Very interesting. Have some feedback though.
- The confusing instruction manual is not good, and it needs basic tutorials. You already have to deal with the difficulties of both doing things in machine code, and actually understanding the level itself.
- There's also the inconsistencies of how the inputs and outputs behave differently from other hexagons. I think making the input/outputs different, like being circles, would help clarify that they're different.
- The hexagons having separate sides really doesn't add anything to the game. It's just unnecessary confusion that doesn't allow any additional capabilities. You could replace the "rotate" and "copy" commands with something like hex copy (like "move", but doesn't clear the source).