Index: includes/common.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/common.inc,v
retrieving revision 1.1017
diff -u -p -r1.1017 common.inc
--- includes/common.inc	13 Oct 2009 21:16:42 -0000	1.1017
+++ includes/common.inc	14 Oct 2009 00:18:04 -0000
@@ -4308,6 +4308,21 @@ function drupal_alter($type, &$data, &$c
     $function = $module . '_' . $hook;
     $function($data, $context1, $context2);
   }
+  // Allow the theme to alter variables after the theme system has been
+  // initialized.
+  if (drupal_get_bootstrap_phase() == DRUPAL_BOOTSTRAP_FULL) {
+    global $theme, $base_theme;
+    $themes = array($theme);
+    foreach ($base_theme as $base) {
+      $themes[] = $base->name;
+    }
+    foreach ($themes as $theme) {
+      $function = $theme . '_' . $hook;
+      if (function_exists($function)) {
+        $function($data, $context1, $context2);
+      }
+    }
+  }
 }
 
 /**
Index: includes/theme.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/theme.inc,v
retrieving revision 1.534
diff -u -p -r1.534 theme.inc
--- includes/theme.inc	13 Oct 2009 05:26:57 -0000	1.534
+++ includes/theme.inc	14 Oct 2009 00:13:32 -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);
 }
 
 /**
Index: includes/theme.maintenance.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/theme.maintenance.inc,v
retrieving revision 1.42
diff -u -p -r1.42 theme.maintenance.inc
--- includes/theme.maintenance.inc	9 Oct 2009 00:59:54 -0000	1.42
+++ includes/theme.maintenance.inc	14 Oct 2009 00:13:32 -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')) {
Index: modules/simpletest/tests/common.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/tests/common.test,v
retrieving revision 1.84
diff -u -p -r1.84 common.test
--- modules/simpletest/tests/common.test	13 Oct 2009 16:38:43 -0000	1.84
+++ modules/simpletest/tests/common.test	14 Oct 2009 00:27:13 -0000
@@ -29,24 +29,24 @@ class DrupalAlterTestCase extends Drupal
 
     // Verify alteration of a single argument.
     $array_copy = $array;
-    $array_expected = array('foo' => 'Drupal');
+    $array_expected = array('foo' => 'Drupal theme');
     drupal_alter('drupal_alter', $array_copy);
     $this->assertEqual($array_copy, $array_expected, t('Single array was altered.'));
 
     $object_copy = clone $object;
     $object_expected = clone $object;
-    $object_expected->foo = 'Drupal';
+    $object_expected->foo = 'Drupal theme';
     drupal_alter('drupal_alter', $object_copy);
     $this->assertEqual($object_copy, $object_expected, t('Single object was altered.'));
 
     // Verify alteration of multiple arguments.
     $array_copy = $array;
-    $array_expected = array('foo' => 'Drupal');
+    $array_expected = array('foo' => 'Drupal theme');
     $object_copy = clone $object;
     $object_expected = clone $object;
-    $object_expected->foo = 'Drupal';
+    $object_expected->foo = 'Drupal theme';
     $array2_copy = $array;
-    $array2_expected = array('foo' => 'Drupal');
+    $array2_expected = array('foo' => 'Drupal theme');
     drupal_alter('drupal_alter', $array_copy, $object_copy, $array2_copy);
     $this->assertEqual($array_copy, $array_expected, t('First argument to drupal_alter() was altered.'));
     $this->assertEqual($object_copy, $object_expected, t('Second argument to drupal_alter() was altered.'));
Index: modules/simpletest/tests/common_test.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/tests/common_test.module,v
retrieving revision 1.5
diff -u -p -r1.5 common_test.module
--- modules/simpletest/tests/common_test.module	13 Oct 2009 16:38:43 -0000	1.5
+++ modules/simpletest/tests/common_test.module	14 Oct 2009 00:29:58 -0000
@@ -101,6 +101,40 @@ function common_test_drupal_alter_alter(
 }
 
 /**
+ * Implement hook_TYPE_alter() on behalf of Garland theme.
+ *
+ * Same as common_test_drupal_alter_alter(), but here, we verify that themes
+ * can also alter and come last.
+ */
+function garland_drupal_alter_alter(&$data, &$arg2 = NULL, &$arg3 = NULL) {
+  // Alter first argument.
+  if (is_array($data)) {
+    $data['foo'] .= ' theme';
+  }
+  elseif (is_object($data)) {
+    $data->foo .= ' theme';
+  }
+  // Alter second argument, if present.
+  if (isset($arg2)) {
+    if (is_array($arg2)) {
+      $arg2['foo'] .= ' theme';
+    }
+    elseif (is_object($arg2)) {
+      $arg2->foo .= ' theme';
+    }
+  }
+  // Try to alter third argument, if present.
+  if (isset($arg3)) {
+    if (is_array($arg3)) {
+      $arg3['foo'] .= ' theme';
+    }
+    elseif (is_object($arg3)) {
+      $arg3->foo .= ' theme';
+    }
+  }
+}
+
+/**
  * Implement hook_theme().
  */
 function common_test_theme() {