Nice, thoughtful article. Thanks for the insight.
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I also found on a recent playthrough that if you get a missile pack before you're supposed to, you'll be unable to pick up the one to the left of the downdraft fan (where you're supposed to first get missiles). I made the mistake of grabbing the missile pack from the hole in the roof of the missile turret room using an infinite foam ladder, but then found much later that I couldn't pick up that initial missile pack later in the game.