The --initialize flag is responsible for creating a new Drive at the server_url. If this is not done after changing the --domain or --server-url setting, the user can be met with a resource not found error. This is frustrating to new users, and we should make sure we can deal with this automatically.
Re-run initialize when server_url is different
This seems to be a decent solution. Note that this way there can be multiple /setup invites, but each is scoped to its own drive, so it should not be a problem.