diff --git a/core/includes/bootstrap.inc b/core/includes/bootstrap.inc
index c81ccf1..eac1995 100644
--- a/core/includes/bootstrap.inc
+++ b/core/includes/bootstrap.inc
@@ -890,7 +890,7 @@ function drupal_get_filename($type, $name, $filename = NULL) {
     // because this function is called during installation.
     if (drupal_container()->hasDefinition('keyvalue') && function_exists('db_query')) {
       try {
-        $file_list = state()->get('system.' . $type . '_file_list');
+        $file_list = state()->get('system.' . $type . '.files');
         if ($file_list && isset($file_list[$name]) && file_exists(DRUPAL_ROOT . '/' . $file_list[$name])) {
           $files[$type][$name] = $file_list[$name];
         }
@@ -901,7 +901,6 @@ function drupal_get_filename($type, $name, $filename = NULL) {
         // completely.
       }
     }
-
     // Fallback to searching the filesystem if the database could not find the
     // file or the file returned by the database is not found.
     if (!isset($files[$type][$name])) {
@@ -2101,15 +2100,14 @@ function drupal_bootstrap($phase = NULL, $new_phase = TRUE) {
   );
   // Not drupal_static(), because the only legitimate API to control this is to
   // call drupal_bootstrap() with a new phase parameter.
-  static $final_phase = -1;
+  static $final_phase;
   // Not drupal_static(), because it's impossible to roll back to an earlier
   // bootstrap state.
   static $stored_phase = -1;
 
-  // When not recursing, store the phase name so it's not forgotten during
-  // recursion. Additionally, ensure that $final_phase is never rolled back to an
-  // earlier bootstrap state.
-  if ($new_phase && $phase > $final_phase) {
+  // When not recursing, store the phase name so it's not forgotten while
+  // recursing.
+  if ($new_phase) {
     $final_phase = $phase;
   }
   if (isset($phase)) {
@@ -2390,7 +2388,7 @@ function _drupal_bootstrap_page_header() {
  * @see drupal_bootstrap()
  */
 function drupal_get_bootstrap_phase() {
-  return drupal_bootstrap(NULL, FALSE);
+  return drupal_bootstrap();
 }
 
 /**
diff --git a/core/includes/common.inc b/core/includes/common.inc
index df744b3..ef63042 100644
--- a/core/includes/common.inc
+++ b/core/includes/common.inc
@@ -6830,6 +6830,11 @@ function drupal_flush_all_caches() {
   // actually loaded.
   module_load_all();
 
+  // Update the list of bootstrap modules.
+  // Allows developers to get new hook_boot() implementations registered without
+  // having to write a hook_update_N() function.
+  _system_update_bootstrap_status();
+
   // Rebuild the schema and cache a fully-built schema based on new module data.
   // This is necessary for any invocation of index.php, because setting cache
   // table entries requires schema information and that occurs during bootstrap
diff --git a/core/includes/install.inc b/core/includes/install.inc
index 860ac3d..89ee357 100644
--- a/core/includes/install.inc
+++ b/core/includes/install.inc
@@ -413,14 +413,13 @@ function drupal_install_system() {
     drupal_container()
       ->get('keyvalue')
       ->get('system.module.schema')
-      ->set('system', max($system_versions));
+      ->set('system', max($system_versions));         
   }
-  config('system.module')
+  config('system.module')      
     ->set('system', 0)
     ->save();
 
-  // Clear out module list and hook implementation statics before calling
-  // system_rebuild_theme_data().
+  // Clear out module list and hook implementation statics.
   system_list_reset();
   module_list_reset();
   module_implements_reset();
diff --git a/core/includes/module.inc b/core/includes/module.inc
index 30fa096..eea8088 100644
--- a/core/includes/module.inc
+++ b/core/includes/module.inc
@@ -15,14 +15,24 @@
  *   Whether to load only the reduced set of modules loaded in "bootstrap mode"
  *   for cached pages. See bootstrap.inc. Pass NULL to only check the current
  *   status without loading of modules.
+ * @param bool $reset
+ *   (optional) Internal use only. Whether to reset the internal statically
+ *   cached flag of whether modules have been loaded. If TRUE, all modules are
+ *   (re)loaded in the same call. Used by the testing framework to override and
+ *   persist a limited module list for the duration of a unit test (in which no
+ *   module system exists).
  *
  * @return bool
  *   A Boolean indicating whether all modules have been loaded. This means all
  *   modules; the load status of bootstrap modules cannot be checked.
  */
-function module_load_all($bootstrap = FALSE) {
+function module_load_all($bootstrap = FALSE, $reset = FALSE) {
   static $has_run = FALSE;
 
+  if ($reset) {
+    $has_run = FALSE;
+  }
+
   // Unless $boostrap is NULL, load the requested set of modules.
   if (isset($bootstrap) && !$has_run) {
     $type = $bootstrap ? 'bootstrap' : 'module_enabled';
@@ -135,20 +145,22 @@ function system_list($type) {
       return $lists['bootstrap'];
     }
     if ($cached = cache('bootstrap')->get('bootstrap_modules')) {
-      $lists['bootstrap'] = $cached->data;
-      // To avoid a separate database lookup for the filepath, prime the
-      // drupal_get_filename() static cache for bootstrap modules only.
-      // The rest is stored separately to keep the bootstrap module cache small.
-      foreach ($lists['bootstrap'] as $module => $filename) {
-        _system_list_warm('module', $module, $filename);
-      }
+      $bootstrap_list = $cached->data;
     }
     else {
-      $lists = _system_list_prepare();
+      $bootstrap_list = state()->get('system.bootstrap_modules') ?: array();
+      cache('bootstrap')->set('bootstrap_modules', $bootstrap_list);
+    }
+    // To avoid a separate database lookup for the filepath, prime the
+    // drupal_get_filename() static cache for bootstrap modules only.
+    // The rest is stored separately to keep the bootstrap module cache small.
+    foreach ($bootstrap_list as $module) {
+      drupal_classloader_register($module->name, dirname($module->filename));
+      drupal_get_filename('module', $module->name, $module->filename);
     }
     // We only return the module names here since module_list() doesn't need
     // the filename itself.
-    $lists['bootstrap'] = array_keys($lists['bootstrap']);
+    $lists['bootstrap'] = array_keys($bootstrap_list);
   }
   // Otherwise build the list for enabled modules and themes.
   elseif (!isset($lists['module_enabled'])) {
@@ -156,130 +168,93 @@ function system_list($type) {
       $lists = $cached->data;
     }
     else {
-      $lists = _system_list_prepare();
-      $lists['bootstrap'] = array_keys($lists['bootstrap']);
-    }
-    foreach ($lists['filepaths'] as $item) {
-      _system_list_warm($item['type'], $item['name'], $item['filepath']);
-    }
-  }
-
-  return $lists[$type];
-}
-
-/**
- * Prepares the system list data structure.
- *
- * @return
- *   An associative array of modules and themes, keyed by list type: bootstrap,
- *   module_enabled, theme, filepaths.
- */
-function _system_list_prepare() {
-  // The module name (rather than the filename) is used as the fallback
-  // weighting in order to guarantee consistent behavior across different
-  // Drupal installations, which might have modules installed in different
-  // locations in the file system. The ordering here must also be
-  // consistent with the one used in module_implements().
-  $enabled_themes = config('system.theme')->get();
-  $enabled_modules = config('system.module')->get();
-  _system_list_warm('module', 'system', 'core/modules/system.module', TRUE);
-
-  $module_file_list = state()->get('system.module_file_list');
-  $theme_data = state()->get('system.themes');
-  // As themes do not need to be installed to be used there is an issue during
-  // installation. The state entry for system.themes does not exist and we need
-  // theme data in order for installation to work. This will be resolved by
-  // http://drupal.org/node/1067408.
-  if (empty($theme_data)) {
-    $theme_data = system_rebuild_theme_data(FALSE);
-  }
-  $lists = array(
-    'bootstrap' => array(),
-    'module_enabled' => array(),
-    'theme' => array(),
-    'filepaths' => array(),
-  );
-  foreach ($theme_data as $key => $theme) {
-    $lists['theme'][$key] = $theme;
-    $status = isset($enabled_themes[$key]);
-    $lists['theme'][$key]->status = $status;
-    $lists['theme'][$key]->name = $key;
-    // Build a list of filenames so drupal_get_filename can use it.
-    if ($status) {
-      $lists['filepaths'][] = array(
-        'type' => 'theme',
-        'name' => $key,
-        'filepath' => $theme->filename
+      $lists = array(
+        'module_enabled' => array(),
+        'theme' => array(),
+        'filepaths' => array(),
       );
-    }
-  }
-  foreach ($lists['theme'] as $key => $theme) {
-    if (!empty($theme->info['base theme'])) {
-      // Make a list of the theme's base themes.
-      require_once DRUPAL_ROOT . '/core/includes/theme.inc';
-      $lists['theme'][$key]->base_themes = drupal_find_base_themes($lists['theme'], $key);
-      // Don't proceed if there was a problem with the root base theme.
-      if (!current($lists['theme'][$key]->base_themes)) {
-        continue;
-      }
-      // Determine the root base theme.
-      $base_key = key($lists['theme'][$key]->base_themes);
-      // Add to the list of sub-themes for each of the theme's base themes.
-      foreach (array_keys($lists['theme'][$key]->base_themes) as $base_theme) {
-        $lists['theme'][$base_theme]->sub_themes[$key] = $lists['theme'][$key]->info['name'];
+      // The module name (rather than the filename) is used as the fallback
+      // weighting in order to guarantee consistent behavior across different
+      // Drupal installations, which might have modules installed in different
+      // locations in the file system. The ordering here must also be
+      // consistent with the one used in module_implements().
+      $modules = config('system.module')->get();
+      $module_files = state()->get('system.module.files');
+      foreach ($modules as $name => $weight) {
+        // Build a list of all enabled modules.
+        $lists['module_enabled'][$name] = $name;
+        // Build a list of filenames so drupal_get_filename can use it.
+        $lists['filepaths'][] = array(
+          'type' => 'module',
+          'name' => $name,
+          'filepath' => $module_files[$name],
+        );
       }
-      // Add the base theme's theme engine info.
-      $lists['theme'][$key]->info['engine'] = $lists['theme'][$base_key]->info['engine'];
-    }
-    else {
-      // A plain theme is its own base theme.
-      $base_key = $key;
-    }
-    // Set the theme engine prefix.
-    $lists['theme'][$key]->prefix = ($lists['theme'][$key]->info['engine'] == 'theme') ? $base_key : $lists['theme'][$key]->info['engine'];
-  }
 
-  foreach ($enabled_modules as $name => $weight) {
-    // Build a list of all enabled modules.
-    $lists['module_enabled'][$name] = $name;
-    $filename = $module_file_list[$name];
-    // Build a list of filenames so drupal_get_filename can use it.
-    $lists['filepaths'][] = array(
-      'type' => 'module',
-      'name' => $name,
-      'filepath' => $filename,
-    );
-    _system_list_warm('module', $name, $filename, TRUE);
-    foreach (bootstrap_hooks() as $hook) {
-      if (function_exists($name .'_' . $hook)) {
-        $lists['bootstrap'][$name] = $filename;
+      // Build a list of themes.
+      // Themes include all themes, including disabled and not installed ones.
+      // @see http://drupal.org/node/1067408
+      /*
+      $themes = config('system.theme')->get();
+      $theme_files = state()->get('system.theme.files');
+      */
+      $theme_data = state()->get('system.theme.data');
+      if (empty($theme_data)) {
+        $theme_data = system_rebuild_theme_data();
+        state()->set('system.theme.data', $theme_data);
       }
+      foreach ($theme_data as $key => $theme) {
+        $lists['theme'][$key] = $theme;
+        $status = isset($enabled_themes[$key]);
+        $lists['theme'][$key]->status = $status;
+        $lists['theme'][$key]->name = $key;
+        // Build a list of filenames so drupal_get_filename can use it.
+        if ($status) {
+          $lists['filepaths'][] = array(
+            'type' => 'theme',
+            'name' => $key,
+            'filepath' => $theme->filename,
+          );
+        }
+      }
+      // @todo Move into list_themes(). Read info for a *particular* requested
+      //   theme from state instead.
+      foreach ($lists['theme'] as $key => $theme) {
+        if (!empty($theme->info['base theme'])) {
+          // Make a list of the theme's base themes.
+          require_once DRUPAL_ROOT . '/core/includes/theme.inc';
+          $lists['theme'][$key]->base_themes = drupal_find_base_themes($lists['theme'], $key);
+          // Don't proceed if there was a problem with the root base theme.
+          if (!current($lists['theme'][$key]->base_themes)) {
+            continue;
+          }
+          // Determine the root base theme.
+          $base_key = key($lists['theme'][$key]->base_themes);
+          // Add to the list of sub-themes for each of the theme's base themes.
+          foreach (array_keys($lists['theme'][$key]->base_themes) as $base_theme) {
+            $lists['theme'][$base_theme]->sub_themes[$key] = $lists['theme'][$key]->info['name'];
+          }
+          // Add the base theme's theme engine info.
+          $lists['theme'][$key]->info['engine'] = $lists['theme'][$base_key]->info['engine'];
+        }
+        else {
+          // A plain theme is its own base theme.
+          $base_key = $key;
+        }
+        // Set the theme engine prefix.
+        $lists['theme'][$key]->prefix = ($lists['theme'][$key]->info['engine'] == 'theme') ? $base_key : $lists['theme'][$key]->info['engine'];
+      }
+      cache('bootstrap')->set('system_list', $lists);
+    }
+    // To avoid a separate database lookup for the filepath, prime the
+    // drupal_get_filename() static cache with all enabled modules and themes.
+    foreach ($lists['filepaths'] as $item) {
+      drupal_get_filename($item['type'], $item['name'], $item['filepath']);
+      drupal_classloader_register($item['name'], dirname($item['filepath']));
     }
   }
-  cache('bootstrap')->set('system_list', $lists);
-  cache('bootstrap')->set('bootstrap_modules', $lists['bootstrap']);
-
-  return $lists;
-}
 
-/**
- * Prepares a module for loading and optionally calls drupal_load().
- *
- * @param string $type
- *   The type of the extension (i.e. theme, theme_engine, module, profile).
- * @param string $name
- *   The name of the extension.
- * @param string $filename
- *   The filename of the extension.
- * @param bool $load
- *   (optional) Call drupal_load() for the extension. Defaults to FALSE.
- */
-function _system_list_warm($type, $name, $filename, $load = FALSE) {
-  drupal_classloader_register($name, dirname($filename));
-  drupal_get_filename($type, $name, $filename);
-  if ($load) {
-    drupal_load($type, $name);
-  }
+  return $lists[$type];
 }
 
 /**
@@ -445,28 +420,27 @@ function module_load_all_includes($type, $name = NULL) {
  * @see hook_modules_enabled()
  */
 function module_enable($module_list, $enable_dependencies = TRUE) {
-  // Get all module data so we can find dependencies, sort and copy to the
-  // installed modules config.
-  $all_modules = system_rebuild_module_data();
   if ($enable_dependencies) {
+    // Get all module data so we can find dependencies and sort.
+    $module_data = system_rebuild_module_data();
     // Create an associative array with weights as values.
     $module_list = array_flip(array_values($module_list));
 
     while (list($module) = each($module_list)) {
-      if (!isset($all_modules[$module])) {
+      if (!isset($module_data[$module])) {
         // This module is not found in the filesystem, abort.
         return FALSE;
       }
-      if ($all_modules[$module]->status) {
+      if ($module_data[$module]->status) {
         // Skip already enabled modules.
         unset($module_list[$module]);
         continue;
       }
-      $module_list[$module] = $all_modules[$module]->sort;
+      $module_list[$module] = $module_data[$module]->sort;
 
       // Add dependencies to the list, with a placeholder weight.
       // The new modules will be processed as the while loop continues.
-      foreach (array_keys($all_modules[$module]->requires) as $dependency) {
+      foreach (array_keys($module_data[$module]->requires) as $dependency) {
         if (!isset($module_list[$dependency])) {
           $module_list[$dependency] = 0;
         }
@@ -489,9 +463,9 @@ function module_enable($module_list, $enable_dependencies = TRUE) {
   $modules_installed = array();
   $modules_enabled = array();
   $schema_store = drupal_container()->get('keyvalue')->get('system.module.schema');
+  $config = config('system.module');
+  $disabled_config = config('system.module.disabled');
   foreach ($module_list as $module) {
-    $config = config('system.module');
-    $disabled_config = config('system.module.disabled');
     // Only process modules that are not already enabled.
     $enabled = TRUE;
     $weight = 0;
@@ -519,6 +493,7 @@ function module_enable($module_list, $enable_dependencies = TRUE) {
       // Refresh the module list to include it.
       system_list_reset();
       module_implements_reset();
+      _system_update_bootstrap_status();
       // Refresh the schema to include it.
       drupal_get_schema(NULL, TRUE);
       // Update the theme registry to include it.
@@ -624,17 +599,15 @@ function module_disable($module_list, $disable_dependents = TRUE) {
 
   $invoke_modules = array();
 
+  $config = config('system.module');
+  $disabled_config = config('system.module.disabled');
   foreach ($module_list as $module) {
     if (module_exists($module)) {
-      $config = config('system.module');
-      $disabled_config = config('system.module.disabled');
       module_load_install($module);
       module_invoke($module, 'disable');
-      if ($weight = $config->get($module)) {
-        $disabled_config
-          ->set($module, $weight)
-          ->save();
-      }
+      $disabled_config
+        ->set($module, $config->get($module))
+        ->save();
       $config
         ->clear($module)
         ->setData(module_config_sort($config->get()))
@@ -652,6 +625,7 @@ function module_disable($module_list, $disable_dependents = TRUE) {
     // Invoke hook_modules_disabled before disabling modules,
     // so we can still call module hooks to get information.
     module_invoke_all('modules_disabled', $invoke_modules);
+    _system_update_bootstrap_status();
     // Update the theme registry to remove the newly-disabled module.
     drupal_theme_rebuild();
   }
diff --git a/core/includes/schema.inc b/core/includes/schema.inc
index b9ec5ea..58aa7c4 100644
--- a/core/includes/schema.inc
+++ b/core/includes/schema.inc
@@ -175,7 +175,7 @@ function drupal_get_installed_schema_version($module, $reset = FALSE, $array = F
 
   if (!$versions) {
     if (!$versions = drupal_container()->get('keyvalue')->get('system.module.schema')->getAll()) {
-      $versions= array();
+      $versions = array();
     }
   }
 
diff --git a/core/includes/theme.inc b/core/includes/theme.inc
index d57b323..2195e64 100644
--- a/core/includes/theme.inc
+++ b/core/includes/theme.inc
@@ -1412,19 +1412,19 @@ function theme_render_template($template_file, $variables) {
  */
 function theme_enable($theme_list) {
   drupal_clear_css_cache();
-  $config = config('system.theme');
+  $enabled_themes = config('system.theme');
+  $disabled_themes = config('system.theme.disabled');
   foreach ($theme_list as $key) {
-    // The value is not used, it needs to be consistent with
-    // config('system.module') which uses the value for weight so set all of
-    // them to the same value. 1 looks like 'enabled' so let's use that.
-    $config->set($key, 1);
+    // The value is not used; the weight is ignored for themes currently.
+    $enabled_themes->set($key, 0);
+    $disabled_themes->clear($key);
     // Install default configuration of the theme.
     config_install_default_config('theme', $key);
   }
-  $config->save();
+  $enabled_themes->save();
+  $disabled_themes->save();
 
-  system_list_reset();
-  system_rebuild_theme_data(TRUE);
+  list_themes(TRUE);
   menu_router_rebuild();
   drupal_theme_rebuild();
 
@@ -1449,11 +1449,15 @@ function theme_disable($theme_list) {
 
   drupal_clear_css_cache();
 
-  $config = config('system.theme');
+  $enabled_themes = config('system.theme');
+  $disabled_themes = config('system.theme.disabled');
   foreach ($theme_list as $key) {
-    $config->clear($key);
+    // The value is not used; the weight is ignored for themes currently.
+    $enabled_themes->clear($key);
+    $disabled_themes->set($key, 0);
   }
-  $config->save();
+  $enabled_themes->save();
+  $disabled_themes->save();
 
   list_themes(TRUE);
   menu_router_rebuild();
diff --git a/core/includes/update.inc b/core/includes/update.inc
index e36b9ef..0f0f391 100644
--- a/core/includes/update.inc
+++ b/core/includes/update.inc
@@ -413,9 +413,11 @@ function update_module_enable(array $modules) {
       }
     }
     // Enable the module with a weight of 0.
+    // @todo Missing sorting.         
     config('system.module')
       ->set($module, 0)
       ->save();
+    config('system.module.disabled')->clear($module)->save();
     // Change the schema version from SCHEMA_UNINSTALLED to 0, so any module
     // updates since the module's inception are executed in a core upgrade.
     $store->set($module, 0);
@@ -953,7 +955,7 @@ function update_retrieve_dependencies() {
   $return = array();
   // Get a list of installed modules, arranged so that we invoke their hooks in
   // the same order that module_invoke_all() does.
-  foreach (config('system.module')->get() as $module => $data) {
+  foreach (config('system.module')->get() as $module => $data) {                          
     $function = $module . '_update_dependencies';
     if (function_exists($function)) {
       $result = $function();
diff --git a/core/modules/action/lib/Drupal/action/Tests/LoopTest.php b/core/modules/action/lib/Drupal/action/Tests/LoopTest.php
index fce4f2d..9f3a959 100644
--- a/core/modules/action/lib/Drupal/action/Tests/LoopTest.php
+++ b/core/modules/action/lib/Drupal/action/Tests/LoopTest.php
@@ -67,6 +67,7 @@ protected function triggerActions() {
     $expected[] = 'Stack overflow: too many calls to actions_do(). Aborting to prevent infinite recursion.';
 
     $result = db_query("SELECT message FROM {watchdog} WHERE type = 'action_loop_test' OR type = 'action' ORDER BY wid");
+    $loop_started = FALSE;
     foreach ($result as $row) {
       $expected_message = array_shift($expected);
       $this->assertEqual($row->message, $expected_message, format_string('Expected message %expected, got %message.', array('%expected' => $expected_message, '%message' => $row->message)));
diff --git a/core/modules/block/block.install b/core/modules/block/block.install
index 5ad23aa..ee72e0f 100644
--- a/core/modules/block/block.install
+++ b/core/modules/block/block.install
@@ -213,6 +213,7 @@ function block_schema() {
  * Implements hook_install().
  */
 function block_install() {
+
   // Block should go first so that other modules can alter its output
   // during hook_page_alter(). Almost everything on the page is a block,
   // so before block module runs, there will not be much to alter.
diff --git a/core/modules/help/lib/Drupal/help/Tests/HelpTest.php b/core/modules/help/lib/Drupal/help/Tests/HelpTest.php
index 260768a..7d5d20e 100644
--- a/core/modules/help/lib/Drupal/help/Tests/HelpTest.php
+++ b/core/modules/help/lib/Drupal/help/Tests/HelpTest.php
@@ -108,10 +108,8 @@ protected function verifyHelp($response = 200) {
   protected function getModuleList() {
     $modules = array();
     $module_data = system_rebuild_module_data();
-    foreach (config('system.module')->get() as $module => $data) {
-      if (file_exists($module_data[$module]->filename) && function_exists($module . '_help')) {
-        $modules[$module] = $module_data[$module]->info['name'];
-      }
+    foreach (module_implements('help') as $module) {
+      $modules[$module] = $module_data[$module]->info['name'];
     }
     return $modules;
   }
diff --git a/core/modules/locale/lib/Drupal/locale/LocaleLookup.php b/core/modules/locale/lib/Drupal/locale/LocaleLookup.php
index ee40928..77aa4dd 100644
--- a/core/modules/locale/lib/Drupal/locale/LocaleLookup.php
+++ b/core/modules/locale/lib/Drupal/locale/LocaleLookup.php
@@ -36,16 +36,7 @@ public function __construct($langcode, $context) {
     // Add the current user's role IDs to the cache key, this ensures that, for
     // example, strings for admin menu items and settings forms are not cached
     // for anonymous users.
-    if (isset($GLOBALS['user'])) {
-      $rids = implode(':', array_keys($GLOBALS['user']->roles));
-    }
-    else {
-      // If there is no global user, surely it's an anonymous user. For
-      // example, during update install_ensure_config_directory() calls for
-      // stream wrappers which calls locale_stream_wrappers() which has t()
-      // calls in it.
-      $rids = DRUPAL_ANONYMOUS_RID;
-    }
+    $rids = implode(':', array_keys($GLOBALS['user']->roles));
     parent::__construct("locale:$langcode:$context:$rids", 'cache', array('locale' => TRUE));
   }
 
diff --git a/core/modules/locale/lib/Drupal/locale/Tests/LocaleCompareTest.php b/core/modules/locale/lib/Drupal/locale/Tests/LocaleCompareTest.php
index 323c55d..112fee8 100644
--- a/core/modules/locale/lib/Drupal/locale/Tests/LocaleCompareTest.php
+++ b/core/modules/locale/lib/Drupal/locale/Tests/LocaleCompareTest.php
@@ -77,8 +77,6 @@ function testLocaleCompare() {
 
     // Return the locale test modules back to their hidden state.
     variable_del('locale_translation_test_system_info_alter');
-    // Reset system lists to reflect changes.
-    system_list_reset();
   }
 
 }
diff --git a/core/modules/simpletest/lib/Drupal/simpletest/TestBase.php b/core/modules/simpletest/lib/Drupal/simpletest/TestBase.php
index a10324e..aeff65e 100644
--- a/core/modules/simpletest/lib/Drupal/simpletest/TestBase.php
+++ b/core/modules/simpletest/lib/Drupal/simpletest/TestBase.php
@@ -831,6 +831,7 @@ protected function tearDown() {
 
     // Reset module list and module load status.
     module_list_reset();
+    module_load_all(FALSE, TRUE);
 
     // Restore original in-memory configuration.
     $conf = $this->originalConf;
diff --git a/core/modules/simpletest/lib/Drupal/simpletest/WebTestBase.php b/core/modules/simpletest/lib/Drupal/simpletest/WebTestBase.php
index 71311af..016ffd0 100644
--- a/core/modules/simpletest/lib/Drupal/simpletest/WebTestBase.php
+++ b/core/modules/simpletest/lib/Drupal/simpletest/WebTestBase.php
@@ -9,6 +9,7 @@
 
 use Drupal\Core\DrupalKernel;
 use Drupal\Core\Database\Database;
+use Drupal\Core\Database\ConnectionNotDefinedException;
 use PDO;
 use stdClass;
 use DOMDocument;
@@ -1065,8 +1066,7 @@ protected function drupalGet($path, array $options = array(), array $headers = a
     // options set, it might change the GET into a POST. Make sure we clear out
     // previous options.
     $out = $this->curlExec(array(CURLOPT_HTTPGET => TRUE, CURLOPT_URL => url($path, $options), CURLOPT_NOBODY => FALSE, CURLOPT_HTTPHEADER => $headers));
-    // Ensure that any changes to variables in the other thread are picked up.
-    $this->refreshVariables();
+    $this->refreshVariables(); // Ensure that any changes to variables in the other thread are picked up.
 
     // Replace original page output with new output from redirected page(s).
     if ($new = $this->checkForMetaRefresh()) {
diff --git a/core/modules/simpletest/simpletest.module b/core/modules/simpletest/simpletest.module
index 98b62c9..0c996e7 100644
--- a/core/modules/simpletest/simpletest.module
+++ b/core/modules/simpletest/simpletest.module
@@ -1,7 +1,6 @@
 <?php
 
 use Drupal\Core\Database\Database;
-use Drupal\Component\ArraySelect;
 use Drupal\simpletest\TestBase;
 
 /**
diff --git a/core/modules/system/lib/Drupal/system/Tests/Module/VersionTest.php b/core/modules/system/lib/Drupal/system/Tests/Module/VersionTest.php
index 6867ae8..e328712 100644
--- a/core/modules/system/lib/Drupal/system/Tests/Module/VersionTest.php
+++ b/core/modules/system/lib/Drupal/system/Tests/Module/VersionTest.php
@@ -62,8 +62,9 @@ function testModuleVersions() {
       // Testing extra version. Incompatible.
       'common_test (>2.4-rc0)',
     );
-    foreach ($dependencies as $i => $dependency) {
-      variable_set('dependency', $dependency);
+    variable_set('dependencies', $dependencies);
+    $n = count($dependencies);
+    for ($i = 0; $i < $n; $i++) {
       $this->drupalGet('admin/modules');
       $checkbox = $this->xpath('//input[@id="edit-modules-testing-module-test-enable"]');
       $this->assertEqual(!empty($checkbox[0]['disabled']), $i % 2, $dependencies[$i]);
diff --git a/core/modules/system/lib/Drupal/system/Tests/Upgrade/UpgradePathTestBase.php b/core/modules/system/lib/Drupal/system/Tests/Upgrade/UpgradePathTestBase.php
index 2c64b08..b7e1106 100644
--- a/core/modules/system/lib/Drupal/system/Tests/Upgrade/UpgradePathTestBase.php
+++ b/core/modules/system/lib/Drupal/system/Tests/Upgrade/UpgradePathTestBase.php
@@ -189,7 +189,8 @@ protected function refreshVariables() {
   protected function performUpgrade($register_errors = TRUE) {
 
     // Load the first update screen.
-    $this->getUpdatePhp();
+    $update_url = $GLOBALS['base_url'] . '/core/update.php';
+    $this->drupalGet($update_url, array('external' => TRUE));
     if (!$this->assertResponse(200)) {
       throw new Exception('Initial GET to update.php did not return HTTP 200 status.');
     }
@@ -229,7 +230,7 @@ protected function performUpgrade($register_errors = TRUE) {
     }
 
     // Check if there still are pending updates.
-    $this->getUpdatePhp();
+    $this->drupalGet($update_url, array('external' => TRUE));
     $this->drupalPost(NULL, array(), t('Continue'));
     if (!$this->assertText(t('No pending updates.'), t('No pending updates at the end of the update process.'))) {
       throw new Exception('update.php still shows pending updates after execution.');
@@ -243,6 +244,7 @@ protected function performUpgrade($register_errors = TRUE) {
     // but not on the test client.
     system_list_reset();
     module_implements_reset();
+    module_load_all(FALSE, TRUE);
 
     // Rebuild caches.
     // @todo Remove the try/catch when UpgradePathTestBase::setup() is fixed to
@@ -261,28 +263,4 @@ protected function performUpgrade($register_errors = TRUE) {
     return TRUE;
   }
 
-  /**
-   * Gets update.php without calling url().
-   *
-   * This function is necessary because drupalGet calls t() before the
-   * database is ready for that.
-   */
-  protected function getUpdatePhp() {
-    // We re-using a CURL connection here. If that connection still has certain
-    // options set, it might change the GET into a POST. Make sure we clear out
-    // previous options.
-    $path = $GLOBALS['base_url'] . '/core/update.php';
-    $out = $this->curlExec(array(CURLOPT_HTTPGET => TRUE, CURLOPT_URL => $path, CURLOPT_NOBODY => FALSE));
-    // Ensure that any changes to variables in the other thread are picked up.
-    $this->refreshVariables();
-
-    // Replace original page output with new output from redirected page(s).
-    if ($new = $this->checkForMetaRefresh()) {
-      $out = $new;
-    }
-    $this->verbose('GET request to: update.php' .
-      '<hr />Ending URL: ' . $this->getUrl() .
-      '<hr />' . $out);
-    return $out;
-  }
 }
diff --git a/core/modules/system/system.admin.inc b/core/modules/system/system.admin.inc
index ff9a59a..46c7a36 100644
--- a/core/modules/system/system.admin.inc
+++ b/core/modules/system/system.admin.inc
@@ -792,9 +792,8 @@ function system_modules($form, $form_state = array()) {
 
   // Remove hidden modules from display list.
   $visible_files = $files;
-  $profile = drupal_get_profile();
   foreach ($visible_files as $filename => $file) {
-    if (!empty($file->info['hidden']) || $filename == $profile) {
+    if (!empty($file->info['hidden'])) {
       unset($visible_files[$filename]);
     }
   }
@@ -1253,7 +1252,7 @@ function system_modules_uninstall($form, $form_state = NULL) {
   $all_modules = system_rebuild_module_data();
   $disabled_modules = array();
   foreach ($all_modules as $name => $module) {
-    if (empty($module->status) && drupal_get_installed_schema_version($name) > SCHEMA_UNINSTALLED) {
+    if (empty($module->status) && drupal_get_installed_schema_version($name) > SCHEMA_UNINSTALLED) {    
       $disabled_modules[$name] = $module;
     }
   }
diff --git a/core/modules/system/system.install b/core/modules/system/system.install
index c7b5ad5..b4af5e8 100644
--- a/core/modules/system/system.install
+++ b/core/modules/system/system.install
@@ -435,15 +435,6 @@ function system_requirements($phase) {
   if ($phase == 'update') {
     $profile = drupal_get_profile();
     $files = system_rebuild_module_data();
-    // Build dependencies based on non-system_info_alter-ed info files
-    // if we are fired before the alter could even run.
-    if (drupal_get_bootstrap_phase() < DRUPAL_BOOTSTRAP_CODE) {
-      foreach ($files as $record) {
-        $record->info = $record->parsed_info;
-      }
-      $files = _module_build_dependencies($files);
-    }
-
     foreach ($files as $module => $file) {
       // Ignore disabled modules and installation profiles.
       if (!$file->status || $module == $profile) {
diff --git a/core/modules/system/system.module b/core/modules/system/system.module
index a07a4db..7302126 100644
--- a/core/modules/system/system.module
+++ b/core/modules/system/system.module
@@ -2686,16 +2686,20 @@ function system_check_directory($form_element) {
  */
 function system_get_info($type, $name = NULL) {
   $info = array();
-  $function = 'system_rebuild_' . $type . '_data';
-  $data = $function();
-  foreach (array_keys(config("system.$type")->get()) as $enabled) {
-    $info[$enabled] = $data[$enabled]->info;
+  if ($type == 'module') {
+    $data = system_rebuild_module_data();
+    foreach (module_list() as $module) {
+      $info[$module] = $data[$module]->info;
+    }
   }
-  $profile = drupal_get_profile();
-  if (isset($info[$profile]) && !isset($info[$profile]['distribution_name'])) {
-    $info[$profile]['distribution_name'] = 'Drupal';
+  else {
+    $list = system_list($type);
+    foreach ($list as $shortname => $item) {
+      if (!empty($item->status)) {
+        $info[$shortname] = $item->info;
+      }
+    }
   }
-
   if (isset($name)) {
     return isset($info[$name]) ? $info[$name] : array();
   }
@@ -2729,97 +2733,81 @@ function system_get_module_info($property) {
  * @return
  *   An associative array of module information.
  */
-function _system_rebuild_module_data($state_name = FALSE, $save = FALSE) {
-  static $module_store = array(), $profiles_seen;
+function _system_rebuild_module_data() {
+  // Find modules
+  $modules = drupal_system_listing('/^' . DRUPAL_PHP_FUNCTION_PATTERN . '\.module$/', 'modules', 'name', 0);
+
+  // Find installation profiles.
+  $profiles = drupal_system_listing('/^' . DRUPAL_PHP_FUNCTION_PATTERN . '\.profile$/', 'profiles', 'name', 0);
 
+  // Include the installation profile in modules that are loaded.
   $profile = drupal_get_profile();
-  // Find modules not yet processed.
-  $modules = array();
-  if (empty($module_store) && ($state_name || drupal_valid_test_ua()) && ($data = state()->get($state_name ?: __FUNCTION__))) {
-    // During a test run no modules can move, no info files can change so
-    // speed up test runs by only finding and parsing once.
-    $module_store = $data['module_store'];
-    $profiles_seen = $data['profiles_seen'];
-  }
-  // If this is the first time, start with all modules.
-  if (empty($module_store)) {
-    // Find modules and installation profiles. As these are files, they can't
-    // change within a request. However, it does depend on $profile.
-    $modules = drupal_system_listing('/^' . DRUPAL_PHP_FUNCTION_PATTERN . '\.module$/', 'modules', 'name', 0);
-  }
-  // If this profile is not yet parsed, add it.
-  if (!isset($profiles_seen[$profile])) {
-    $profiles = drupal_system_listing('/^' . DRUPAL_PHP_FUNCTION_PATTERN . '\.profile$/', 'profiles', 'name', 0);
-    // Include the install profile in modules that are loaded.
-    $modules[$profile] = $profiles[$profile];
-    // Install profile hooks are always executed last.
-    $modules[$profile]->weight = 1000;
-    $profiles_seen[$profile] = TRUE;
-  }
-  // Now process the modules if necessary.
-  if ($modules) {
-    // Set defaults for module info.
-    $defaults = array(
-      'dependencies' => array(),
-      'description' => '',
-      'package' => 'Other',
-      'version' => NULL,
-      'php' => DRUPAL_MINIMUM_PHP,
-      'files' => array(),
-      'bootstrap' => 0,
-    );
-    // Read info files for each module.
-    foreach ($modules as $key => $module) {
-      // The module system uses the key 'filename' instead of 'uri' so copy the
-      // value so it will be used by the modules system.
-      $modules[$key]->filename = $module->uri;
-
-      // Look for the info file.
-      $module->parsed_info = drupal_parse_info_file(dirname($module->uri) . '/' . $module->name . '.info');
-
-      // Add the info file modification time, so it becomes available for
-      // contributed modules to use for ordering module lists.
-      $module->parsed_info['mtime'] = filemtime(dirname($module->uri) . '/' . $module->name . '.info');
-
-      // Skip modules that don't provide info.
-      if (empty($module->parsed_info)) {
-        unset($modules[$key]);
-        continue;
-      }
+  $modules[$profile] = $profiles[$profile];
 
-      // Merge in defaults and save.
-      $modules[$key]->parsed_info = $module->parsed_info + $defaults;
+  // Installation profile hooks are always executed last.
+  $modules[$profile]->weight = 1000;
 
-      // Prefix stylesheets and scripts with module path.
-      $path = dirname($module->uri);
-      if (isset($module->parsed_info['stylesheets'])) {
-        $module->parsed_info['stylesheets'] = _system_info_add_path($module->parsed_info['stylesheets'], $path);
-      }
-      if (isset($module->parsed_info['scripts'])) {
-        $module->parsed_info['scripts'] = _system_info_add_path($module->parsed_info['scripts'], $path);
-      }
+  // Set defaults for module info.
+  $defaults = array(
+    'dependencies' => array(),
+    'description' => '',
+    'package' => 'Other',
+    'version' => NULL,
+    'php' => DRUPAL_MINIMUM_PHP,
+    'files' => array(),
+    'bootstrap' => 0,
+  );
 
-      // Install profiles are hidden by default, unless explicitly specified
-      // otherwise in the .info file.
-      if ($key == $profile && !isset($modules[$key]->info['hidden'])) {
-        $modules[$key]->info['hidden'] = TRUE;
-      }
+  // Read info files for each module.
+  foreach ($modules as $key => $module) {
+    // The module system uses the key 'filename' instead of 'uri' so copy the
+    // value so it will be used by the modules system.
+    $modules[$key]->filename = $module->uri;
+
+    // Look for the info file.
+    $module->info = drupal_parse_info_file(dirname($module->uri) . '/' . $module->name . '.info');
+
+    // Add the info file modification time, so it becomes available for
+    // contributed modules to use for ordering module lists.
+    $module->info['mtime'] = filemtime(dirname($module->uri) . '/' . $module->name . '.info');
+
+    // Skip modules that don't provide info.
+    if (empty($module->info)) {
+      unset($modules[$key]);
+      continue;
     }
-    // Store the processed modules.
-    $module_store += $modules;
-  }
-  if ($save || ($modules && drupal_valid_test_ua())) {
-    state()->set($state_name ?: __FUNCTION__, array(
-      'module_store' => $module_store,
-      'profiles_seen' => $profiles_seen,
-    ));
+
+    // Merge in defaults and save.
+    $modules[$key]->info = $module->info + $defaults;
+
+    // Prefix stylesheets and scripts with module path.
+    $path = dirname($module->uri);
+    if (isset($module->info['stylesheets'])) {
+      $module->info['stylesheets'] = _system_info_add_path($module->info['stylesheets'], $path);
+    }
+    if (isset($module->info['scripts'])) {
+      $module->info['scripts'] = _system_info_add_path($module->info['scripts'], $path);
+    }
+
+    // Installation profiles are hidden by default, unless explicitly specified
+    // otherwise in the .info file.
+    if ($key == $profile && !isset($modules[$key]->info['hidden'])) {
+      $modules[$key]->info['hidden'] = TRUE;
+    }
+
+    // Invoke hook_system_info_alter() to give installed modules a chance to
+    // modify the data in the .info files if necessary.
+    $type = 'module';
+    drupal_alter('system_info', $modules[$key]->info, $modules[$key], $type);
   }
-  $modules = $module_store;
-  // Do not return the non-active profile modules. Typically at most one: when
-  // testing switches the profile.
-  foreach ($profiles_seen as $key => $value) {
-    if ($key != $profile) {
-      unset($modules[$key]);
+
+  if (isset($modules[$profile])) {
+    // The installation profile is required, if it's a valid module.
+    $modules[$profile]->info['required'] = TRUE;
+    // Add a default distribution name if the profile did not provide one. This
+    // matches the default value used in install_profile_info().
+    if (!isset($modules[$profile]->info['distribution_name'])) {
+      $modules[$profile]->info['distribution_name'] = 'Drupal';
     }
   }
 
@@ -2834,6 +2822,8 @@ function _system_rebuild_module_data($state_name = FALSE, $save = FALSE) {
  */
 function system_rebuild_module_data($reset = TRUE) {
   $modules_cache = &drupal_static(__FUNCTION__, array());
+  // @todo Revert the majority of the following changes.        
+
   // Only rebuild once per request. $modules and $modules_cache cannot be
   // combined into one variable, because the $modules_cache variable is reset by
   // reference from system_list_reset() during the rebuild.
@@ -2863,7 +2853,7 @@ function system_rebuild_module_data($reset = TRUE) {
     $modules_cache['data'] = $modules;
     // Store module filenames so that if can be retrieved during system_list()
     // without a rebuild or drupal_get_filename() without scanning directories.
-    state()->set('system.module_file_list', $module_file_list);
+    state()->set('system.module.files', $module_file_list);
   }
   // Running the info alter function is not possible before full bootstrap.
   if (!isset($modules_cache['info_alter']) && drupal_get_bootstrap_phase() >= DRUPAL_BOOTSTRAP_CODE) {
@@ -2874,10 +2864,6 @@ function system_rebuild_module_data($reset = TRUE) {
     $type = 'module';
     // It is not impossible a function resets the modules cache. Keep it.
     $modules = $modules_cache['data'];
-    foreach ($modules as $record) {
-       // Copy parsed info.
-      $record->info = $record->parsed_info;
-    }
     foreach (config('system.module')->get() as $module => $weight) {
       $function = $module .'_system_info_alter';
       if (function_exists($function)) {
@@ -2904,6 +2890,23 @@ function system_rebuild_module_data($reset = TRUE) {
 }
 
 /**
+ * Refresh bootstrap column in the system table.
+ *
+ * This is called internally by module_enable/disable() to flag modules that
+ * implement hooks used during bootstrap, such as hook_boot(). These modules
+ * are loaded earlier to invoke the hooks.
+ */
+function _system_update_bootstrap_status() {
+  $bootstrap_modules = array();
+  foreach (bootstrap_hooks() as $hook) {
+    foreach (module_implements($hook) as $module) {
+      $bootstrap_modules[$module] = drupal_get_filename('module', $module);
+    }
+  }
+  state()->set('system.bootstrap_modules', $bootstrap_modules);
+}
+
+/**
  * Helper function to scan and collect theme .info data and their engines.
  *
  * @return
@@ -2998,7 +3001,7 @@ function _system_rebuild_theme_data() {
   // Store theme filenames so that if can be retrieved during
   // drupal_get_filename() without scanning directories.
   if (drupal_container()->hasDefinition('keyvalue') && function_exists('db_query')) {
-    state()->set('system.theme_file_list', $theme_file_list);
+    state()->set('system.theme.files', $theme_file_list);
   }
   // Now that we've established all our master themes, go back and fill in data
   // for subthemes.
@@ -3035,19 +3038,13 @@ function _system_rebuild_theme_data() {
  * @return
  *   Array of all available themes and their data.
  */
-function system_rebuild_theme_data($reset = TRUE) {
+function system_rebuild_theme_data() {
   $themes = _system_rebuild_theme_data();
   ksort($themes);
   $themes_status = config('system.theme')->get();
   foreach ($themes as $theme => $data) {
     $data->status = isset($themes_status[$theme]);
   }
-  if ($reset) {
-    system_list_reset();
-  }
-  // Store theme data so that if can be retrieved during system_list() without
-  // a rebuild.
-  state()->set('system.themes', $themes);
   return $themes;
 }
 
diff --git a/core/modules/system/tests/modules/system_test/system_test.module b/core/modules/system/tests/modules/system_test/system_test.module
index ef06cb7..4949aec 100644
--- a/core/modules/system/tests/modules/system_test/system_test.module
+++ b/core/modules/system/tests/modules/system_test/system_test.module
@@ -247,10 +247,11 @@ function system_test_exit() {
 function system_test_system_info_alter(&$info, $file, $type) {
   // We need a static otherwise the last test will fail to alter common_test.
   static $test;
-  if (($dependency = variable_get('dependency', array())) || $test) {
+  if (($dependencies = variable_get('dependencies', array())) || $test) {
     if ($file->name == 'module_test') {
       $info['hidden'] = FALSE;
-      $info['dependencies'][] = $dependency;
+      $info['dependencies'][] = array_shift($dependencies);
+      variable_set('dependencies', $dependencies);
       $test = TRUE;
     }
     if ($file->name == 'common_test') {