I'm struggling to even set up the basic setup from the first example - is it supposed to feed chocolate in and out of the mine? no matter what I do nothing seems to connect
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Yes, it's supposed to take from the miner and put it back into the miner with the chest as a buffer. You need to make sure that the funnels are right next to the miner and the chest. If there is space between the funnel and the miner/chest, the funnels won't funnel. You can hold space to align buildings to each other and to center miners on veins.