diff -u b/core/modules/breakpoint/lib/Drupal/breakpoint/Entity/BreakpointGroup.php b/core/modules/breakpoint/lib/Drupal/breakpoint/Entity/BreakpointGroup.php
--- b/core/modules/breakpoint/lib/Drupal/breakpoint/Entity/BreakpointGroup.php
+++ b/core/modules/breakpoint/lib/Drupal/breakpoint/Entity/BreakpointGroup.php
@@ -11,6 +11,7 @@
 use Drupal\breakpoint\BreakpointGroupInterface;
 use Drupal\breakpoint\InvalidBreakpointSourceException;
 use Drupal\breakpoint\InvalidBreakpointSourceTypeException;
+use Drupal\Core\Entity\EntityStorageControllerInterface;
 
 /**
  * Defines the BreakpointGroup entity.
@@ -224,2 +225,22 @@
   }
+
+  /**
+   * {@inheritdoc}
+   */
+  public function preSave(EntityStorageControllerInterface $storage_controller) {
+    parent::preSave($storage_controller);
+
+    $this->dependencies = array();
+    if ($this->sourceType == Breakpoint::SOURCE_TYPE_MODULE) {
+      $this->createDependency('module', $this->source);
+    }
+    elseif ($this->sourceType == Breakpoint::SOURCE_TYPE_THEME) {
+      $this->createDependency('theme', $this->source);
+    }
+    $breakpoints = $this->getBreakpoints();
+    foreach ($breakpoints as $breakpoint) {
+      $this->createDependency('module', $breakpoint->getConfigDependencyName());
+    }
+  }
+
 }
diff -u b/core/modules/editor/lib/Drupal/editor/Entity/Editor.php b/core/modules/editor/lib/Drupal/editor/Entity/Editor.php
--- b/core/modules/editor/lib/Drupal/editor/Entity/Editor.php
+++ b/core/modules/editor/lib/Drupal/editor/Entity/Editor.php
@@ -83,6 +83,10 @@
     // Create a dependency of the linked filter.
     $filter = entity_load('filter_format', $this->format);
     $this->createDependency('entity', $filter->getConfigDependencyName());
+    // @todo use EntityWithPluginBagInterface so configuration between config
+    //   entity and dependency on provider is managed automatically.
+    $definition = \Drupal::service('plugin.manager.editor')->createInstance($this->editor)->getPluginDefinition();
+    $this->createDependency('module', $definition['provider']);
     parent::preSave($storage_controller);
   }
 
reverted:
--- b/core/modules/search/config/entity.view_mode.node.search_index.yml
+++ a/core/modules/search/config/entity.view_mode.node.search_index.yml
@@ -3,7 +3,3 @@
 status: false
 cache: true
 targetEntityType: node
-dependencies:
-  module:
-    - node
-    - search
reverted:
--- b/core/modules/search/config/entity.view_mode.node.search_result.yml
+++ a/core/modules/search/config/entity.view_mode.node.search_result.yml
@@ -3,7 +3,3 @@
 status: false
 cache: true
 targetEntityType: node
-dependencies:
-  module:
-    - node
-    - search
diff -u b/core/profiles/standard/config/block.block.bartik_breadcrumbs.yml b/core/profiles/standard/config/block.block.bartik_breadcrumbs.yml
--- b/core/profiles/standard/config/block.block.bartik_breadcrumbs.yml
+++ b/core/profiles/standard/config/block.block.bartik_breadcrumbs.yml
@@ -25,0 +26,2 @@
+  theme:
+    - bartik
diff -u b/core/profiles/standard/config/block.block.bartik_content.yml b/core/profiles/standard/config/block.block.bartik_content.yml
--- b/core/profiles/standard/config/block.block.bartik_content.yml
+++ b/core/profiles/standard/config/block.block.bartik_content.yml
@@ -25,0 +26,2 @@
+  theme:
+    - bartik
diff -u b/core/profiles/standard/config/block.block.bartik_footer.yml b/core/profiles/standard/config/block.block.bartik_footer.yml
--- b/core/profiles/standard/config/block.block.bartik_footer.yml
+++ b/core/profiles/standard/config/block.block.bartik_footer.yml
@@ -25 +25,3 @@
-    - system
\ No newline at end of file
+    - system
+  theme:
+    - bartik
diff -u b/core/profiles/standard/config/block.block.bartik_help.yml b/core/profiles/standard/config/block.block.bartik_help.yml
--- b/core/profiles/standard/config/block.block.bartik_help.yml
+++ b/core/profiles/standard/config/block.block.bartik_help.yml
@@ -25 +25,3 @@
-    - system
\ No newline at end of file
+    - system
+  theme:
+    - bartik
diff -u b/core/profiles/standard/config/block.block.bartik_login.yml b/core/profiles/standard/config/block.block.bartik_login.yml
--- b/core/profiles/standard/config/block.block.bartik_login.yml
+++ b/core/profiles/standard/config/block.block.bartik_login.yml
@@ -25,0 +26,2 @@
+  theme:
+    - bartik
diff -u b/core/profiles/standard/config/block.block.bartik_powered.yml b/core/profiles/standard/config/block.block.bartik_powered.yml
--- b/core/profiles/standard/config/block.block.bartik_powered.yml
+++ b/core/profiles/standard/config/block.block.bartik_powered.yml
@@ -25 +25,3 @@
-    - system
\ No newline at end of file
+    - system
+  theme:
+    - bartik
diff -u b/core/profiles/standard/config/block.block.bartik_search.yml b/core/profiles/standard/config/block.block.bartik_search.yml
--- b/core/profiles/standard/config/block.block.bartik_search.yml
+++ b/core/profiles/standard/config/block.block.bartik_search.yml
@@ -25,0 +26,2 @@
+  theme:
+    - bartik
diff -u b/core/profiles/standard/config/block.block.bartik_tools.yml b/core/profiles/standard/config/block.block.bartik_tools.yml
--- b/core/profiles/standard/config/block.block.bartik_tools.yml
+++ b/core/profiles/standard/config/block.block.bartik_tools.yml
@@ -25 +25,3 @@
-    - system
\ No newline at end of file
+    - system
+  theme:
+    - bartik
diff -u b/core/profiles/standard/config/block.block.seven_breadcrumbs.yml b/core/profiles/standard/config/block.block.seven_breadcrumbs.yml
--- b/core/profiles/standard/config/block.block.seven_breadcrumbs.yml
+++ b/core/profiles/standard/config/block.block.seven_breadcrumbs.yml
@@ -25,0 +26,2 @@
+  theme:
+    - seven
diff -u b/core/profiles/standard/config/block.block.seven_content.yml b/core/profiles/standard/config/block.block.seven_content.yml
--- b/core/profiles/standard/config/block.block.seven_content.yml
+++ b/core/profiles/standard/config/block.block.seven_content.yml
@@ -25,0 +26,2 @@
+  theme:
+    - seven
diff -u b/core/profiles/standard/config/block.block.seven_help.yml b/core/profiles/standard/config/block.block.seven_help.yml
--- b/core/profiles/standard/config/block.block.seven_help.yml
+++ b/core/profiles/standard/config/block.block.seven_help.yml
@@ -25,0 +26,2 @@
+  theme:
+    - seven
diff -u b/core/profiles/standard/config/block.block.seven_login.yml b/core/profiles/standard/config/block.block.seven_login.yml
--- b/core/profiles/standard/config/block.block.seven_login.yml
+++ b/core/profiles/standard/config/block.block.seven_login.yml
@@ -25,0 +26,2 @@
+  theme:
+    - seven
diff -u b/core/profiles/standard/config/editor.editor.basic_html.yml b/core/profiles/standard/config/editor.editor.basic_html.yml
--- b/core/profiles/standard/config/editor.editor.basic_html.yml
+++ b/core/profiles/standard/config/editor.editor.basic_html.yml
@@ -46,0 +47,2 @@
+  module:
+    - ckeditor
diff -u b/core/profiles/standard/config/editor.editor.full_html.yml b/core/profiles/standard/config/editor.editor.full_html.yml
--- b/core/profiles/standard/config/editor.editor.full_html.yml
+++ b/core/profiles/standard/config/editor.editor.full_html.yml
@@ -58,0 +59,2 @@
+  module:
+    - ckeditor
only in patch2:
unchanged:
--- a/core/lib/Drupal/Core/Extension/ThemeHandler.php
+++ b/core/lib/Drupal/Core/Extension/ThemeHandler.php
@@ -169,6 +169,11 @@ public function disable(array $theme_list) {
 
     $this->clearCssCache();
 
+    // Remove configuration.
+    foreach ($theme_list as $key) {
+      \Drupal::service('config.manager')->uninstall('theme', $key);
+    }
+
     $theme_config = $this->configFactory->get('system.theme');
     $disabled_themes = $this->configFactory->get('system.theme.disabled');
     foreach ($theme_list as $key) {
only in patch2:
unchanged:
--- a/core/modules/block/custom_block/lib/Drupal/custom_block/Entity/CustomBlock.php
+++ b/core/modules/block/custom_block/lib/Drupal/custom_block/Entity/CustomBlock.php
@@ -103,7 +103,7 @@ public function getTheme() {
    */
   public function preSave(EntityStorageControllerInterface $storage_controller) {
     parent::preSave($storage_controller);
-
+    $this->createDependency('theme', $this->theme);
     // Before saving the custom block, set changed time.
     $this->set('changed', REQUEST_TIME);
   }
only in patch2:
unchanged:
--- a/core/modules/block/lib/Drupal/block/Entity/Block.php
+++ b/core/modules/block/lib/Drupal/block/Entity/Block.php
@@ -11,6 +11,7 @@
 use Drupal\block\BlockPluginBag;
 use Drupal\block\BlockInterface;
 use Drupal\Core\Config\Entity\EntityWithPluginBagInterface;
+use Drupal\Core\Entity\EntityStorageControllerInterface;
 
 /**
  * Defines a Block configuration entity class.
@@ -172,4 +173,12 @@ public static function sort($a, $b) {
     return strcmp($a->label(), $b->label());
   }
 
+  /**
+   * {@inheritdoc}
+   */
+  public function preSave(EntityStorageControllerInterface $storage_controller) {
+    parent::preSave($storage_controller);
+    $this->createDependency('theme', $this->theme);
+  }
+
 }
only in patch2:
unchanged:
--- a/core/modules/block/tests/modules/block_test/config/block.block.test_block.yml
+++ b/core/modules/block/tests/modules/block_test/config/block.block.test_block.yml
@@ -18,3 +18,8 @@ visibility:
     roles: {  }
   node_type:
     types: {  }
+dependencies:
+  module:
+    - block_test
+  theme:
+    - stark
only in patch2:
unchanged:
--- a/core/modules/breakpoint/breakpoint.module
+++ b/core/modules/breakpoint/breakpoint.module
@@ -39,106 +39,6 @@ function breakpoint_help($path, $arg) {
 }
 
 /**
- * Implements hook_themes_disabled().
- *
- * @param array $theme_list
- *   An array of theme names.
- *
- * @see _breakpoint_delete_breakpoints()
- *
- * @todo: This should be removed if https://drupal.org/node/1813110 is resolved.
- */
-function breakpoint_themes_disabled($theme_list) {
-  _breakpoint_delete_breakpoints($theme_list, Breakpoint::SOURCE_TYPE_THEME);
-}
-
-/**
- * Implements hook_modules_uninstalled().
- *
- * @param array $modules
- *   An array of the modules that were uninstalled.
- *
- * @see _breakpoint_delete_breakpoints()
- *
- * @todo: This should be removed if https://drupal.org/node/1813110 is resolved.
- */
-function breakpoint_modules_uninstalled($modules) {
-  _breakpoint_delete_breakpoints($modules, Breakpoint::SOURCE_TYPE_MODULE);
-}
-
-/**
- * Remove breakpoints from all disabled themes or uninstalled modules.
- *
- * The source type has to match the original source type, otherwise the group
- * will not be deleted. All groups created by the theme or module will be
- * deleted as well.
- *
- * @param array $list
- *   A list of modules or themes that are disabled.
- * @param string $source_type
- *   Either Breakpoint::SOURCE_TYPE_THEME or Breakpoint::SOURCE_TYPE_MODULE.
- */
-function _breakpoint_delete_breakpoints($list, $source_type) {
-  $ids = \Drupal::configFactory()->listAll('breakpoint.breakpoint_group.' . $source_type . '.');
-  $entity_manager = \Drupal::entityManager();
-  $entity_type = $entity_manager->getDefinition('breakpoint_group');
-
-  // Remove the breakpoint.breakpoint part of the breakpoint identifier.
-  foreach ($ids as &$id) {
-    $id = ConfigStorageController::getIDFromConfigName($id, $entity_type->getConfigPrefix());
-  }
-  $breakpoint_groups = entity_load_multiple('breakpoint_group', $ids);
-
-  foreach ($breakpoint_groups as $breakpoint_group) {
-    if ($breakpoint_group->sourceType == $source_type && in_array($breakpoint_group->source, $list)) {
-      // Delete the automatically created breakpoint group.
-      $breakpoint_group->delete();
-
-      // Get all breakpoints defined by this theme/module.
-      $breakpoint_ids = \Drupal::service('config.storage')->listAll('breakpoint.breakpoint.' . $source_type . '.' . $breakpoint_group->id() . '.');
-      $entity_type = $entity_manager->getDefinition('breakpoint');
-
-      // Remove the breakpoint.breakpoint part of the breakpoint identifier.
-      foreach ($breakpoint_ids as &$breakpoint_id) {
-        $breakpoint_id = ConfigStorageController::getIDFromConfigName($breakpoint_id, $entity_type->getConfigPrefix());
-      }
-      $breakpoints = entity_load_multiple('breakpoint', $breakpoint_ids);
-
-      // Make sure we only delete breakpoints defined by this theme/module.
-      foreach ($breakpoints as $breakpoint) {
-        if ($breakpoint->sourceType == $source_type && $breakpoint->source == $breakpoint_group->name) {
-          $breakpoint->delete();
-        }
-      }
-    }
-  }
-
-  // Delete groups defined by a module/theme even if that module/theme didn't
-  // define any breakpoints.
-  foreach ($ids as $id) {
-    // Delete all breakpoint groups defined by the theme or module.
-    _breakpoint_delete_breakpoint_groups($id, $source_type);
-  }
-}
-
-/**
- * Remove breakpoint groups from all disabled themes or uninstalled modules.
- *
- * @param array $group_id
- *   Machine readable name of the breakpoint group.
- * @param string $source_type
- *   Either Breakpoint::SOURCE_TYPE_THEME or Breakpoint::SOURCE_TYPE_MODULE.
- */
-function _breakpoint_delete_breakpoint_groups($group_id, $source_type) {
-  $breakpoint_groups = entity_load_multiple('breakpoint_group');
-  foreach ($breakpoint_groups as $breakpoint_group) {
-    if ($breakpoint_group->sourceType == $source_type && $breakpoint_group->source == $group_id) {
-      $breakpoint_group->delete();
-    }
-  }
-}
-
-/**
  * Load one breakpoint by its identifier.
  *
  * @param int $id
only in patch2:
unchanged:
--- a/core/modules/breakpoint/config/schema/breakpoint.schema.yml
+++ b/core/modules/breakpoint/config/schema/breakpoint.schema.yml
@@ -39,6 +39,9 @@ breakpoint.breakpoint.*.*.*:
     status:
       type: boolean
       label: 'Enabled'
+    dependencies:
+      type: config_dependency
+      label: 'Dependencies'
 
 breakpoint.breakpoint_group.*.*.*:
   type: mapping
@@ -74,3 +77,6 @@ breakpoint.breakpoint_group.*.*.*:
     status:
       type: boolean
       label: 'Enabled'
+    dependencies:
+      type: config_dependency
+      label: 'Dependencies'
only in patch2:
unchanged:
--- a/core/modules/breakpoint/lib/Drupal/breakpoint/BreakpointGroupInterface.php
+++ b/core/modules/breakpoint/lib/Drupal/breakpoint/BreakpointGroupInterface.php
@@ -51,7 +51,7 @@ public function addBreakpoints($breakpoints);
   /**
    * Gets the array of breakpoints for the breakpoint group.
    *
-   * @return array
+   * @return \Drupal\breakpoint\Entity\Breakpoint[]
    *   The array of breakpoints for the breakpoint group.
    */
   public function getBreakpoints();
only in patch2:
unchanged:
--- a/core/modules/breakpoint/lib/Drupal/breakpoint/Entity/Breakpoint.php
+++ b/core/modules/breakpoint/lib/Drupal/breakpoint/Entity/Breakpoint.php
@@ -14,6 +14,7 @@
 use Drupal\breakpoint\InvalidBreakpointSourceException;
 use Drupal\breakpoint\InvalidBreakpointSourceTypeException;
 use Drupal\breakpoint\InvalidBreakpointMediaQueryException;
+use Drupal\Core\Entity\EntityStorageControllerInterface;
 
 /**
  * Defines the Breakpoint entity.
@@ -276,4 +277,19 @@ public static function isValidMediaQuery($media_query) {
     }
     throw new InvalidBreakpointMediaQueryException('Media query is empty.');
   }
+
+  /**
+   * {@inheritdoc}
+   */
+  public function preSave(EntityStorageControllerInterface $storage_controller) {
+    parent::preSave($storage_controller);
+    $this->dependencies = array();
+    if ($this->sourceType == static::SOURCE_TYPE_MODULE) {
+      $this->createDependency('module', $this->source);
+    }
+    elseif ($this->sourceType == static::SOURCE_TYPE_THEME) {
+      $this->createDependency('theme', $this->source);
+    }
+  }
+
 }
only in patch2:
unchanged:
--- a/core/modules/search/config/entity.view_mode.node.search_index.yml
+++ b/core/modules/node/config/entity.view_mode.node.search_index.yml
@@ -3,3 +3,6 @@ label: 'Search index'
 status: false
 cache: true
 targetEntityType: node
+dependencies:
+  module:
+    - node
only in patch2:
unchanged:
--- a/core/modules/search/config/entity.view_mode.node.search_result.yml
+++ b/core/modules/node/config/entity.view_mode.node.search_result.yml
@@ -3,3 +3,6 @@ label: 'Search result'
 status: false
 cache: true
 targetEntityType: node
+dependencies:
+  module:
+    - node
only in patch2:
unchanged:
--- a/core/modules/picture/config/schema/picture.schema.yml
+++ b/core/modules/picture/config/schema/picture.schema.yml
@@ -37,6 +37,9 @@ picture.mappings.*:
     langcode:
       type: string
       label: 'Default language'
+    dependencies:
+      type: config_dependency
+      label: 'Dependencies'
 
 entity_view_display.field.picture:
   type: entity_field_view_display_base
only in patch2:
unchanged:
--- a/core/modules/picture/lib/Drupal/picture/Entity/PictureMapping.php
+++ b/core/modules/picture/lib/Drupal/picture/Entity/PictureMapping.php
@@ -8,6 +8,7 @@
 namespace Drupal\picture\Entity;
 
 use Drupal\Core\Config\Entity\ConfigEntityBase;
+use Drupal\Core\Entity\EntityStorageControllerInterface;
 use Drupal\picture\PictureMappingInterface;
 
 /**
@@ -85,6 +86,21 @@ public function __construct(array $values, $entity_type) {
   }
 
   /**
+   * {@inheritdoc}
+   */
+  public function preSave(EntityStorageControllerInterface $storage_controller) {
+    parent::preSave($storage_controller);
+    $this->dependencies = array();
+    if (isset($this->breakpointGroup)) {
+      // @todo Implement getExportProperties() so we do not have reload the
+      //   entity since this property is changed in
+      //   \Drupal\picture\PictureMapping::save().
+      $breakpoint_group = entity_load('breakpoint_group', $this->breakpointGroup);
+      $this->createDependency('entity', $breakpoint_group->getConfigDependencyName());
+    }
+  }
+
+  /**
    * Overrides Drupal\Core\Entity::save().
    */
   public function save() {
only in patch2:
unchanged:
--- a/core/modules/tour/config/schema/tour.schema.yml
+++ b/core/modules/tour/config/schema/tour.schema.yml
@@ -34,6 +34,9 @@ tour.tour.*:
       sequence:
         - type: tour.tip.[plugin]
           label: 'Tour tip'
+    dependencies:
+      type: config_dependency
+      label: 'Dependencies'
 
 tour.tip:
   type: mapping
only in patch2:
unchanged:
--- a/core/modules/tour/lib/Drupal/tour/Entity/Tour.php
+++ b/core/modules/tour/lib/Drupal/tour/Entity/Tour.php
@@ -8,6 +8,7 @@
 namespace Drupal\tour\Entity;
 
 use Drupal\Core\Config\Entity\ConfigEntityBase;
+use Drupal\Core\Entity\EntityStorageControllerInterface;
 use Drupal\tour\TipsBag;
 use Drupal\tour\TourInterface;
 
@@ -168,4 +169,18 @@ public function resetKeyedRoutes() {
     unset($this->keyedRoutes);
   }
 
+  /**
+   * {@inheritdoc}
+   */
+  public function preSave(EntityStorageControllerInterface $storage_controller) {
+    parent::preSave($storage_controller);
+
+    foreach($this->tipsBag as $instance) {
+      $definition = $instance->getPluginDefinition();
+      $this->createDependency('module', $definition['provider']);
+    }
+
+    $this->createDependency('module', $this->module);
+  }
+
 }
only in patch2:
unchanged:
--- a/core/modules/views_ui/config/tour.tour.views-ui.yml
+++ b/core/modules/views_ui/config/tour.tour.views-ui.yml
@@ -87,3 +87,6 @@ tips:
     location: left
     attributes:
       data-id: views-display-extra-actions
+dependencies:
+  module:
+    - views_ui
only in patch2:
unchanged:
--- a/core/profiles/minimal/config/block.block.stark_admin.yml
+++ b/core/profiles/minimal/config/block.block.stark_admin.yml
@@ -18,3 +18,8 @@ visibility:
     roles: {  }
   node_type:
     types: {  }
+dependencies:
+  module:
+    - system
+  theme:
+    - stark
only in patch2:
unchanged:
--- a/core/profiles/minimal/config/block.block.stark_login.yml
+++ b/core/profiles/minimal/config/block.block.stark_login.yml
@@ -18,3 +18,8 @@ visibility:
     roles: {  }
   node_type:
     types: {  }
+dependencies:
+  module:
+    - user
+  theme:
+    - stark
only in patch2:
unchanged:
--- a/core/profiles/minimal/config/block.block.stark_tools.yml
+++ b/core/profiles/minimal/config/block.block.stark_tools.yml
@@ -18,3 +18,8 @@ visibility:
     roles: {  }
   node_type:
     types: {  }
+dependencies:
+  module:
+    - system
+  theme:
+    - stark