I don't use the plugin's sidebar BTW - I haven't even noticed that there is one till now.
Just curious - what are you using the plugin for then?
I'd also be fine with an option to disable to plugin/directory traversal on a per project basis
I can do that - IMO that makes more sense than ignoring the whole project based on the ignored directory patterns. To be clear, this option would disable the whole plugin completely for certain projects because when ProjectOrganizer cannot see files in the project directory, it cannot do anything useful.
although I actually think projectorganizer does lookups on just the open tabs even without the index from what I've seen in the code
I'm not aware of that, could you point me to the code? In any case, the documents in open tabs are opened and parsed by Geany already so the files have to be transferred over network anyway.