We (finally) implement the XXX comment. It requires a bit of care not
to reparent all of the possible toplevel messages. There is some
slightly naughty low level access to the list structures here that can
be cleaned up in a later commit.
---
 lib/thread.cc               | 53 ++++++++++++++++++-------------------
 test/T510-thread-replies.sh |  1 -
 2 files changed, 26 insertions(+), 28 deletions(-)

diff --git a/lib/thread.cc b/lib/thread.cc
index 85ca00ae..e4ab4319 100644
--- a/lib/thread.cc
+++ b/lib/thread.cc
@@ -467,12 +467,6 @@ _resolve_thread_relationships (notmuch_thread_t *thread)
 	    _notmuch_message_list_add_message (maybe_toplevel_list, message);
     }
 
-    for (notmuch_messages_t *roots = _notmuch_messages_create (maybe_toplevel_list);
-	 notmuch_messages_valid (roots);
-	 notmuch_messages_move_to_next (roots)) {
-	notmuch_message_t *message = notmuch_messages_get (roots);
-	_parent_or_toplevel (thread, message);
-    }
     /*
      * if we reach the end of the list without finding a top-level
      * message, that means the thread is a cycle (or set of cycles)
@@ -481,36 +475,41 @@ _resolve_thread_relationships (notmuch_thread_t *thread)
      */
     if (first_node) {
 	message = first_node->message;
-	if (! thread->toplevel_list->head ||
+	DEBUG_PRINTF("checking first message  %s\n",
+		     notmuch_message_get_message_id (message));
+
+	if (! maybe_toplevel_list->head ||
 	    ! _parent_via_in_reply_to (thread, message)) {
-	    /*
-	     * If the oldest message happens to be in-reply-to a
-	     * missing message, we only check for references if there
-	     * is some other candidate for root message.
-	     */
-	    if (thread->toplevel_list->head)
-		_parent_or_toplevel (thread, message);
-	    else
-		_notmuch_message_list_add_message (thread->toplevel_list, message);
+	    DEBUG_PRINTF("adding first message as toplevel = %s\n",
+		     notmuch_message_get_message_id (message));
+	    _notmuch_message_list_add_message (maybe_toplevel_list, message);
 	}
     }
 
+    for (notmuch_messages_t *messages = _notmuch_messages_create (maybe_toplevel_list);
+	 notmuch_messages_valid (messages);
+	 notmuch_messages_move_to_next (messages))
+    {
+	notmuch_message_t *message = notmuch_messages_get (messages);
+	_notmuch_message_label_depths (message, 0);
+    }
+
+    for (notmuch_messages_t *roots = _notmuch_messages_create (maybe_toplevel_list);
+	 notmuch_messages_valid (roots);
+	 notmuch_messages_move_to_next (roots)) {
+	notmuch_message_t *message = notmuch_messages_get (roots);
+	/* XXX TODO: cleaner way to test iterator for last, list for emptiness  */
+	if (roots->iterator->next || thread->toplevel_list->head)
+	    _parent_or_toplevel (thread, message);
+	else
+	    _notmuch_message_list_add_message (thread->toplevel_list, message);
+    }
+
     /* XXX this could be made conditional on messages being inserted
      * (out of order) in later passes
      */
     thread->toplevel_list = _notmuch_message_sort_subtrees (thread, thread->toplevel_list);
 
-
-    /* XXX: After scanning through the entire list looking for parents
-     * via "In-Reply-To", we should do a second pass that looks at the
-     * list of messages IDs in the "References" header instead. (And
-     * for this the parent would be the "deepest" message of all the
-     * messages found in the "References" list.)
-     *
-     * Doing this will allow messages and sub-threads to be positioned
-     * correctly in the thread even when an intermediate message is
-     * missing from the thread.
-     */
     talloc_free (local);
 }
 
diff --git a/test/T510-thread-replies.sh b/test/T510-thread-replies.sh
index c244054a..915e68ef 100755
--- a/test/T510-thread-replies.sh
+++ b/test/T510-thread-replies.sh
@@ -174,7 +174,6 @@ EOF
 test_expect_equal_file EXPECTED OUTPUT
 
 test_begin_subtest "reply to ghost (tree view)"
-test_subtest_known_broken
 test_emacs '(notmuch-tree "id:000-real-root@example.org")
 	    (notmuch-test-wait)
 	    (test-output)
-- 
2.18.0

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