Why do I always miss stuff. My biggest gripe with mutt was that it couldn’t sort threads by the last message received in each thread. Turns out it can. ‘set sort_aux=last-message-received’
Update: Along the same lines.. it turns out that if sort_re is set, then message will only be threaded if they both match the reply_regexp regular expression in the same way. You have to unset it to make it check the unmatched part of the subject line. And it’s set by default. Double doh.
With this new knowledge in hand, now mutt does exactly what I want it to. Double True.

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