Thanks for reporting as @pkiller mentioned this should be fixed if you create the system folder. I have also fixed it on master as well as the error messages so you should get a better error message if the upload fails.
@julian Supporting just one use case would give the possibility to anyone with a cheap vps dedicated to nodebb to adapt to it.
If it could backup all configurations and installed plugins, with a way to restore it in another fresh installed instance, that would be very good.
@PitaJ I was able to do it by giving the nav button a unique ID in the ID section and then just controlling the tooltip/button action in JS under the custom JS section. Surprisingly easy to do as it turns out.