The rune system is quite criticised and it’s mostly because of how clunky it is to use.
I suggest you add a rune library at the enchantress. We then:
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add runes to the library by extracting them from a piece of gear (destroying it in the process)
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pay with money + materials the cost of adding a rune, without having to go through the motions of remembering which weapon has it, crafting the weapon, and removing the rune from the weapon.