last week on Thursday I worked with TJ to reorganize  the whole project in order to bring it in line with coding standards and to make it easier to find objects, materials, etc. it went well for the most part moving folders and objects had no problems. but renaming scripts broke almost everything since unity forgets anything that was attached. So we had to put it all back together and that to forever. So I would say break your projects and clean it up now before it becomes a tangled mess later.