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Addons on in addition to this one were jcxxp_123.pk, a hexen64 music file and an item pack. None of which should cause changes in weapons.
i really love your weapons, but could you perhaps split the weapons and the items into two pk3s?
i always use psychikons items and they collide with the one in your pk3, and the way you made it you have to use both your weapons and items or neither.
so could you perhaps split them and make 2 PK3s out of them, one with the weapon-stuffs and one with the vial and flash?
Its strange, but i can't see your models in the game.