diff --git a/devel/TODO b/devel/TODO
index f2124834..1cf4089f 100644
--- a/devel/TODO
+++ b/devel/TODO
@@ -14,11 +14,6 @@ sender's name containing ';' which causes emacs to drop a search
 result.) This may require removing the outer array from the current
 "notmuch search --format=json" results.
 
-Fix '*' to work by simply calling '+' or '-' on a region consisting of
-the entire buffer, (this would avoid one race condition---while still
-leaving other race conditions---but could also potentially make '*' a
-very expensive operation).
-
 Add a global keybinding table for notmuch, and then view-specific
 tables that add to it.
 	
diff --git a/emacs/notmuch.el b/emacs/notmuch.el
index b11ef60b..c9bc2f22 100644
--- a/emacs/notmuch.el
+++ b/emacs/notmuch.el
@@ -400,14 +400,25 @@ If BARE is set then do not prefix with \"thread:\""
   (let ((thread (plist-get (notmuch-search-get-result) :thread)))
     (when thread (concat (unless bare "thread:") thread))))
 
-(defun notmuch-search-find-thread-id-region (beg end)
-  "Return a list of threads for the current region"
-  (mapcar (lambda (thread) (concat "thread:" thread))
-	  (notmuch-search-properties-in-region :thread beg end)))
+(defun notmuch-search-find-stable-query ()
+  "Return the stable queries for the current thread.
 
-(defun notmuch-search-find-thread-id-region-search (beg end)
-  "Return a search string for threads for the current region"
-  (mapconcat 'identity (notmuch-search-find-thread-id-region beg end) " or "))
+This returns a list (MATCHED-QUERY UNMATCHED-QUERY) for the
+matched and unmatched messages in the current thread."
+  (plist-get (notmuch-search-get-result) :query))
+
+(defun notmuch-search-find-stable-query-region (beg end &optional only-matched)
+  "Return the stable query for the current region.
+
+If ONLY-MATCHED is non-nil, include only matched messages.  If it
+is nil, include both matched and unmatched messages."
+  (let ((query-list nil) (all (not only-matched)))
+    (dolist (queries (notmuch-search-properties-in-region :query beg end))
+      (when (first queries)
+	(push (first queries) query-list))
+      (when (and all (second queries))
+	(push (second queries) query-list)))
+    (concat "(" (mapconcat 'identity query-list ") or (") ")")))
 
 (defun notmuch-search-find-authors ()
   "Return the authors for the current thread"
@@ -499,17 +510,20 @@ Returns (TAG-CHANGES REGION-BEGIN REGION-END)."
 	   (notmuch-search-get-tags-region beg end) prompt initial-input)
 	  region)))
 
-(defun notmuch-search-tag (tag-changes &optional beg end)
+(defun notmuch-search-tag (tag-changes &optional beg end only-matched)
   "Change tags for the currently selected thread or region.
 
 See `notmuch-tag' for information on the format of TAG-CHANGES.
 When called interactively, this uses the region if the region is
 active.  When called directly, BEG and END provide the region.
 If these are nil or not provided, this applies to the thread at
-point."
+point.
+
+If ONLY-MATCHED is non-nil, only tag matched messages."
   (interactive (notmuch-search-interactive-tag-changes))
   (unless (and beg end) (setq beg (point) end (point)))
-  (let ((search-string (notmuch-search-find-thread-id-region-search beg end)))
+  (let ((search-string (notmuch-search-find-stable-query-region
+			beg end only-matched)))
     (notmuch-tag search-string tag-changes)
     (notmuch-search-foreach-result beg end
       (lambda (pos)
@@ -779,7 +793,7 @@ See `notmuch-tag' for information on the format of TAG-CHANGES."
   (interactive
    (list (notmuch-read-tag-changes
 	  (notmuch-search-get-tags-region (point-min) (point-max)) "Tag all")))
-  (notmuch-tag notmuch-search-query-string tag-changes))
+  (notmuch-search-tag tag-changes (point-min) (point-max) t))
 
 (defun notmuch-search-buffer-title (query)
   "Returns the title for a buffer with notmuch search results."
@@ -883,7 +897,7 @@ the configured default sort order."
       (save-excursion
 	(let ((proc (notmuch-start-notmuch
 		     "notmuch-search" buffer #'notmuch-search-process-sentinel
-		     "search" "--format=sexp" "--format-version=1"
+		     "search" "--format=sexp" "--format-version=2"
 		     (if oldest-first
 			 "--sort=oldest-first"
 		       "--sort=newest-first")
diff --git a/test/emacs b/test/emacs
index 7503e962..3b3b14d7 100755
--- a/test/emacs
+++ b/test/emacs
@@ -889,7 +889,7 @@ $PWD/notmuch_fail exited with status 1 (see *Notmuch errors* for more details)
 ---
 [XXX]
 $PWD/notmuch_fail exited with status 1
-command: $PWD/notmuch_fail search --format\=sexp --format-version\=1 --sort\=newest-first tag\:inbox
+command: $PWD/notmuch_fail search --format\=sexp --format-version\=2 --sort\=newest-first tag\:inbox
 exit status: 1"
 
 test_begin_subtest "Search handles subprocess warnings"
@@ -923,7 +923,6 @@ This is a warning
 This is another warning"
 
 test_begin_subtest "Search thread tag operations are race-free"
-test_subtest_known_broken
 add_message '[subject]="Search race test"'
 gen_msg_id_1=$gen_msg_id
 generate_message '[in-reply-to]="<'$gen_msg_id_1'>"' \
@@ -937,7 +936,6 @@ output=$(notmuch search --output=messages 'tag:search-thread-race-tag')
 test_expect_equal "$output" "id:$gen_msg_id_1"
 
 test_begin_subtest "Search global tag operations are race-free"
-test_subtest_known_broken
 generate_message '[in-reply-to]="<'$gen_msg_id_1'>"' \
 	    '[references]="<'$gen_msg_id_1'>"' \
 	    '[subject]="Re: Search race test"'