diff -u b/core/includes/common.inc b/core/includes/common.inc
--- b/core/includes/common.inc
+++ b/core/includes/common.inc
@@ -7379,6 +7379,14 @@
   // Important: This rebuild must happen last, so the menu router is guaranteed
   // to be based on up to date information.
   menu_rebuild();
+
+  // Re-initialize the maintenance theme, if the current request attempted to
+  // use it. Unlike regular usages of this function, the installer and update
+  // scripts need to flush all caches during GET requests/page building.
+  if (function_exists('_drupal_maintenance_theme')) {
+    unset($GLOBALS['theme']);
+    drupal_maintenance_theme();
+  }
 }
 
 /**
diff -u b/core/includes/install.core.inc b/core/includes/install.core.inc
--- b/core/includes/install.core.inc
+++ b/core/includes/install.core.inc
@@ -1526,7 +1526,7 @@
   // Add JS to show / hide the 'Email administrator about site updates' elements
   drupal_add_js('jQuery(function () { Drupal.hideEmailAdministratorCheckbox() });', 'inline');
   // Build menu to allow clean URL check.
-  menu_rebuild();
+  menu_router_rebuild();
 
   // Cache a fully-built schema. This is necessary for any invocation of
   // index.php because: (1) setting cache table entries requires schema
@@ -1586,11 +1586,6 @@
   // registered by the install profile are registered correctly.
   drupal_flush_all_caches();
 
-  // Re-initialize the maintenance theme for the final installation page.
-  // @see drupal_flush_all_caches()
-  unset($GLOBALS['theme']);
-  drupal_maintenance_theme();
-
   drupal_set_title(st('@drupal installation complete', array('@drupal' => drupal_install_profile_distribution_name())), PASS_THROUGH);
 
   $messages = drupal_set_message();
diff -u b/core/modules/simpletest/drupal_web_test_case.php b/core/modules/simpletest/drupal_web_test_case.php
--- b/core/modules/simpletest/drupal_web_test_case.php
+++ b/core/modules/simpletest/drupal_web_test_case.php
@@ -1014,7 +1014,7 @@
 
     $saved_type = node_type_save($type);
     node_types_rebuild();
-    menu_rebuild();
+    menu_router_rebuild();
     node_add_body_field($type);
 
     $this->assertEqual($saved_type, SAVED_NEW, t('Created content type %type.', array('%type' => $type->type)));
diff -u b/core/modules/system/system.test b/core/modules/system/system.test
--- b/core/modules/system/system.test
+++ b/core/modules/system/system.test
@@ -2184,7 +2184,7 @@
     // Enable our test module. Flush all caches, which we assert is the only
     // thing necessary to use the rebuilt {system}.info.
     module_enable(array('module_test'), FALSE);
-    drupal_flush_all_caches();
+    $this->resetAll();
     $this->assertTrue(module_exists('module_test'), t('Test module is enabled.'));
 
     $info = $this->getSystemInfo('seven', 'theme');
@@ -2199,7 +2199,7 @@
 
     // Disable the module and verify that {system}.info is rebuilt without it.
     module_disable(array('module_test'), FALSE);
-    drupal_flush_all_caches();
+    $this->resetAll();
     $this->assertFalse(module_exists('module_test'), t('Test module is disabled.'));
 
     $info = $this->getSystemInfo('seven', 'theme');
only in patch2:
unchanged:
--- a/core/includes/gettext.inc
+++ b/core/includes/gettext.inc
@@ -61,7 +61,7 @@ function _locale_import_po($file, $langcode, $overwrite_options, $customized = L
   cache()->deletePrefix('locale:');
 
   // Rebuild the menu, strings may have changed.
-  menu_rebuild();
+  menu_router_rebuild();
 
   drupal_set_message(t('The translation was successfully imported. There are %number newly created translated strings, %update strings were updated and %delete strings were removed.', array('%number' => $additions, '%update' => $updates, '%delete' => $deletes)));
   watchdog('locale', 'Imported %file into %locale: %number new strings added, %update updated and %delete removed.', array('%file' => $file->filename, '%locale' => $langcode, '%number' => $additions, '%update' => $updates, '%delete' => $deletes));
only in patch2:
unchanged:
--- a/core/includes/lock.inc
+++ b/core/includes/lock.inc
@@ -13,9 +13,10 @@
  * In most environments, multiple Drupal page requests (a.k.a. threads or
  * processes) will execute in parallel. This leads to potential conflicts or
  * race conditions when two requests execute the same code at the same time. A
- * common example of this is a rebuild like menu_rebuild() where we invoke many
- * hook implementations to get and process data from all active modules, and
- * then delete the current data in the database to insert the new afterwards.
+ * common example of this is a rebuild like menu_router_rebuild() where we
+ * invoke many hook implementations to get and process data from all active
+ * modules, and then delete the current data in the database to insert the new
+ * afterwards.
  *
  * This is a cooperative, advisory lock system. Any long-running operation
  * that could potentially be attempted in parallel by multiple requests should
only in patch2:
unchanged:
--- a/core/includes/menu.inc
+++ b/core/includes/menu.inc
@@ -301,7 +301,7 @@ const MENU_PREFERRED_LINK = '1cf698d64d1aa4b83907cf6ed55db3a7f8e92c91';
  * then the 1011 bitstring represents node/%/edit/foo where % means that
  * any argument matches that part. We limit ourselves to using binary
  * numbers that correspond the patterns of wildcards of router items that
- * actually exists. This list of 'masks' is built in menu_rebuild().
+ * actually exists. This list of 'masks' is built in menu_router_rebuild().
  *
  * @param $parts
  *   An array of path parts, for the above example
@@ -450,7 +450,7 @@ function menu_get_item($path = NULL, $router_item = NULL) {
     // Rebuild if we know it's needed, or if the menu masks are missing which
     // occurs rarely, likely due to a race condition of multiple rebuilds.
     if (variable_get('menu_rebuild_needed', FALSE) || !variable_get('menu_masks', array())) {
-      menu_rebuild();
+      menu_router_rebuild();
     }
     $original_map = arg(NULL, $path);
 
@@ -2657,12 +2657,12 @@ function menu_reset_static_cache() {
  *   TRUE if the menu was rebuilt, FALSE if another thread was rebuilding
  *   in parallel and the current thread just waited for completion.
  */
-function menu_rebuild() {
-  if (!lock_acquire('menu_rebuild')) {
+function menu_router_rebuild() {
+  if (!lock_acquire(__FUNCTION__)) {
     // Wait for another request that is already doing this work.
     // We choose to block here since otherwise the router item may not
     // be available in menu_execute_active_handler() resulting in a 404.
-    lock_wait('menu_rebuild');
+    lock_wait(__FUNCTION__);
     return FALSE;
   }
 
@@ -2683,7 +2683,7 @@ function menu_rebuild() {
     watchdog_exception('menu', $e);
   }
 
-  lock_release('menu_rebuild');
+  lock_release(__FUNCTION__);
   return TRUE;
 }
 
only in patch2:
unchanged:
--- a/core/includes/theme.inc
+++ b/core/includes/theme.inc
@@ -1489,7 +1489,7 @@ function theme_enable($theme_list) {
   }
 
   list_themes(TRUE);
-  menu_rebuild();
+  menu_router_rebuild();
   drupal_theme_rebuild();
 
   // Invoke hook_themes_enabled() after the themes have been enabled.
@@ -1522,7 +1522,7 @@ function theme_disable($theme_list) {
   }
 
   list_themes(TRUE);
-  menu_rebuild();
+  menu_router_rebuild();
   drupal_theme_rebuild();
 
   // Invoke hook_themes_disabled after the themes have been disabled.
only in patch2:
unchanged:
--- a/core/modules/aggregator/aggregator.test
+++ b/core/modules/aggregator/aggregator.test
@@ -893,7 +893,7 @@ class AggregatorRenderingTestCase extends AggregatorTestCase {
     $feed->block = 0;
     aggregator_save_feed((array) $feed);
     // It is nescessary to flush the cache after saving the number of items.
-    drupal_flush_all_caches();
+    $this->resetAll();
     // Check that the block is no longer displayed.
     $this->drupalGet('node');
     $this->assertNoText(t($block['title']), 'Feed block is not displayed on the page when number of items is set to 0.');
only in patch2:
unchanged:
--- a/core/modules/block/block.test
+++ b/core/modules/block/block.test
@@ -391,7 +391,7 @@ class BlockTestCase extends DrupalWebTestCase {
     // Disable caching for this block.
     variable_set('block_test_caching', DRUPAL_NO_CACHE);
     // Flushing all caches should call _block_rehash().
-    drupal_flush_all_caches();
+    $this->resetAll();
     // Verify that the database is updated with the new caching mode.
     $current_caching = db_query("SELECT cache FROM {block} WHERE module = 'block_test' AND delta = 'test_cache'")->fetchField();
     $this->assertEqual($current_caching, DRUPAL_NO_CACHE, t("Test block's database entry updated to DRUPAL_NO_CACHE."));
@@ -833,7 +833,7 @@ class BlockHiddenRegionTestCase extends DrupalWebTestCase {
     $theme = 'block_test_theme';
     theme_enable(array($theme));
     variable_set('theme_default', $theme);
-    menu_rebuild();
+    menu_router_rebuild();
 
     // Ensure that "block_test_theme" is set as the default theme.
     $this->drupalGet('admin/structure/block');
only in patch2:
unchanged:
--- a/core/modules/entity/tests/entity.test
+++ b/core/modules/entity/tests/entity.test
@@ -222,7 +222,7 @@ class EntityAPIInfoTestCase extends DrupalWebTestCase  {
     // Change the label of the test entity type and make sure changes appear
     // after flushing caches.
     variable_set('entity_cache_test_label', 'New label.');
-    drupal_flush_all_caches();
+    $this->resetAll();
     $info = entity_get_info('entity_cache_test');
     $this->assertEqual($info['label'], 'New label.', 'New label appears in entity info.');
 
only in patch2:
unchanged:
--- a/core/modules/field_ui/field_ui.module
+++ b/core/modules/field_ui/field_ui.module
@@ -52,7 +52,7 @@ function field_ui_help($path, $arg) {
 function field_ui_field_attach_rename_bundle($entity_type, $bundle_old, $bundle_new) {
   // The Field UI relies on entity_get_info() to build menu items for entity
   // field administration pages. Ensure that the menu is rebuilt.
-  menu_rebuild();
+  menu_router_rebuild();
 }
 
 /**
only in patch2:
unchanged:
--- a/core/modules/menu/menu.install
+++ b/core/modules/menu/menu.install
@@ -66,6 +66,6 @@ function menu_install() {
  * Implements hook_uninstall().
  */
 function menu_uninstall() {
-  menu_rebuild();
+  menu_router_rebuild();
 }
 
only in patch2:
unchanged:
--- a/core/modules/menu/menu.module
+++ b/core/modules/menu/menu.module
@@ -180,7 +180,7 @@ function menu_theme() {
  * Add a link for each custom menu.
  */
 function menu_enable() {
-  menu_rebuild();
+  menu_router_rebuild();
   $base_link = db_query("SELECT mlid AS plid, menu_name FROM {menu_links} WHERE link_path = 'admin/structure/menu' AND module = 'system'")->fetchAssoc();
   $base_link['router_path'] = 'admin/structure/menu/manage/%';
   $base_link['module'] = 'menu';
only in patch2:
unchanged:
--- a/core/modules/node/content_types.inc
+++ b/core/modules/node/content_types.inc
@@ -355,7 +355,7 @@ function node_type_form_submit($form, &$form_state) {
   $status = node_type_save($type);
 
   node_types_rebuild();
-  menu_rebuild();
+  menu_router_rebuild();
   $t_args = array('%name' => $type->name);
 
   if ($status == SAVED_UPDATED) {
@@ -458,7 +458,7 @@ function node_type_delete_confirm_submit($form, &$form_state) {
   watchdog('menu', 'Deleted content type %name.', $t_args, WATCHDOG_NOTICE);
 
   node_types_rebuild();
-  menu_rebuild();
+  menu_router_rebuild();
 
   $form_state['redirect'] = 'admin/structure/types';
   return;
only in patch2:
unchanged:
--- a/core/modules/search/search.test
+++ b/core/modules/search/search.test
@@ -1225,7 +1225,7 @@ class SearchKeywordsConditions extends SearchWebTestCase {
     $this->drupalLogin($this->searching_user);
     // Test with all search modules enabled.
     variable_set('search_active_modules', array('node' => 'node', 'user' => 'user', 'search_extra_type' => 'search_extra_type'));
-    menu_rebuild();
+    menu_router_rebuild();
   }
 
   /**
@@ -1936,7 +1936,7 @@ class SearchPageOverride extends SearchWebTestCase {
 
     // Enable the extra type module for searching.
     variable_set('search_active_modules', array('node' => 'node', 'user' => 'user', 'search_extra_type' => 'search_extra_type'));
-    menu_rebuild();
+    menu_router_rebuild();
   }
 
   function testSearchPageHook() {
only in patch2:
unchanged:
--- a/core/modules/shortcut/shortcut.install
+++ b/core/modules/shortcut/shortcut.install
@@ -36,7 +36,7 @@ function shortcut_install() {
   // Drupal is already installed (i.e., we are not in the installer).
   // @see http://drupal.org/node/1376150
   if (variable_get('install_task', '') != 'done') {
-    menu_rebuild();
+    menu_router_rebuild();
   }
   shortcut_set_save($shortcut_set);
 }
only in patch2:
unchanged:
--- a/core/modules/system/system.admin.inc
+++ b/core/modules/system/system.admin.inc
@@ -327,12 +327,13 @@ function system_theme_default() {
       // Set the default theme.
       variable_set('theme_default', $theme);
 
-      // Rebuild the menu. This duplicates the menu_rebuild() in theme_enable().
-      // However, modules must know the current default theme in order to use
-      // this information in hook_menu() or hook_menu_alter() implementations,
-      // and doing the variable_set() before the theme_enable() could result
-      // in a race condition where the theme is default but not enabled.
-      menu_rebuild();
+      // Rebuild the menu. This duplicates the menu_router_rebuild() in
+      // theme_enable(). However, modules must know the current default theme in
+      // order to use this information in hook_menu() or hook_menu_alter()
+      // implementations, and doing the variable_set() before the theme_enable()
+      // could result in a race condition where the theme is default but not
+      // enabled.
+      menu_router_rebuild();
 
       // The status message depends on whether an admin theme is currently in use:
       // a value of 0 means the admin theme is set to be the default theme.
only in patch2:
unchanged:
--- a/core/modules/system/tests/menu.test
+++ b/core/modules/system/tests/menu.test
@@ -395,7 +395,7 @@ class MenuRouterTestCase extends DrupalWebTestCase {
     // Change the menu_name parameter in menu_test.module, then force a menu
     // rebuild.
     menu_test_menu_name('changed');
-    menu_rebuild();
+    menu_router_rebuild();
 
     $sql = "SELECT menu_name FROM {menu_links} WHERE router_path = 'menu_name_test'";
     $name = db_query($sql)->fetchField();