Procedure is quite entangled. I keep my XML source in files.. I periodically recreate BaseX database from folder that contain all my XML files and use it to perform queries, that analyse my data. When I find something I need - I have to go back to file, and perform search there to find once more therexml element . already retrieved at BaseX query.

I weight to move from files to BaseX database and keep all info there. 

But... Here is a catch: Files I can keep in version control system (IBM Rational Cynnergy system)

Is there some way to keep versions track of data - kept in BaseX database? Some interface with standard Version control systems, or any other way?