There are a number of file manager applications in the App Store, all intended to help organize or at least manage file storage. Given your sister's lack of discipline in keeping things organized one of those apps might be just what she is looking for. I have looked at several of them, but I would hesitate to recommend any one of them because each seems to target a particular way of organizing or disorganizing and you need to find one your sister can live with.
The best suggestion I can make is to go to the App Store and search on file manager or file management and then spend some time with your sister looking at the various offerings to find one that appeals to her. You will find some that work hard to create order out of chaos and others that don't give a care where the files are and focus on being able to perform complex searches to find what the user is looking for. One of the latter types might be just what the doctor ordered for your sister. She could dump everything into one undivided Documents folder and use to tool to find what she wants. (Caution) this type of tool often relies on file tags to narrow the search and it takes at least some discipline to create the tags along with the file.
Another possibility might be a database such as Evernote to store and organize the files. That still requires some user discipline, but the GUI might create a visual picture your sister can relate to.
