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With the release of psychic disciplines in 6th, and the fact that they make very little mention to Codex powers in the rulebook, could it be possible that they are phasing out the Codex powers and completely replacing them with the discipline system?

No way. As an Ork player I'd be a little upset.

Notice that the card holder is only half full with the rulebook discipline cards?

I can guarantee they won't pass up the opportunity to sell more cheap to make psychic decks.

I also think it's unlikely. I think what we're seeing is an expansion of psykers being a more important part of the game (and thus getting a bunch of new stuff), rather than stuff just getting consolidated.

They're going to be bringing in army-specific psychic disciplines in every codex.

Pretty much a carbon copy of the system they use for Magic in WHFB. You have a generic set of disciplines in the BRB and then each army has their own flavor of magic, or in this case warp spawned powers, to chose from.