During update / reconfigure, overwrite Procfile by default?

With !989 (merged) and !990 (merged) we have wide support for remembering (via gdk.yml) that a user wants to run services that are off by default.

Is this a good time to change things so that gdk reconfigure and gdk update overwrite Procfile? The default is still to complain if there are changes.

I'm proposing this because we have told too many people, too often, to run rm Procfile; make Procfile to fix their GDK. If we always overwrite Procfile this happens automatically.