******Spoiler Alert!*****************************************
Commenting here just in case anyone gets stuck at any point in the game! Here's a quick breakdown of how to complete a few of the more complex puzzles.
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First Room: You need to "use" the knife (pressing X twice) to open it, followed by using the opened knife on the nearby plants. Follow up by combining the stick with knife, to create a crowbar in order to open the sarcophagus.
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Floor Trap: Use/Inspect the skull in your inventory, the correct pathway is engraved on its forehead.
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Switch that is blocked by Plants: First you'll have to drink some of your Blue Nebula, followed by cutting off a piece of clothing from the Corpse in the main room near the Floor Trap entrance. Combine the drink and the rag, after completing the One-Eyed Statue (see below) you will use this rag in bottle with the statue to create a Molotov cocktail - use this with the plants to burn them away.
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One-Eyed Statue: Use your knife with the skull to remove a gemstone, place that gemstone into the One-Eyed Statue.
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Lever surrounded by Fish: Cut off some vines, from the nearby wall and combine with your knife to create a grappling hook. Use this in front of the water to pull the switch.