Some, perhaps not all, of these folders were made undeletable a long time ago by Don at DeeDee's request. I think the problem was that sometimes her class admins would delete them and then other actions threw errors because they expected these folders to be there.
Perhaps the better fix would have been to remove the dependencies, but it was a long time ago when there were a lot of bugs and we were trying to fix them as fast as possible, and I believe this is the behavior DeeDee wanted anyway, so it made sense at the time.
