I can't remember where I heard about this. On one of the nook boards, someone posted that they found a freeware program that sorts files in external dries. They used it to sort files in their nook My Documents folder so that they ended up in alphabetical order by title.
Does anyone know what this program is? It's not Calibre -- it's a smaller and simpler program. Probably too simple, but sometimes simple is what you need.
