC's explorer and drag and drop folders to their new locations. I have not done this for many years now so have no idea how successful it might be today.
You could also import all of the related files to the library, be they cover art, txt files, pdf, log files etc., then create a working view that includes all of the required media types. You can tag them all accordingly in line with their audio counterparts, then select those files and perform the rename operation on all of them to have MC move the whole lot in one go, and automatically remove the empty folder at the end of the operation.