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In the eldar codex it says

" farseer mat take any of the following"

under autarch it says:

"may take up to two of the following"

where does it state you cant take the same upgrade twice.

you can take two plasma pistols in the marine codex. two chain swords for an autach. they wont do much but hey....

am i just trying to rules lawyer better farseers or is there a legit reason why i cant take 3 runes??

This is a permissive rule set, you need to be told what you can do, not what you can't (other wise you can just declare your self the winner since it doesn't say you can't)

If you examine the end your codex carefully where it lists that they my take options, Under Auratchs and Farseers It has an item and the points value for that item. If you look at something like a Wraithlord it has an item, and "# pts each". This is how you can tell whether or not you can take multiples of items in your codex.