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I was playing this single player. I'm not sure which cubes I went through, but I managed to get the cyan key after getting the green and red keys. Then I went through the cyan gate and got the pyramid level cube, and went back and found that the connecting room changed.
So I think the cyan key was meant to be the last key, but I got it early. Is something like this supposed to happen?

Also, I think I was supposed to connect the cubes in one of the three given orders and connect the pyramid at the end, but I just connected the pyramid directly to the starting cube. Then as the left brain, I went through the door, hoping to enter the pyramid. But the left screen went yellow, and the right screen went red for a while and the game restarted to the begining. What happened? Did I win?

I saw a few people mention a VVVVVV level mapper. I think it would show a player made level as a minimap (like in the main game's pause menu) but I can't find it anywhere. Where is this mapper?

I already saw the instructions to add or update the levels at "my documents". So that's what I've been doing.
But I noticed that the original 10 player made levels files could also be found at "program files".

For "a new dimension", I have an old version at "program files", and the new version at "my documents".

What are the files located at "program files" for if the game apparently uses the files from "my documents"?