Why is it called the Junk Yard?
Short answer: The "junk" is the throwaway snippets you copy all day. The Junk Yard holds them for a while and clears them on a timer; it has nothing to do with junk files on your disk.
Because it's meant for throwaway bits — the snippets, links, screenshots and notes you need for a little while and then don't. The board catches them and lets them go on a timer, the way a yard of odds and ends gets cleared out.
It isn't about junk files on your disk. The Junk Yard never scans or deletes anything on your drives; it only holds scraps. If you want something permanently, save it somewhere proper — the board is designed to clear itself.