This is one of those cases where the warning looks absolutely correct,
(complaining about a free variable), but I'm left wondering how the
original code could have worked at all.
From what I can tell, this code wasn't actually being called by any
of the current code in notmuch.
Initially this file provides one main function
notmuch-query-get-threads, which takes a set of search terms, and
returns a parsed set of matching threads as a lisp data structure.
A set of notmuch-query-map-* functions are provided to help map
functions over the data structure.
The function notmuch-query-get-message-ids uses this machinery to get
the set of message-ids matching a query.
Edited-by: Carl Worth <cworth@cworth.org>: Change comment syntax,
(";;" rather than ";" to make emacs-lisp mode happy), and eliminate
some excess whitespace, as suggested by David Edmonson.