Inconsistency between tag database and notmuch search

[Navin Kabra]

I've managed to get my notmuch tag database in an inconsistent 
state and
can't figure out how to fix it. Because of this I have "unread" 
messages sitting in my inbox permanently and I can't get rid of 
them.

Specifically, I have a few threads/messages that don't have any 
tags,
but still show up in notmuch search for those tags. And using
notmuch tag to remove (or add) any tags on these threads has no 
effect. Doing a `notmuch compact` does not fix this issue.

(I believe I managed to do this by running some notmuch commands 
while a
`xapian-compact` was running in the background.)

Here are some commands that demonstrate the problem:

    ~$ notmuch --version
    notmuch 0.23.5

    ~$ notmuch search thread:0000000000058ca0
    thread:0000000000058ca0  February 22 [1/1] Mandar Joshi; 
    Announcing TiECon Pune 2017 - Pune's largest, most energizing 
    startup event! ()

    ~$ notmuch search thread:0000000000058ca0 and tag:inbox
    thread:0000000000058ca0  February 22 [1/1] Mandar Joshi; 
    Announcing TiECon Pune 2017 - Pune's largest, most energizing 
    startup event! ()

    ~$ notmuch tag -inbox thread:0000000000058ca0 

    ~$ notmuch search thread:0000000000058ca0 
    thread:0000000000058ca0  February 22 [1/1] Mandar Joshi; 
    Announcing TiECon Pune 2017 - Pune's largest, most energizing 
    startup event! ()

    ~$ notmuch tag +inbox thread:0000000000058ca0 

    ~$ notmuch search thread:0000000000058ca0 
    thread:0000000000058ca0  February 22 [1/1] Mandar Joshi; 
    Announcing TiECon Pune 2017 - Pune's largest, most energizing 
    startup event! ()


As you can see from the `()` at the end of the notmuch search 
output, this thread has no tags associated with it. And still, it 
is showing up in the notmuch search output.

What should I do to get rid of these messages from the notmuch 
search output?