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When I'm looking right, save the game, and restart, I'm looking down. This breaks some original glitches/features of the game like being able to get back on the SS Anne after it was left. I have no idea why this is no longer saving player direction, does anyone know where this is?
I think you misunderstand the original glitch. The game always loads you facing down, even if you saved while facing right.
To use the SS Anne surfing glitch, you have to save while pressing right, not just save while facing right. Then when the game reloads, you will be facing right instead of down.