It would be nice if the autosave files created by emacs or other editors were not picked up by arduino as being part of a sketch. In this case, emacs is naming autosaves something like ".#filename.c", and arduino comes along and says "ends in '.c', must be source code." I think it should ignore anything starting with '.'
Good idea. I put it on the list: https://developer.berlios.de/bugs/?func=detailbug&bug_id=11943&group_id=3590.