The new customization variable, notmuch-search-exclude-deleted, when
set to t, will exclude any messages with the "deleted" tag from
searches.

Additionally, specifying "tag:deleted" in the search directly will
override the exclusion and will included deleted messages in the
search results.
---
 emacs/notmuch.el                                   |    8 ++++
 test/emacs                                         |   42 ++++++++++++++++++++
 .../notmuch-search-tag-inbox-deleted-excluded      |   24 +++++++++++
 3 files changed, 74 insertions(+), 0 deletions(-)
 create mode 100644 
test/emacs.expected-output/notmuch-search-tag-inbox-deleted-excluded

diff --git a/emacs/notmuch.el b/emacs/notmuch.el
index fde2377..c519687 100644
--- a/emacs/notmuch.el
+++ b/emacs/notmuch.el
@@ -905,6 +905,11 @@ PROMPT is the string to prompt with."
       (read-from-minibuffer prompt nil keymap nil
                            'notmuch-query-history nil nil))))

+(defcustom notmuch-search-exclude-deleted nil
+  "Exclude deleted messages (with \"deleted\" tag) from search results."
+  :group 'notmuch
+  :type 'boolean)
+
 ;;;###autoload
 (defun notmuch-search (query &optional oldest-first target-thread target-line 
continuation)
   "Run \"notmuch search\" with the given query string and display results.
@@ -927,6 +932,9 @@ The optional parameters are used as follows:
     (set 'notmuch-search-target-thread target-thread)
     (set 'notmuch-search-target-line target-line)
     (set 'notmuch-search-continuation continuation)
+    (when (and notmuch-search-exclude-deleted
+              (not (string-match "tag:deleted[ )]*" query)))
+      (setq query (concat query " and not tag:deleted")))
     (let ((proc (get-buffer-process (current-buffer)))
          (inhibit-read-only t))
       (if proc
diff --git a/test/emacs b/test/emacs
index a06c223..1d78fbe 100755
--- a/test/emacs
+++ b/test/emacs
@@ -35,6 +35,48 @@ test_emacs '(notmuch-search "tag:inbox")
            (test-output)'
 test_expect_equal_file OUTPUT $EXPECTED/notmuch-search-tag-inbox

+test_begin_subtest "Exclude \"deleted\" messages from search"
+notmuch tag +deleted id:1258506353-20352-1-git-send-email-stewart at 
flamingspork.com
+# we "delete" a second message that's part of a multi-message thread
+# to make sure the rest of the thread is still returned
+notmuch tag +deleted id:1258471718-6781-1-git-send-email-dottedmag at 
dottedmag.net
+test_emacs '(let ((notmuch-search-exclude-deleted t))
+             (notmuch-search "tag:inbox")
+             (notmuch-test-wait)
+             (test-output))'
+notmuch tag -deleted id:1258506353-20352-1-git-send-email-stewart at 
flamingspork.com
+notmuch tag -deleted id:1258471718-6781-1-git-send-email-dottedmag at 
dottedmag.net
+test_expect_equal_file OUTPUT 
$EXPECTED/notmuch-search-tag-inbox-deleted-excluded
+
+test_begin_subtest "Exclude \"deleted\" messages from search, manual override"
+notmuch tag +deleted id:1258506353-20352-1-git-send-email-stewart at 
flamingspork.com
+notmuch tag +deleted id:1258471718-6781-1-git-send-email-dottedmag at 
dottedmag.net
+cat <<EOF >EXPECTED
+  2009-11-18 [1/1]   Stewart Smith        [notmuch] [PATCH] Fix linking with 
gcc to use g++ to link in C++ libs. (deleted inbox unread)
+  2009-11-17 [1/5]   Mikhail Gusarov, Carl Worth, Keith Packard  [notmuch] 
[PATCH 1/2] Close message file after parsing message headers (deleted inbox 
unread)
+End of search results.
+EOF
+test_emacs '(let ((notmuch-search-exclude-deleted t))
+             (notmuch-search "tag:inbox and tag:deleted")
+             (notmuch-test-wait)
+             (test-output))'
+notmuch tag -deleted id:1258506353-20352-1-git-send-email-stewart at 
flamingspork.com
+notmuch tag -deleted id:1258471718-6781-1-git-send-email-dottedmag at 
dottedmag.net
+test_expect_equal_file OUTPUT EXPECTED
+
+test_begin_subtest "Exclude \"deleted\" messages from search, but not 
\"deleted*\""
+notmuch tag +deleted-patch id:1258506353-20352-1-git-send-email-stewart at 
flamingspork.com
+cat <<EOF >EXPECTED
+  2009-11-18 [1/1]   Stewart Smith        [notmuch] [PATCH] Fix linking with 
gcc to use g++ to link in C++ libs. (deleted-patch inbox unread)
+End of search results.
+EOF
+test_emacs '(let ((notmuch-search-exclude-deleted t))
+             (notmuch-search "tag:inbox and tag:deleted-patch")
+             (notmuch-test-wait)
+             (test-output))'
+notmuch tag -deleted-patch id:1258506353-20352-1-git-send-email-stewart at 
flamingspork.com
+test_expect_equal_file OUTPUT EXPECTED
+
 test_begin_subtest "Navigation of notmuch-hello to search results"
 test_emacs '(notmuch-hello)
            (goto-char (point-min))
diff --git 
a/test/emacs.expected-output/notmuch-search-tag-inbox-deleted-excluded 
b/test/emacs.expected-output/notmuch-search-tag-inbox-deleted-excluded
new file mode 100644
index 0000000..39b4c51
--- /dev/null
+++ b/test/emacs.expected-output/notmuch-search-tag-inbox-deleted-excluded
@@ -0,0 +1,24 @@
+  2010-12-29 [1/1]   Fran?ois Boulogne    [aur-general] Guidelines: cp, mkdir 
vs install (inbox unread)
+  2010-12-16 [1/1]   Olivier Berger       Essai accentu? (inbox unread)
+  2009-11-18 [1/1]   Chris Wilson         [notmuch] [PATCH 1/2] Makefile: 
evaluate pkg-config once (inbox unread)
+  2009-11-18 [2/2]   Alex Botero-Lowry, Carl Worth  [notmuch] [PATCH] Error 
out if no query is supplied to search instead of going into an infinite loop 
(attachment inbox unread)
+  2009-11-18 [2/2]   Ingmar Vanhassel, Carl Worth  [notmuch] [PATCH] Typsos 
(inbox unread)
+  2009-11-18 [3/3]   Adrian Perez de Castro, Keith Packard, Carl Worth  
[notmuch] Introducing myself (inbox signed unread)
+  2009-11-18 [3/3]   Israel Herraiz, Keith Packard, Carl Worth   [notmuch] New 
to the list (inbox unread)
+  2009-11-18 [3/3]   Jan Janak, Carl Worth        [notmuch] What a great idea! 
(inbox unread)
+  2009-11-18 [2/2]   Jan Janak, Carl Worth        [notmuch] [PATCH] Older 
versions of install do not support -C. (inbox unread)
+  2009-11-18 [3/3]   Aron Griffis, Keith Packard, Carl Worth     [notmuch] 
archive (inbox unread)
+  2009-11-18 [2/2]   Keith Packard, Carl Worth    [notmuch] [PATCH] Make 
notmuch-show 'X' (and 'x') commands remove inbox (and unread) tags (inbox 
unread)
+  2009-11-18 [7/7]   Lars Kellogg-Stedman, Mikhail Gusarov, Keith Packard, 
Carl Worth  [notmuch] Working with Maildir storage? (inbox signed unread)
+  2009-11-18 [4/5]   Mikhail Gusarov, Carl Worth, Keith Packard  [notmuch] 
[PATCH 1/2] Close message file after parsing message headers (deleted inbox 
unread)
+  2009-11-18 [2/2]   Keith Packard, Alexander Botero-Lowry    [notmuch] 
[PATCH] Create a default notmuch-show-hook that highlights URLs and uses 
word-wrap (inbox unread)
+  2009-11-18 [1/1]   Alexander Botero-Lowry  [notmuch] request for pull (inbox 
unread)
+  2009-11-18 [4/4]   Jjgod Jiang, Alexander Botero-Lowry      [notmuch] Mac OS 
X/Darwin compatibility issues (inbox unread)
+  2009-11-18 [1/1]   Rolland Santimano    [notmuch] Link to mailing list 
archives ? (inbox unread)
+  2009-11-18 [1/1]   Jan Janak            [notmuch] [PATCH] notmuch new: 
Support for conversion of spool subdirectories into tags (inbox unread)
+  2009-11-18 [1/1]   Stewart Smith        [notmuch] [PATCH] count_files: sort 
directory in inode order before statting (inbox unread)
+  2009-11-18 [1/1]   Stewart Smith        [notmuch] [PATCH 2/2] Read mail 
directory in inode number order (inbox unread)
+  2009-11-18 [2/2]   Lars Kellogg-Stedman [notmuch] "notmuch help" outputs to 
stderr? (attachment inbox signed unread)
+  2009-11-17 [1/1]   Mikhail Gusarov      [notmuch] [PATCH] Handle rename of 
message file (inbox unread)
+  2009-11-17 [2/2]   Alex Botero-Lowry, Carl Worth  [notmuch] preliminary 
FreeBSD support (attachment inbox unread)
+End of search results.
-- 
1.7.7.3

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