Index: includes/bootstrap.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/bootstrap.inc,v
retrieving revision 1.284
diff -u -p -r1.284 bootstrap.inc
--- includes/bootstrap.inc	26 May 2009 09:12:28 -0000	1.284
+++ includes/bootstrap.inc	27 May 2009 23:15:59 -0000
@@ -1163,11 +1163,15 @@ function watchdog($type, $message, $vari
  *   - 'status'
  *   - 'warning'
  *   - 'error'
+ * @param $message_key
+ *   The message key of the message. This key is used to identify the message
+ *   in hook_message_alter.
+ *
  * @param $repeat
  *   If this is FALSE and the message is already set, then the message won't
  *   be repeated.
  */
-function drupal_set_message($message = NULL, $type = 'status', $repeat = TRUE) {
+function drupal_set_message($message = NULL, $type = 'status', $message_key = NULL, $repeat = TRUE) {
   if ($message) {
     if (!isset($_SESSION['messages'])) {
       drupal_set_session('messages', array());
@@ -1178,7 +1182,12 @@ function drupal_set_message($message = N
     }
 
     if ($repeat || !in_array($message, $_SESSION['messages'][$type])) {
-      $_SESSION['messages'][$type][] = $message;
+      if (isset($message_key)) {
+        $_SESSION['messages'][$type][$message_key] = $message;
+      }
+      else {
+        $_SESSION['messages'][$type][] = $message;
+      }
     }
   }
 
@@ -1206,6 +1215,7 @@ function drupal_get_messages($type = NUL
         unset($_SESSION['messages'][$type]);
       }
       if (isset($messages[$type])) {
+        drupal_alter('message', $messages[$type]);
         return array($type => $messages[$type]);
       }
     }
@@ -1213,6 +1223,7 @@ function drupal_get_messages($type = NUL
       if ($clear_queue) {
         unset($_SESSION['messages']);
       }
+      drupal_alter('message', $messages);
       return $messages;
     }
   }
Index: includes/menu.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/menu.inc,v
retrieving revision 1.325
diff -u -p -r1.325 menu.inc
--- includes/menu.inc	24 May 2009 17:39:30 -0000	1.325
+++ includes/menu.inc	27 May 2009 23:15:59 -0000
@@ -2728,7 +2728,7 @@ function _menu_site_is_offline() {
       // page redirects], and specifically suppress its display on the site
       // maintenance page.
       if (drupal_get_normal_path($_GET['q']) != 'admin/settings/maintenance-mode') {
-        drupal_set_message(t('Operating in maintenance mode. <a href="@url">Go online.</a>', array('@url' => url('admin/settings/maintenance-mode'))), 'status', FALSE);
+        drupal_set_message(t('Operating in maintenance mode. <a href="@url">Go online.</a>', array('@url' => url('admin/settings/maintenance-mode'))), 'status', NULL, FALSE);
       }
     }
     else {
Index: includes/theme.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/theme.inc,v
retrieving revision 1.491
diff -u -p -r1.491 theme.inc
--- includes/theme.inc	26 May 2009 10:41:06 -0000	1.491
+++ includes/theme.inc	27 May 2009 23:16:00 -0000
@@ -1181,7 +1181,8 @@ function theme_status_messages($display 
       $output .= " </ul>\n";
     }
     else {
-      $output .= $messages[0];
+      // Need to shift array since key of the first element is unknown.
+      $output .= array_shift($messages);
     }
     $output .= "</div>\n";
   }