Ok, adds arcane damage.
Are there damage interactions? Like, what happens when arcane and holy damage are fused? Does my holy crossbow have an issue with me turning into a dark spirit and doing dark damage? What would happen if I made an attack that dealt both fire damage and ice damage?
Arcane + other damage types adds up their effects, arcane can be converted to elemental as well. Dark cancels holy and vice versa. When you are a dark spirit, you deal dark damage only, everything gets converted into dark. Elemental damage in high amounts cancel each other when you use antagonistic elements. Casting a fire storm and frost nova will get you some water droplets sprayed around. In small amounts, you cast a spell that shots a firebolt, but it gets weakened by a tiny fraction when affected by your ice aura.
1) The crystals are clearly a trap
2) What can I upgrade with amethyst in my inventory? Is there enough to upgrade everything? Does a roll determine the result? If yes, would a 1 permanently ruin my stuff, make it worse, etc?
1) Rolls will show...
2) You can upgrade literally everything. Weapons, armors, charms. Each thing will require using it in different form. Like, if you want to upgrade your tome, then you need amethyst powder or getting it encrusted with gems. Weapons can have them as gems placed in sockets or powder mixed into the alloy. With charms you use powder on them or just strap the gem to them, or use amethyst as a gem in ring/amulet. 1 gem = 1 upgrade. Roll does determine result and there's chance to damage your item. It can go as bad as to a need to reforge weapon/get new item.