Any way to preserve changes in the users.xml ? Maybe allow for a <custom> section or similar?
Currently no. Maybe something like this could be added in a future version. Indeed I had similar thoughts in the past. One problem might be that this file is only parsed if BaseX is started (subsequent changes at runtime will be overwritten if the file is updated by BaseX). However, it could make sense to extend the User Module with a function for handling custom user data. How do you currently work with users?
By the way: what was the reason users.xml is not stored as a basex database but on the file system?
I wanted to keep BaseX initialization as simple and fast as possible.