Al Haji-Ali <abdo.haji.ali@gmail.com> writes:

> I changed the message, removed "B" from "References" and deleted the
> files of all old (and intermediate) drafts that have "B" in
> "References".  But no matter what I do, I have "B" grouped with "D"
> and any other messages which I create with "In-Reply-To" being "A".

How did you find the files to delete? One trap to watch out for is that
if using notmuch, you should use notmuch search --exlude=false, to make
sure messages are not being hidden because of their tags.

> I suspect that somewhere in the database the IDs of "A" and "B" are
> linked now. Is there a way (short of deleting the database and
> re-indexing) to correct this and remove this connection?

The database does not store relationships explicitely, only via messages
with references to other messages. At a high level you can try the
attached script to get a picture of the corresponding thread.

If you can't run the script, or it doesn't help, you can interrogate the
database directly without going through notmuch.

if the message-id of B is 'foo@example.org' you can search with for
replies with xapian-delve (in xapian-tools on Debian and derivatives).

xapian-delve -d .local/share/notmuch/default/xapian \
             -t 'XREPLYTOfoo@example.org'

and for references

xapian-delve -d .local/share/notmuch/default/xapian \
             -t 'XREFERENCEfoo@example.org'

That will give you Xapian record numbers, and you can turn those into
files with something like

xapian-delve -d .local/share/notmuch/default/xapian -r 801793 -1 | \
             perl -ne  's/XF(D|O).*?:// && print'

For records with multiple files, you will have to figure out with file
goes with which directory (or just find the file names, which supposed
ot be unique).