If geany was written in Perl or Python I would try my luck. I'm not versed in C at all.

Well, geany.conf is just a plain text file, so you can write a script to remove the entries from a copy that you VCS and put geany.conf in .gitignore. And a script to restore all but the session info.

In general storing tool configs for general purpose tools like editors in shared VCS is frowned upon, not everyone wants to use the same editor, though you can of course do anything with your own stuff.

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