The settings are stored in the prefs.xml files in the .java folder. But If I change a setting the file will be removed and re-created. So I can’t keep the file in my dotfiles sync with it. Can I change the behavior so that the file can be kept as a symlink? Thanks!
If you create a fork of JabRef, then yes you can customize your settings arbitrarily.
If you think other users would also profit from this change, you might try to open a pull-request. You will likely receive valuable feedback from the more knowledgeable JabRef maintainers
I didn’t mean to change the code but some config or env vars… Not a Java dev so 
You can export and import your preferences to an xml file and there is a cli option: