I suggest you raise an issue on the Geany repo explaining your use case, the problems with the existing system, your proposal etc. and see what people say.

Are you aware of the stash system, how does this interact? Having a billion [exaggeration for effect] pref handling systems will make the code more difficult to follow than it already is.

This could all be implemented in a plugin to manage its own settings as proof of concept to ensure that it makes sense before modifying Geany.

Plugins already manage their own settings, I'm not sure what you mean?

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