Re: Possible some threads are not complete due to bug?

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+References:\r
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+Date: Wed, 23 Sep 2015 20:55:32 -0400\r
+Message-ID:\r
+ <CAJhTkNhp=mMPsD7hkGKW4eY9WWOuS2pf=x4sDiLnx9ref9JTew@mail.gmail.com>\r
+Subject: Re: Possible some threads are not complete due to bug?\r
+From: Xu Wang <xuwang762@gmail.com>\r
+To: David Bremner <david@tethera.net>\r
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+On Wed, Sep 23, 2015 at 6:44 PM, David Bremner <david@tethera.net> wrote:\r
+> Xu Wang <xuwang762@gmail.com> writes:\r
+>\r
+>> Because when I do a notmuch search for that message by message ID with\r
+>> --output=threads, it gives a different thread ID.\r
+>>\r
+>>> Isn't that what your first command tells you?\r
+>> Well yes, but I wanted to confirm that that is indeed the reason. I\r
+>> have heard in someone saying that debugging is process of confirming\r
+>> things that should be true.\r
+>\r
+> I'm still confused. It sounds like you gave the same command twice and\r
+> got different answers. Can you maybe show the complete sequence of\r
+> commands and output (assuming it's not too large)?\r
+\r
+Dear David, thank you for your kind persistence. I apologize for the\r
+lack of clarity in my writing. Below is the full sequence of commands\r
+(I just subsitute MYMSGID and MYMSGIDREPLY for two message IDs) as\r
+well as my thought process.\r
+\r
+$ notmuch search --output=threads "id:MYMSGID"\r
+thread:000000000000a125\r
+$ notmuch search --output=messages "thread:000000000000a125"\r
+id:MYMSGID\r
+$\r
+# I know that MYMSGIDREPLY did respond to that message. I have it in\r
+my mutt mailbox and it shows the down-right arrow signifying this. I\r
+inspect the headers and there is indeed a header in MYMSGIDREPLY that\r
+says "In-Reply-To: <MYMSGID>". I then do...\r
+$ notmuch search --output=threads "id:MYMSGIDREPLY"\r
+thread:000000000000c125\r
+$ notmuch search --output=messages "thread:000000000000c125"\r
+id:MYMSGIDREPLY\r
+$\r
+\r
+# What I expected (and did not get) was the following output:\r
+$ notmuch search --output=threads "id:MYMSGID"\r
+thread:000000000000a125\r
+$ notmuch search --output=messages "thread:000000000000a125"\r
+id:MYMSGID\r
+id:MYMSGIDREPLY\r
+$\r
+\r
+# after regenerating the notmuch database, I did indeed get the output\r
+that I expected.\r
+\r
+Kind regards,\r
+\r
+Xu\r