As it stands now, the user has to upload the files individually to the server, in the correct places, while this is not particularly hard, it could be easier. Since we already upload an addon.xml file to actually install the mod, we might as well upload a .zip that contains both the php files and the xml file
Implementation wise, we already use library/ for almost everything, we could have another directory called addons/ which would be added to the php search path, and, ready, addons with auto-install without ever conflicting with the main code (an addon cannot upload a rogue XenForo_ControllerPublic since everything would go to a different directory). Since already data and internal_data are chmod 777 adding one more directory to that should not be that much of a problem
This would make installing and uninstalling addons a really pleasant experience. It could actually be one click to deleting the relevant files.