I got a new Husk of the Pit today and grinded it up to an Eidolon Ally and it says it still needs a crux of crota to upgrade? It also didn't start the exotic quest line for me.
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I'm guessing it's the Y1 version. You'll know you have the Y3 version because •It drops from Ogres •It has an axe symbol on its icon •It'll start up the exotic quest