diff -u b/core/lib/Drupal/Core/Config/ConfigImporter.php b/core/lib/Drupal/Core/Config/ConfigImporter.php
--- b/core/lib/Drupal/Core/Config/ConfigImporter.php
+++ b/core/lib/Drupal/Core/Config/ConfigImporter.php
@@ -295,32 +295,30 @@
       return $module_data[$module]->sort;
     }, $module_list);
 
-    // Work out what to install and uninstall.
-    $current_modules = $this->storageComparer->getTargetStorage()->read('system.module');
-    $new_modules = $this->storageComparer->getSourceStorage()->read('system.module');
-    $install = array();
-    $uninstall = array();
-    if (isset($current_modules['enabled'], $new_modules['enabled']) && is_array($current_modules['enabled']) && is_array($new_modules['enabled'])) {
-      $uninstall = array_diff(array_keys($current_modules['enabled']), array_keys($new_modules['enabled']));
-      $install = array_diff(array_keys($new_modules['enabled']), array_keys($current_modules['enabled']));
-      // Sort the module list by their weights. So that dependencies
-      // are uninstalled last.
-      asort($module_list);
-      $uninstall = array_intersect(array_keys($module_list), $uninstall);
-      // Sort the module list by their weights (reverse). So that dependencies
-      // are installed first.
-      arsort($module_list);
-      $install = array_intersect(array_keys($module_list), $install);
-    }
-
-    $current_themes = $this->storageComparer->getTargetStorage()->read('system.theme');
-    $new_themes = $this->storageComparer->getSourceStorage()->read('system.theme');
-    $enable = array();
-    $disable = array();
-    if (isset($current_themes['enabled'], $new_themes['enabled']) && is_array($current_themes['enabled']) && is_array($new_themes['enabled'])) {
-      $enable = array_diff(array_keys($new_themes['enabled']), array_keys($current_themes['enabled']));
-      $disable = array_diff(array_keys($current_themes['enabled']), array_keys($new_themes['enabled']));
-    }
+    // Read the extensions information to determine changes.
+    $current_extensions = $this->storageComparer->getTargetStorage()->read('core.extension');
+    $new_extensions = $this->storageComparer->getSourceStorage()->read('core.extension');
+
+    // Probably an empty staging directory.
+    if (!$new_extensions) {
+      return;
+    }
+
+    // Work out what modules to install and uninstall.
+    $uninstall = array_diff(array_keys($current_extensions['module']), array_keys($new_extensions['module']));
+    $install = array_diff(array_keys($new_extensions['module']), array_keys($current_extensions['module']));
+    // Sort the module list by their weights. So that dependencies
+    // are uninstalled last.
+    asort($module_list);
+    $uninstall = array_intersect(array_keys($module_list), $uninstall);
+    // Sort the module list by their weights (reverse). So that dependencies
+    // are installed first.
+    arsort($module_list);
+    $install = array_intersect(array_keys($module_list), $install);
+
+    // Work out what themes to enable and to disable.
+    $enable = array_diff(array_keys($new_extensions['theme']), array_keys($current_extensions['theme']));
+    $disable = array_diff(array_keys($current_extensions['theme']), array_keys($new_extensions['theme']));
 
     $this->extensionChangelist = array(
       'module' => array(
diff -u b/core/modules/config/lib/Drupal/config/Tests/ConfigImportRecreateTest.php b/core/modules/config/lib/Drupal/config/Tests/ConfigImportRecreateTest.php
--- b/core/modules/config/lib/Drupal/config/Tests/ConfigImportRecreateTest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigImportRecreateTest.php
@@ -45,14 +45,6 @@
     $this->installSchema('system', 'config_snapshot');
     $this->installSchema('node', 'node');
 
-    $theme_data = $this->container->get('config.storage')->read('system.theme');
-    if (empty($theme_data['enabled'])) {
-      $this->container->get('config.storage')->write('system.theme', array('admin' => '', 'default' => 'start', 'enabled' => array('stark')));
-    }
-    $module_data = $this->container->get('config.storage')->read('system.module');
-    if (empty($module_data['enabled'])) {
-      $this->container->get('config.storage')->write('system.module', array('enabled' => array('system')));
-    }
     $this->copyConfig($this->container->get('config.storage'), $this->container->get('config.storage.staging'));
 
     // Set up the ConfigImporter object for testing.
diff -u b/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php b/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php
--- b/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php
@@ -75,19 +75,19 @@
     // during the install. Options and Text are there in ensure modules are
     // installed with the correct dependencies. Options depends on Text so Text
     // should be installed first.
-    $system_module = \Drupal::config('system.module')->get();
-    $system_module['enabled']['action'] = 0;
-    $system_module['enabled']['ban'] = 0;
-    $system_module['enabled'] = module_config_sort($system_module['enabled']);
-    $staging->write('system.module', $system_module);
+    $core_extension = \Drupal::config('core.extension')->get();
+    $core_extension['module']['action'] = 0;
+    $core_extension['module']['ban'] = 0;
+    $core_extension['module'] = module_config_sort($core_extension['module']);
+    $core_extension['theme']['bartik'] = 0;
+    $staging->write('core.extension', $core_extension);
 
     // Use the install storage so that we can read configuration from modules
     // and themes that are not installed.
     $install_storage = new InstallStorage();
 
-    // Enable the bartik theme and set it as default.
+    // Set the Bartik theme as default.
     $system_theme = \Drupal::config('system.theme')->get();
-    $system_theme['enabled']['bartik'] = 0;
     $system_theme['default'] = 'bartik';
     $staging->write('system.theme', $system_theme);
     $staging->write('bartik.settings', $install_storage->read('bartik.settings'));
@@ -96,15 +96,19 @@
     $action_settings = $install_storage->read('action.settings');
     $action_settings['recursion_limit'] = 50;
     $staging->write('action.settings', $action_settings);
-
     // Disable the Options and Text modules to ensure that dependencies are handled
     // correctly.
     \Drupal::moduleHandler()->uninstall(array('text', 'options'));
+
+    // Set the state system to record installations and uninstallations.
+    \Drupal::state()->set('ConfigImportUITest.core.extension.modules_installed', array());
+    \Drupal::state()->set('ConfigImportUITest.core.extension.modules_uninstalled', array());
+
     // Verify that both appear as ready to import.
     $this->drupalGet('admin/config/development/configuration');
     $this->assertText($name);
     $this->assertText($dynamic_name);
-    $this->assertText('system.module');
+    $this->assertText('core.extension');
     $this->assertText('system.theme');
     $this->assertText('action.settings');
     $this->assertText('bartik.settings');
@@ -114,7 +118,7 @@
     $this->drupalPostForm(NULL, array(), t('Import all'));
     $this->assertNoText($name);
     $this->assertNoText($dynamic_name);
-    $this->assertNoText('system.module');
+    $this->assertNoText('core.extension');
     $this->assertNoText('system.theme');
     $this->assertNoText('action.settings');
     $this->assertNoText('bartik.settings');
@@ -143,10 +147,12 @@
     $theme_info = \Drupal::service('theme_handler')->listInfo();
     $this->assertTrue($theme_info['bartik']->status, 'Bartik theme enabled during import.');
 
-    // The configuration object system.theme will be saved twice during config
-    // import. Once during enabling the system and once during importing the
-    // new default setting.
-    $this->assertEqual(\Drupal::state()->get('ConfigImportUITest.system.theme.save', 0), 2, 'The system.theme configuration saved twice during import.');
+    // Ensure installations and uninstallation occur as expected.
+    $installed = \Drupal::state()->get('ConfigImportUITest.core.extension.modules_installed', array());
+    $uninstalled = \Drupal::state()->get('ConfigImportUITest.core.extension.modules_uninstalled', array());
+    $expected = array('ban', 'action', 'text', 'options');
+    $this->assertIdentical($expected, $installed, 'Ban, Action, Text and Options modules installed in the correct order.');
+    $this->assertTrue(empty($uninstalled), 'No modules uninstalled during import');
 
     // Verify that the action.settings configuration object was only written
     // once during the import process and only with the value set in the staged
@@ -156,37 +162,36 @@
     $recursion_limit_values = \Drupal::state()->get('ConfigImportUITest.action.settings.recursion_limit', array());
     $this->assertIdentical($recursion_limit_values, array(50));
 
-    $system_module = \Drupal::config('system.module')->get();
-    unset($system_module['enabled']['action']);
-    unset($system_module['enabled']['ban']);
-    unset($system_module['enabled']['options']);
-    unset($system_module['enabled']['text']);
-    $staging->write('system.module', $system_module);
+    $core_extension = \Drupal::config('core.extension')->get();
+    unset($core_extension['module']['action']);
+    unset($core_extension['module']['ban']);
+    unset($core_extension['module']['options']);
+    unset($core_extension['module']['text']);
+    unset($core_extension['theme']['bartik']);
+    $core_extension['disabled']['theme']['bartik'] = 0;
+    $staging->write('core.extension', $core_extension);
     $staging->delete('action.settings');
     $staging->delete('text.settings');
 
     $system_theme = \Drupal::config('system.theme')->get();
-    unset($system_theme['enabled']['bartik']);
     $system_theme['default'] = 'stark';
     $system_theme['admin'] = 'stark';
     $staging->write('system.theme', $system_theme);
-    $staging->write('system.theme.disabled', array('bartik' => 0));
 
-    // Reset counter.
-    \Drupal::state()->set('ConfigImportUITest.system.theme.save', 0);
+    // Set the state system to record installations and uninstallations.
+    \Drupal::state()->set('ConfigImportUITest.core.extension.modules_installed', array());
+    \Drupal::state()->set('ConfigImportUITest.core.extension.modules_uninstalled', array());
 
     // Verify that both appear as ready to import.
     $this->drupalGet('admin/config/development/configuration');
-    $this->assertText('system.module');
+    $this->assertText('core.extension');
     $this->assertText('system.theme');
-    $this->assertText('system.theme.disabled');
     $this->assertText('action.settings');
 
     // Import and verify that both do not appear anymore.
     $this->drupalPostForm(NULL, array(), t('Import all'));
-    $this->assertNoText('system.module');
+    $this->assertNoText('core.extension');
     $this->assertNoText('system.theme');
-    $this->assertNoText('system.theme.disabled');
     $this->assertNoText('action.settings');
 
     $this->rebuildContainer();
@@ -195,9 +200,13 @@
     $this->assertFalse(\Drupal::moduleHandler()->moduleExists('action'), 'Action module uninstalled during import.');
     $this->assertFalse(\Drupal::moduleHandler()->moduleExists('options'), 'Options module uninstalled during import.');
     $this->assertFalse(\Drupal::moduleHandler()->moduleExists('text'), 'Text module uninstalled during import.');
-    // This is because it will be updated to change the default and admin theme,
-    // and then remove Bartik.
-    $this->assertEqual(\Drupal::state()->get('ConfigImportUITest.system.theme.save', 0), 2, 'The system.theme configuration saved twice during import.');
+
+    // Ensure installations and uninstallation occur as expected.
+    $installed = \Drupal::state()->get('ConfigImportUITest.core.extension.modules_installed', array());
+    $uninstalled = \Drupal::state()->get('ConfigImportUITest.core.extension.modules_uninstalled', array());
+    $expected = array('options', 'text', 'ban', 'action');
+    $this->assertIdentical($expected, $uninstalled, 'Options, Text, Action and Ban modules uninstalled in the correct order.');
+    $this->assertTrue(empty($installed), 'No modules installed during import');
 
     $theme_info = \Drupal::service('theme_handler')->listInfo();
     $this->assertTrue(isset($theme_info['bartik']) && !$theme_info['bartik']->status, 'Bartik theme disabled during import.');
diff -u b/core/modules/config/lib/Drupal/config/Tests/ConfigImporterTest.php b/core/modules/config/lib/Drupal/config/Tests/ConfigImporterTest.php
--- b/core/modules/config/lib/Drupal/config/Tests/ConfigImporterTest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigImporterTest.php
@@ -50,14 +50,6 @@
     // so it has to be cleared out manually.
     unset($GLOBALS['hook_config_test']);
 
-    $theme_data = $this->container->get('config.storage')->read('system.theme');
-    if (empty($theme_data['enabled'])) {
-      $this->container->get('config.storage')->write('system.theme', array('admin' => '', 'default' => 'stark', 'enabled' => array('stark')));
-    }
-    $module_data = $this->container->get('config.storage')->read('system.module');
-    if (empty($module_data['enabled'])) {
-      $this->container->get('config.storage')->write('system.module', array('enabled' => array('system')));
-    }
     $this->copyConfig($this->container->get('config.storage'), $this->container->get('config.storage.staging'));
 
     // Set up the ConfigImporter object for testing.
diff -u b/core/modules/config/tests/config_import_test/lib/Drupal/config_import_test/EventSubscriber.php b/core/modules/config/tests/config_import_test/lib/Drupal/config_import_test/EventSubscriber.php
--- b/core/modules/config/tests/config_import_test/lib/Drupal/config_import_test/EventSubscriber.php
+++ b/core/modules/config/tests/config_import_test/lib/Drupal/config_import_test/EventSubscriber.php
@@ -56,9 +56,23 @@
       $values[] = $config->get('recursion_limit');
       $this->state->set('ConfigImportUITest.action.settings.recursion_limit', $values);
     }
-    if ($config->getName() == 'system.theme') {
-      $value = $this->state->get('ConfigImportUITest.system.theme.save', 0);
-      $this->state->set('ConfigImportUITest.system.theme.save', $value + 1);
+
+    if ($config->getName() == 'core.extension') {
+      $installed = $this->state->get('ConfigImportUITest.core.extension.modules_installed', array());
+      $uninstalled = $this->state->get('ConfigImportUITest.core.extension.modules_uninstalled', array());
+      $original = $config->getOriginal('module');
+      $data = $config->get('module');
+      $install = array_diff_key($data, $original);
+      if (!empty($install)) {
+        $installed[] = key($install);
+      }
+      $uninstall = array_diff_key($original, $data);
+      if (!empty($uninstall)) {
+        $uninstalled[] = key($uninstall);
+      }
+
+      $this->state->set('ConfigImportUITest.core.extension.modules_installed', $installed);
+      $this->state->set('ConfigImportUITest.core.extension.modules_uninstalled', $uninstalled);
     }
   }
 
diff -u b/core/modules/forum/forum.install b/core/modules/forum/forum.install
--- b/core/modules/forum/forum.install
+++ b/core/modules/forum/forum.install
@@ -34,7 +34,7 @@
           ),
         ),
       ))->save();
-  
+
       // Create a default forum so forum posts can be created.
       $term = entity_create('taxonomy_term', array(
         'name' => t('General discussion'),
@@ -44,7 +44,7 @@
         'forum_container' => 0,
       ));
       $term->save();
-  
+
       // Create the instance on the bundle.
       entity_create('field_instance_config', array(
         'field_name' => 'taxonomy_forums',
@@ -53,14 +53,14 @@
         'bundle' => 'forum',
         'required' => TRUE,
       ))->save();
-  
-        // Assign form display settings for the 'default' form mode.
-        entity_get_form_display('node', 'forum', 'default')
-          ->setComponent('taxonomy_forums', array(
-            'type' => 'options_select',
-          ))
-          ->save();
-  
+
+      // Assign form display settings for the 'default' form mode.
+      entity_get_form_display('node', 'forum', 'default')
+        ->setComponent('taxonomy_forums', array(
+          'type' => 'options_select',
+        ))
+        ->save();
+
       // Assign display settings for the 'default' and 'teaser' view modes.
       entity_get_display('node', 'forum', 'default')
         ->setComponent('taxonomy_forums', array(
@@ -68,6 +68,7 @@
           'weight' => 10,
         ))
         ->save();
+
       entity_get_display('node', 'forum', 'teaser')
         ->setComponent('taxonomy_forums', array(
           'type' => 'taxonomy_term_reference_link',
reverted:
--- b/core/modules/system/config/schema/system.schema.yml
+++ a/core/modules/system/config/schema/system.schema.yml
@@ -466,8 +466,6 @@
           type: boolean
           label: 'Use default'
 
-# The weight for disabled themes is ignored but the same format for
-# system.theme:enabled is used for consistency.
 system.theme.disabled:
   type: sequence
   label: 'Disabled themes'
reverted:
--- b/core/modules/system/config/system.theme.disabled.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-# An empty array representing no disabled themes. This file needs to exist since
-# all simple configuration must exist.
-{  }
\ No newline at end of file
only in patch2:
unchanged:
--- a/core/modules/config/lib/Drupal/config/Tests/ConfigOverrideTest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigOverrideTest.php
@@ -32,6 +32,7 @@ public static function getInfo() {
   public function setUp() {
     parent::setUp();
     $this->installSchema('system', 'config_snapshot');
+    $this->copyConfig($this->container->get('config.storage'), $this->container->get('config.storage.staging'));
   }
 
   /**
only in patch2:
unchanged:
--- a/core/modules/config/lib/Drupal/config/Tests/ConfigSnapshotTest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigSnapshotTest.php
@@ -36,6 +36,7 @@ public function setUp() {
     // Update the config snapshot. This allows the parent::setUp() to write
     // configuration files.
     \Drupal::service('config.manager')->createSnapshot(\Drupal::service('config.storage'), \Drupal::service('config.storage.snapshot'));
+    $this->copyConfig($this->container->get('config.storage'), $this->container->get('config.storage.staging'));
   }
 
   /**
only in patch2:
unchanged:
--- a/core/modules/simpletest/lib/Drupal/simpletest/DrupalUnitTestBase.php
+++ b/core/modules/simpletest/lib/Drupal/simpletest/DrupalUnitTestBase.php
@@ -148,7 +148,7 @@ protected function setUp() {
     // \Drupal\Core\Config\ConfigInstaller::installDefaultConfig() to work.
     // Write directly to active storage to avoid early instantiation of
     // the event dispatcher which can prevent modules from registering events.
-    \Drupal::service('config.storage')->write('core.extension', array('module' => array()));
+    \Drupal::service('config.storage')->write('core.extension', array('module' => array(), 'theme' => array()));
 
     // Collect and set a fixed module list.
     $class = get_class($this);