Man, that blows. I find the current model (and only one I can remember? Maybe I did use it when it worked that way, and just didn't realize it) of keeping all user packages totally separate from the core system and just linking them in better and safer than what e.g. most Linux package managers do—now that I'm used to my package manager not really being able to mess up my base system, I wish all the rest worked that way, too :-/