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I am running a squad of shining spears, and i was wondering whether i should run them with a farseer for fortune or an autarch for some CC punch?

As far as I know the support spells from the farseer will give you more millage. I would wait for a more seasoned Eldar players input though.

Farseer all the way. It can do more for the Spears and the army as a whole. Some people like using Divination, I prefer the codex powers, mainly fortune. Survivability is important for Spears as they are few in number likely to be shot to ribbons if the enemy gets the chance. However if you're feeling lucky you could try and roll for that 4++ inv sv one which I could see being very useful if you're assaulting anything that can hit back hard.

Also Runes of Warding.

An Autarch can't do these things, a Farseer can.

Any opinions on guide for them too? Plain farseers can take it right?

Guide is good for a shooting squad( dire avengers , dark reapers , etc.) fortune and doom are my favourites .

Farseer all the way. You may just want to keep it cheap and just take fortune. Otherwise doom is usually better.

This is actually a reasonably effective unit to clear backfield fire power as you can turbo boost first turn.

Just do not whatever you do charge a dedicated CC unit like a wraithstar. They will eat you alive.

Why not both? The farseer will add survivability and versatility while the Autarch will significantly improve their killing capabilities in close combats with the flurry of blows that s/he can dish out.

I have often used a shining spears squad with an autarch, and I found that a farseer was almost necessary to stop them being shot up (by using Fortune). Without it, the squad is just far too fragile for its cost. Even with fortune, eeeeh.

Frankly you're better off not taking shining spears at all. Hate to be a killjoy, I love the idea of the unit, but they just get slaughtered. Units that are expensive, fragile, and only sort of good on one round of combat if they get the charge, are just not a good idea. If you want a jetbike close combat unit, try warlocks.

I would also argue using prescience and trying to get foreboding ( I think, the 4+ invul) since you can re roll while in combat as well while you get that lovely 4++

Well, Shining Spears are too expensive for what they can achieve. At the competitive level, I'd run a squad of Jetlocks led by a Fortuneseer.
Shining Spears could be used to target isolated squads or squads (shooters or objective holders) in the enemy back field. Fortune will keep this unit longer alive. An Autarch is too fragile.

I agree, Farseer. The Autarch is a... well, I hate em. As an HQ I feel they are mediocre. The Farseer is great for Psyker, plus he helps DTW, PLUS his Awesome Fortune and all, PLUS the Spear of Doom (singing spears terrify folks I play, killed several FLYERS with em lol...) AND he's got the Invuln. On a bike, even more scary, plus a nice retinue. Expensive, yeah, but dang they work well.