I haven't personally run into circular dependencies in Godot yet, but in a way that makes me even more concerned because I know they've gotta hit someday
And yes! Git! Git is my favorite thing in the world, Git is great, Git saves lives!
I *have* run into really weird 2D lighting issues in Godot though, I think that particular chunk of the engine has not received proper love over the year, it all felt kinda broken and backwards when I used it in the past. I think a lot of people completely disregard it and program their own 2D lighting because it's so bad.
When I was still in college I had a class where we had to make a game for a "client" aka another student with an idea. Our client wanted us to make a relaxation game, with breathing exercises and 6 different mini-games to help with different negative emotions. But the kicker is we had to program the whole thing from scratch in Java with no game framework! This game really reminded me of working on that project, but I'm just rambling lol.
Anyway, I really liked your game! I struggled a bit at first understanding what was going on because the mouse indicator didn't show up until screen 2, but it was fine from there!