Custom configurations management question

We have, as other users do I guess, more than one file installed with the XWiki packages modified for our needs.
I wonder how this is dealt with, when it comes to superseeding changes from new packages?

Usually in Linux distributions we can often find some this_dir.d directory where costum configuration are stored.

In our XWiki install which are not yet in production we have some parts imported from Confluence, but not all, and some of the imports need modification such as notifications disabled in /etc/xwiki/, and some other files are meant to have their modification kept when it will be in production, at some point in the future.

So is there a way to make it easy to maintain the updated files belonging to the XWiki packages, once it will be in production while we get updates from the xwiki repository?