I was very frustrated at first that I didn't understand anything, and then I got it with the readme!
I never could finish stage 1, maybe I did not get everything but after dying 3 times because the red area is totally isolated, I feel that your automata should have a little tweaks to always let a way in.
Anyway, well played, it's a great idea to include a cellular automata in a game like this, I never played a game like this, so thank you!