(SPOILER) The nail does serve a purpose. If you click the wall behind the alien with the pristine nail, you'll notice that it makes that strange marking on the note. Look closely at the wall markings. there is a //// with a slash through it that means 5. People who are trapped in places like prison make these slash marks to mark one day and count the days. usually there are a lot of those marks, but instead, there is the symbol instead, suggesting that the symbol = 5. The nail mark was to show that the alien Jay was slowly turning mad and drawing those symbols himself. The code includes a number with that designates the symbol drawn on the chalkboard, so you needed the nail to know that the symbol was 5. Although I guess you can just do a trial and error :P Just trying to defend the creator with his logic and that he did not create useless stuff in this game. Big fan! Can't wait for the last Submachine game.
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