Are there any magic systems in the cosmere that aren’t shard based?
This depends on definitions. The effects of Adonalsium permeate everything, and Adonalsium is also the source of the Shards. It is possible to find a magic that isn’t DIRECTLY powered by a specific shard, however, though most of these would have been set up before the shattering and would be much smaller in scope than things like Allomancy and Surgebinding.
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