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Deformation skeleton before rig


Is there a way to create shifter rig on preexisting Deformation skeleton (for games) and the extending it while adding joints? Or the i create joint and attach shifter to it afterwards. Also can i change hierarchy of twist joints so that they are all parented to upper arm or lower armo jnts and etc. ?? Or do you think its better to actually create another deformations skeleton just for the game engine ?