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Ah yeah, this was something I coded up because I assumed it would fulfill the 95% use case. Maybe some people actually do want to handle _deleted documents, though (e.g. if you are manually adding _deleting: true instead of remove()ing). I'd accept a PR to add a configuration option for this, e.g.:
Using crypto-pouch documents being replicated to pouch that are tagged as deleted don't get transformed: calvinmetcalf/crypto-pouch#19 (comment)
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