On Wed, Mar 17, 2021 at 10:43:07PM +0100, Ben Engbers scripsit:

To my knowledge there is no need to remove the data directory. I have never done this and have never had any problems

Well, data/ is in the archive empty and I need to retain the existing data from the incumbent basex when I update BaseX.

I find it's simpler to promote data/ to being a sibling of basex/ and use a symbolic link from inside basex/ to find it so I don't have to argue with the defaults. (I am far from sure you can argue with the defaults to the extent of putting the data directory outside of basex/.)

So, if you have no need to retain data = no need to do anything with data/. But if you do need to retain data/, giving whatever archive tool a chance to drop an empty data/ over it on upgrade is maybe not the best plan.