Then you're missing the Graveyard, the Crystal Path and the Tower Keep.
The Tower Keep is at the top of where the shopkeeper is. The bulk of it is a puzzle platformer, so experiment a lot with back and forth.
The Crystal Cave and Graveyard are found in the opposite direction of the Machine where you fight Clemantis. There's a path to the right from the save point at the Left/Right split.
well there is a door with the shopkeeper but i'm missing the key.
also where is "Clemantis"? i cannot find a boss in the gallery with that name. when i go backwards from the boss of the metal area (krystal) there is a very vertical room with a bunch of those "rejected" guys and a safe crystal, but the left entrance of the room is locked and i don't see a way to get to the other side to flip the lever.
i feel like i cheesed the game a bit and went through that area backwards because in the bottom of the dungeon you have tiles that look like the metal area but with a sign saying that it's the end of the content, but in the gallery the metal area room was unlocked for so i teleported directly to the boss and went on from there.
how are you intended/supposed to get to the metal/machine area?
i also went through the entire corrupt matrix but there was nothing there besides another sign.