In the thread at id:87fsfuuxwn.fsf@thinkbox, a bug is discussed where
the point and hl-line overlay get out of sync, leading the user to
open the wrong message. As far as I can tell this is caused by
notmuch-hl-mode being invoked too early.

This change bypasses the logic preventing notmuch-search-hook being
called only once, so that the overlay is updated later after after the
buffer is full(er).

This change may lead to the overlay being updated multiple times; if
this is annoying we can add a similar buffer local variable to ensure
it is only called once.

The extra logic to check notmuch-search-target-line reduces the
flicker somewhat by not highlighting the first line every time.
---
 emacs/notmuch.el | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/emacs/notmuch.el b/emacs/notmuch.el
index f55e9b42..108bccec 100644
--- a/emacs/notmuch.el
+++ b/emacs/notmuch.el
@@ -126,13 +126,17 @@ there will be called at other points of notmuch 
execution."
   :type 'file
   :group 'notmuch)
 
-(defcustom notmuch-search-hook '(notmuch-hl-line-mode)
+(defcustom notmuch-search-hook nil
   "List of functions to call when notmuch displays the search results."
   :type 'hook
-  :options '(notmuch-hl-line-mode)
   :group 'notmuch-search
   :group 'notmuch-hooks)
 
+(defcustom notmuch-hl-line t
+  "Use hl-line-mode to highlight current thread / message"
+  :type 'boolean
+  :group 'notmuch)
+
 ;;; Mime Utilities
 
 (defun notmuch-foreach-mime-part (function mm-handle)
@@ -925,6 +929,11 @@ sets the :orig-tag property."
        (notmuch-sexp-parse-partial-list 'notmuch-search-append-result
                                         results-buf))
       (with-current-buffer results-buf
+       (when (and notmuch-hl-line
+                  (>=
+                   (line-number-at-pos (point-max) t)
+                   (or notmuch-search-target-line -1)))
+         (notmuch-hl-line-mode))
        (notmuch--search-hook-wrapper)))))
 
 ;;; Commands (and some helper functions used by them)
-- 
2.43.0

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