>> I haven't tracked through all the logic of the existing algorithm for
>> this case. But I don't like hearing that notmuch constructs different
>> threads for the same messages presented in different orders. This sounds
>> like a bug separate from what we've discussed above. 

I think I have now found this bug and it is separate from the malformed
In-Reply-To problems.

The problem is that when we merge threads we update all the thread-ids
of documents in the loser thread. But we don't (if I understand the code
correctly) update dangling "metadata" references to threads which don't
(yet) have any documents.

To make this explicit consider the 2 messages 17,18 in the set. 

Message 17 has id <[email protected]> and has no
references/in-reply-to so has no parents.

Message 18 has a reference to <[email protected]>
and an in-reply-to to <[email protected]> and
<[email protected]>

If you add 17 first then it gets thread-id 1 and then when you add 18 message 
18 gets
thread-id 2 as does the dangling link to the "unseen" message
[email protected], and then message 17 is moved to thread-id 2.

However, if you add 18 first then it gets thread-id 1 and the dangling
link gets id 1. When 17 is added it gets thread-id 2, message 18 gets
thread-id updated to 2 *but* the dangling link to [email protected] does
not get updated so stays thread-id 1.

In particular when 52 comes along with its link to [email protected]
then:

        In the first case it gets put in thread-id 3 and the other two
        messages get moved into thread 3.

        In the second case, message 52 gets put in thread 3 and thread 1
        (the dangling link) gets moved into thread 3 leaving thread 2
        (containing messages 17 and 18) untouched.

Best wishes

Mark





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