Documentation - SkinEditor docs must state that end-users should not create files/folders within a skin's folder

While SkinEditor is an exceptional tool it does have a rather serious shortcoming or at a minimum a quirk that really should be documented. I have begun the rather comprehensive undertaking of creating a new skin using an existing skin as a workflow template - keeping me on track of what needs to be done, what requires graphics and what is done with properties etc. Otherwise the skin is completely from scratch.
So far so good. I edit the graphics opening them in PhotShop, look at the existing graphic to assertain the states needed and then create a new one. This new graphic is then saved as .PNG while the original .PSD file is saved alongside it so I can revise the graphics keeping the original layers intact. This is where the problem comes in… at some point, either when closing SkinEditor or when changing element, the files not directly used by SkinEditor are deleted from the folder structure. That is fine if you want to keep a tidy project but not so fine when there are support files in those folders. Definitely not fine. All my .PSD files vanished and I had gotten all the way down to Editors!
Proposed Solution:
There are two solutions that spring to mind: One is to at least inform the user of this behaviour to avoid a painful learning experience. The other is to make this folder tidying optional and settable from the Options menu. The latter would be a welcome change indeed.
I now get around it by having a parallel folder structure but that is not quite enough because PhotoShop and indeed every other editor I know of, opens the last used folder. Opening a graphic from SkinEditor would make that the project folder making it necessary to specifically navigate out of that folder to open a .PSD original.