The fediverse is the overarching architecture. So lemmy is part of the fediverse. It is a federated collection of servers that are somewhat independent, but still part of the system. I'm going to make a very poor analogy, but think of it like your spice cabinet. The individual spices are instances while the cabinet itself is the fediverse. Or at least that's my understanding of it. If I'm mistaken, please someone enlighten me.
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