1) Books by Folder doesn't show the root of the IM, but the /database/media/books. If there are no other cards, the IM is chosen automatically.
2) The current structure is meant only for beta testing and quick updates. I am still not sure what's the best way for the release. Whether I'll keep the js files in IM or include them in /opt etc.
I doubt it's that easy, but will give it a try.