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What forms of HP are meant to be taken into account for Giant Gene's multiplication? Just for ease, I'll note the ones that I can remember.
Stat Point Allocation
Base VIT
Base SAN
Bonus VIT (EX Equipment and Traits)
Bonus SAN from all-around stat buffs (EX Ki Awoken)
HP Bonuses from Equipment (Gloves, Tarrasque Shell)
HP Bonuses from Classes (Hexer's Endurance, Soldier's Tenacity, Ghost's Afflicted Spectre)
Exceptional Health
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Giant gene adds to your base HP amount, so it'd be HP granted by VIT/SAN and exceptional VIT trait, and thats it.
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It applies at the same time as other item-based modifiers to HP, depending on the order you equipped them it might apply before or after other HP modifiers. Could be changed to factor only base HP, or a little less chaotic order, but that's how it works now.
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For the sake of uniformity, I think it would be nice if it either applied either only to scaled vit/san/base or to hp after all modifiers, but if it's possible to fix just with equip order it's not a big deal.
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Ideally the player shouldn't have to worry about that, though, especially since it's not-obvious, so I think I will go ahead and separate all of the property boosts to HP into separate loops so that there's some consistency.