Are you suggesting that all but the oldest message should be considered replies to the oldest message, even though they are not, even though they and the oldest message are replies to a message that is not in your folder?

(In reply to comment #1)
> Are you suggesting that all but the oldest message should be considered
> replies to the oldest message, even though they are not, even though they
> and the oldest message are replies to a message that is not in your folder?

Exactly. Otherwise, such thread will not be considered as thread.

In practice, Such kind of "thread" are produced by certain applications (like Jira or Discourse) that send emails about user's comments to it's threads. 
Well, bugzilla seems sends such kind of "threads" too.

Could you dummy up a virtual message that says, "Threading appears to be broken.  There are N sub-threads that might (or might not) be replies to a missing message."?

Jira became pretty popular, so it would be very nice if this could be implemented.

(In reply to comment #4)
> Jira became pretty popular, so it would be very nice if this could be
> implemented.

Maybe a bug report against jira is needed, then?

No, other mail GUIs can handle email threads created by Jira fine (e.g. thunderbird, outlook (as I was told)).

(In reply to comment #6)
> No, other mail GUIs can handle email threads created by Jira fine (e.g.
> thunderbird, outlook (as I was told)).

That means nothing in itself.

*** This bug has been marked as a duplicate of bug 2258 ***

Harri please take a look and comment on bug http://www.thewildbeast.co.uk/claws-mail/bugzilla/show_bug.cgi?id=2258. There is a patch proposal there, please comment if you're interested.