So the tip being, when you are within a common area, such as your documents, it is a good idea to have everything in some folder and anything that is not within a folder is to be considered a 'system file' or 'common file' for the system. Why is this a good idea? Because from a technical point of view, any file that is not in the folder is quickly identifiable and in the case of any malware (for example) you would more quickly be able to determine just why this file is not in a folder. This could also happen for any new program you have installed.
I notice this sort of maintenance as being useful for such folders as your 'download' folder within a MAC or any folder you may choose as your 'internet downloads' folder.