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> When I want to reply to someone, do I email the list or the person?

Reply to person, CC the list.

> How do I make sure the emails are threaded properly?

Using In-Reply-To header that references parent Message-ID. Git asks for it when sending a patch.

I disrecommend using In-Reply-To when sending a revised patchset. Just start a new thread. Mailing lists which prefer In-Reply-To are in the minority.

The git mailing list seems to be a mix between the two and their submitting patches document doesn't seem to indicate which convention is preferred.

Which mailing lists recommend against using the In-Reply-To header referencing the previous cover letter?

All lists on lists.sr.ht, for one.

Using the In-Reply-To header requires foreknowledge of email headers, the purpose of Message-ID, and how to find it. It's not very approachable. Most mailing lists who have thought about it don't ask users to do it.

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