@dgmz Shame on me - took me ages to look at your patches :-(.
In general, I really like the added features and the implementation looks good too. I've just made some extra patches on top of yours with some minor fixes here:
https://github.com/techee/geany-plugins/tree/projorg_file_ops
Please let me know what you think about them.
The only thing I dislike is that empty directories are shown now - but at the same time this is necessary when you want to have the "create directory" functionality and allow users to add files to the empty directories. So it will probably have to stay this way.