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As for the Codex zone - I've only played around with it a bit but it seems like the answer is yes, you have to drag the cards to your zone for your codex. It's also annoying that there's just one copy of each faction because with multi-color decks often two players have the same specs.
I'm not sure the module is being maintained though... I wouldn't count on any updates for tokens etc.
Also, could you make it so that the token stacks are "infinite bags" or whatever the TTS terminology is?