ProjectOrganizer could actually be a nice name for my plugin as well
Great!
This is something I did on purpose in my plugin because I made it primarily for big projects and it's almost impossible to manually organize thousands of files (and keep them organized while other team members add/remove/rename files). In my opinion, the file system is where the files should be organized properly and there shouldn't be any need to map one file tree to another.
Understood - and your plugin is super-helpful with big projects, etc.
I typically work on smaller codebases, and want to 'get oriented' as quickly as possible (and many of the files won't get put into the custom hierarchy - it's there for clarification, not completeness). For instance the project-tree plugin page itself (https://github.com/mdda/geany-project-tree) shows how the file directories effectively remove oneself a little from the purpose of the different files, whereas the 'collected' version makes more sense (to me at least).
Of course, there's nothing to stop someone from installing them both : Which is why I don't plan on expanding functionality much (though the hooks are there in the Python code if someone does want to).
All the Best - Martin :-)