Well, it really wasn't. You'd program by punching the cards, and then insert them into the computer. If they brought the boards from a terminal (or replicator), and switched the old ones to the new ones, the entire thing would make sense.

It's a bit similar to how people programed analogical computers at the 50s. But it's actually a lot like programing old sewing machines. The thing those have in common is that their programs were always an order of magnitude smaller than this comment.