I got a report from one of our users of the open source mailing list that phab's mail threading breaks for Apple Mail's "Organize by Conversation". There are enough people on the list that use Apple Mail that this is really important for us to get right. I'm happy to help investigating.
"""the e-mails that go to cfe-commits don't seem to get coalesced by Apple Mail's "Organize by Conversation" feature, even though they have the same subject."""
"""Quickly scanning over my inbox shows none of them working -- or rather, it's grouping them if they have the same sender, but not otherwise. So for "[PATCH] Add script to update AST matcher reference", I see your e-mails in one group and Dmitri's in another. I'm going to backpedal on what I said previously because I /do/ see "In-reply-to" and "References" fields in both e-mails now (not sure how I missed that, or maybe it's new). So now I'm confused.
I hope it's not trying to do something intelligent with the Thread-index header and failing, or simply choking on the long reply message name. I'll file a bug on our side too and see who figures it out first.