Probably handle it similarly to how Chrome handles an extension asking for new permissions. It disables the add-on and gives the user a small non-intrusive notification on the options menu. Opening the notification notified the user about the change in permissions and asks them if they want to re-enable the add-on or remove it from Chrome.
Good solution, perhaps two simple options at browser install: Default / Custom. That way you don’t have to uninstall all the stuff at the end.
But how should they handle a version update where a given addon is added. A popup?
Probably handle it similarly to how Chrome handles an extension asking for new permissions. It disables the add-on and gives the user a small non-intrusive notification on the options menu. Opening the notification notified the user about the change in permissions and asks them if they want to re-enable the add-on or remove it from Chrome.