1. I added open externally to make it easier to open the `geany.glade` file. What actually happens depends on what command the user specifies. I don't know what `xdg-open` does with scripts. I'll check when I'm at a real computer.
2. I agree the commands would be better as general plugin configs, but project organizer doesn't currently have a general config. Adding it would have been too much effort, especially if the feature ends up being rejected.
3. I can remove the toolbar buttons. Maybe "add external folder" can also be removed from the toolbar since it's probably infrequently used. (The only button I use much is the reload button.)
4. Why this preference? While I don't necessarily object to moving them, next to "Delete" is not a good place because of the potential for accidental data loss, even when the Trash is used. "Open" menu items are also almost universally placed at the beginning of menus.