1.2 upgrade problem -- controller auto loading?

First - apologies if the core group is an inappropriate place to
repost this. I'm still looking for a definitive answer, and I'm
hoping you might help.

Well, it’s somewhat designed. I lost many many hours on this one (long time ago). After some research, it turned out that this was happening:

I had a plugin controller in myplugin/lib directory. That controller inherited from the ApplicationController. Now, the way dependencies work is that they unload stuff in development mode in certain directories like app/controllers, but not anyplugin/lib. So, ApplicationController would get unloaded, but not my controller that inherited from it. This made Dependencies choke, and it was exactly triggered by a before_filter in my case also!