j is in the global notmuch keymap bound to notmuch jump. In tree-mode
it makes sense to close the message pane first (otherwise the new
search runs in the small top pane of tree-mode).
(define-key map [remap notmuch-search] 'notmuch-tree-to-search)
;; Override because we want to close message pane first.
(define-key map [remap notmuch-mua-new-mail] (notmuch-tree-close-message-pane-and #'notmuch-mua-new-mail))
+ ;; Override because we want to close message pane first.
+ (define-key map [remap notmuch-jump-search] (notmuch-tree-close-message-pane-and #'notmuch-jump-search))
(define-key map "S" 'notmuch-search-from-tree-current-query)