All clans that have come up with sets of clan gear should now be able to trade in the base item for their clan equivalent at their clan's armorer. Cloaks and Master Weapons are to be issued and turned in at your clan head from now on.
If you acquire a piece of clan gear (not cloaks!) and wish to trade it in for its base item, try giving it to one of the shopkeepers or smiths in the nearest city.