One of the most unique entries of this jam, I really enjoyed it. It is hard to understand at first, but once you get it it is really rewarding, great job !
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It is the hardest part in jams, because you struggle to make your gameplay loop to work, and then you have to think about how the player is gonna perceive it. I am no professionnal in user experience design, but you could firstmake a linear loop: the player only has one gem, he must replicate a pattern you give them, then you point out the scanner and testing features. And finally when they got throught it all you let them experiment freely to find this mysterious symbol ? You can check how mobile games explains their mechanics: it is usually a derivative of this pattern. But like I said, I don't know much, it is just how I would do it !