Really nice idea, I don't know if the checkpoint not working was simply where you got to in the development process but nevertheless it's a clever mechanic you've got going on.
I would have liked some way to reset with a clean slate once I figured out my current objective, otherwise it got sort of overwhelming with the clones when I was in the "figure out what to do next" phase and made it difficult to systematically experiment. But this is a good start, good job guys!
loved programmer art