You do know that when you insert an image into Hype it copies it to the resource folder for you. 
rather than keep a reference. This is only if you've added it via the insert menu or the background image in the Element inspector or via a drag and drop from your file system.
Not to take this away from the thread of having a smart folder system. Just thought you would like to know. Not knowing your setup I can't imagine why you have files and folders everywhere.