Imagine the situation, when you have two folders never being synchronized, but that contain pretty similiar information. For example, two photo albums — on your notebook and home PC, distributives or music collection. At the current time they have a lot of similar information stored in same folders in hierarchy, but also a lot of similar information stored in different folders. If you sync them now you will have a lot of dups. So at the moment of sync you need tool, that can lead you to choose correct directory structure of synchronized collection.