Hi,

1. `org-notmuch-store-link' does not allow to store links to email at
point in tree view.  Easy fix:

--8<---------------cut here---------------start------------->8---
(defun org-notmuch-store-link ()
  "Store a link to a notmuch search or message."
-  (when (eq major-mode 'notmuch-show-mode)
+  (when (or (eq major-mode 'notmuch-show-mode)
+            (eq major-mode 'notmuch-tree-mode))
    (let* ((message-id (notmuch-show-get-message-id t))
--8<---------------cut here---------------end--------------->8---

2. A while back
https://lists.gnu.org/archive/html/emacs-orgmode/2014-07/msg00380.html
was merged.  I think using a defcustom here is not very intuitive for
people who use both the tree view and the thread view.  I would expect
the following:

- Opening a tree link will open the tree view.
- Opening a search link will open the search view.

It's easy to implement:

- Deprecate the former defcustom.
- Copy/paste the org-notmuch-search* code to org-notmuch-tree*.

Thoughts?

-- 
Pierre Neidhardt
https://ambrevar.xyz/