=== modified file 'includes/common.inc'
--- includes/common.inc	2009-09-30 13:09:29 +0000
+++ includes/common.inc	2009-10-01 01:38:12 +0000
@@ -3922,6 +3922,9 @@ function _drupal_bootstrap_full() {
   // this before invoking hook_init(), since any modules which initialize the
   // theme system will prevent a custom theme from being correctly set later.
   menu_set_custom_theme();
+  if (!defined('MAINTENANCE_MODE') && !_menu_site_is_offline()) {
+    drupal_theme_initialize();
+  }
   // Let all modules take action before menu system handles the request
   // We do not want this while running update.php.
   if (!defined('MAINTENANCE_MODE') || MAINTENANCE_MODE != 'update') {

=== modified file 'includes/module.inc'
--- includes/module.inc	2009-09-29 18:08:28 +0000
+++ includes/module.inc	2009-09-30 16:26:45 +0000
@@ -346,6 +346,7 @@ function module_hook($module, $hook) {
  * @see module_implements_write_cache().
  */
 function module_implements($hook, $sort = FALSE, $reset = FALSE) {
+  global $theme, $base_theme;
   $implementations = &drupal_static(__FUNCTION__, array());
 
   // We maintain a persistent cache of hook implementations in addition to the
@@ -378,6 +379,12 @@ function module_implements($hook, $sort 
   if (!isset($implementations[$hook])) {
     $implementations[$hook] = array();
     $list = module_list(FALSE, FALSE, $sort);
+    if ($theme && substr($hook, -6) == '_alter') {
+      $list[] = $theme;
+      foreach ($base_theme as $base) {
+        $list[] = $base->name;
+      }
+    }
     foreach ($list as $module) {
       if (module_hook($module, $hook)) {
         $implementations[$hook][$module] = $module;

=== modified file 'includes/theme.inc'
--- includes/theme.inc	2009-09-30 13:09:29 +0000
+++ includes/theme.inc	2009-09-30 15:05:00 +0000
@@ -55,7 +55,7 @@ function drupal_theme_access($theme) {
  * Initialize the theme system by loading the theme.
  */
 function drupal_theme_initialize() {
-  global $theme, $user, $theme_key;
+  global $theme, $user, $theme_key, $base_theme;
 
   // If $theme is already set, assume the others are set, too, and do nothing
   if (isset($theme)) {
@@ -84,7 +84,8 @@ function drupal_theme_initialize() {
     $base_theme[] = $new_base_theme = $themes[$themes[$ancestor]->base_theme];
     $ancestor = $themes[$ancestor]->base_theme;
   }
-  _drupal_theme_initialize($themes[$theme], array_reverse($base_theme));
+  $base_theme = array_reverse($base_theme);
+  _drupal_theme_initialize($themes[$theme], $base_theme);
 }
 
 /**

=== modified file 'includes/theme.maintenance.inc'
--- includes/theme.maintenance.inc	2009-09-11 13:56:56 +0000
+++ includes/theme.maintenance.inc	2009-09-30 15:04:32 +0000
@@ -15,7 +15,7 @@
  * $conf variable in order to change the maintenance theme.
  */
 function _drupal_maintenance_theme() {
-  global $theme, $theme_key;
+  global $theme, $theme_key, $base_theme;
 
   // If $theme is already set, assume the others are set too, and do nothing.
   if (isset($theme)) {
@@ -30,6 +30,7 @@ function _drupal_maintenance_theme() {
   require_once DRUPAL_ROOT . '/includes/module.inc';
   require_once DRUPAL_ROOT . '/includes/database/database.inc';
   unicode_check();
+  $base_theme = array();
 
   // Install and update pages are treated differently to prevent theming overrides.
   if (defined('MAINTENANCE_MODE') && (MAINTENANCE_MODE == 'install' || MAINTENANCE_MODE == 'update')) {

=== modified file 'modules/simpletest/tests/form.test'
--- modules/simpletest/tests/form.test	2009-09-29 15:31:12 +0000
+++ modules/simpletest/tests/form.test	2009-09-30 16:00:05 +0000
@@ -363,6 +363,33 @@ class FormsFormCleanIdFunctionalTest ext
 }
 
 /**
+ * Test hook_form_alter for themes.
+ */
+class FormsAlterThemeTest extends DrupalWebTestCase {
+
+  public static function getInfo() {
+    return array(
+      'name' => 'hook_form_alter by themes test',
+      'description' => 'Test the capability of themes to alter forms.',
+      'group' => 'Form API',
+    );
+  }
+
+  function setUp() {
+    parent::setUp('form_test');
+  }
+
+  /**
+   * Test that the form description we add appears.
+   */
+  function testFormCleanId() {
+    $this->drupalGet('admin/form_test');
+    $this->assertText('Seven form alter');
+  }
+
+}
+
+/**
  * Test using drupal_form_submit in a batch.
  */
 class FormAPITestCase extends DrupalWebTestCase {

=== modified file 'modules/simpletest/tests/form_test.module'
--- modules/simpletest/tests/form_test.module	2009-09-18 00:12:45 +0000
+++ modules/simpletest/tests/form_test.module	2009-09-30 16:03:27 +0000
@@ -68,6 +68,14 @@ function form_test_menu() {
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
+  
+  $items['admin/form_test'] = array(
+    'title' => 'admin theme form test',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('form_test_test_form'),
+    'access arguments' => array('access content'),
+    'type' => MENU_CALLBACK,
+  );
 
   return $items;
 }
@@ -95,6 +103,13 @@ function form_test_test_form($form, &$fo
 }
 
 /**
+ * Implement a hook_form_alter in the name of Seven.
+ */
+function seven_form_form_test_test_form_alter(&$form) {
+  $form['input']['#description'] = 'Seven form alter';
+}
+
+/**
  * Create a header and options array. Helper function for callbacks.
  */
 function _form_test_tableselect_get_data() {