They basically removed gear from the game that was impossible to balance. Go to a city guard and ask them for the Master Crafter, it will put a ping on your map where to find them. Trade them the tokens, the one in academic circle is especially hard to find since their name is up in the roof and you can't see it. It is a mordesh female. Trade your tokens in for gear. Then go to the rune crafting station, there should be a shack right next to it with a few red box like machines called 'rune exchange' where you exchange the rune tokens for runes. I would suggest watching the video posted on the previous page which details how to rune gear before you actually try to rune the gear and 'ruin' it or waste runes. If you had any crafted gear they basically gave you back all the crafting mats. empty your mailbox, put the gear on and go have fun.
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Also they removed all the pvp crafted gear and I noticed there was no ability to make cloth anymore. So you won't have them in your tech tree anymore. I use to have 5-6 levels of bonuses to crafting but now I have 2 and I had to pick the bonus I wanted. You basically lose any points you may of built up by completing the tech tree for recipies that were removed. You may have to start over again for the most part but the good news is they gave you mats back to get the ball rolling.