in reply to Bad conscience
It's too late to save your job by obfuscating. Your boss has downloaded the code. So you may as well do what you know to be the right thing. As soon as your boss notices you changing your style, you will be out of the door without a reference.
But, as a moral individual who always works with the best interests of his employer at heart (stop laughing in the cheap seats), what about your boss's behaviour? Depending on who's who on the food chain, I would be very tempted to go to HIS boss (or someone higher. Do you have an internal audit department? Compliance? Even external auditors if they're due in soon anyway) and say something like "I'm sure he's just doing his job and checking my work, but you do know about all these downloads, don't you? I'd hate to think that someone was blackmailing him into betraying company secrets & we didn't help. Whenever I've asked, I've been brushed off".