Exactly (on the first two paragraphs). I (almost) never type anything into the REPL window itself. I might type a "5" and evaluate it just to see if the REPL i

Exactly (on the first two paragraphs). I (almost) never type anything into the REPL window itself. I might type a "5" and evaluate it just to see if the REPL is busy or not, but otherwise, everything the REPL evaluates comes from an emacs source code buffer, sent via CIDER to the REPL. At most, it might be in a "Rich comment" and thus not evaluated next time I load that file, but those tend to be small, interactive tests and not defns. Unless emacs crashes with the buffer unsaved, there's nothing the REPL has that the source file doesn't.