diff --git a/core/lib/Drupal/Core/Menu/MenuLinkBase.php b/core/lib/Drupal/Core/Menu/MenuLinkBase.php
index 031b272..9796b84 100644
--- a/core/lib/Drupal/Core/Menu/MenuLinkBase.php
+++ b/core/lib/Drupal/Core/Menu/MenuLinkBase.php
@@ -91,13 +91,6 @@ public function isExpanded() {
   /**
    * {@inheritdoc}
    */
-  public function isDiscovered() {
-    return (bool) $this->pluginDefinition['discovered'];
-  }
-
-  /**
-   * {@inheritdoc}
-   */
   public function isResetable() {
     return FALSE;
   }
diff --git a/core/lib/Drupal/Core/Menu/MenuLinkDefault.php b/core/lib/Drupal/Core/Menu/MenuLinkDefault.php
index aea7b12..5cd52d2 100644
--- a/core/lib/Drupal/Core/Menu/MenuLinkDefault.php
+++ b/core/lib/Drupal/Core/Menu/MenuLinkDefault.php
@@ -67,8 +67,8 @@ public static function create(ContainerInterface $container, array $configuratio
    * {@inheritdoc}
    */
   public function isResetable() {
-    // The link can be reset if it was discovered and has an override.
-    return $this->pluginDefinition['discovered'] && $this->staticOverride->loadOverride($this->getPluginId());
+    // The link can be reset if it has an override.
+    return $this->staticOverride->loadOverride($this->getPluginId());
   }
 
   /**
diff --git a/core/lib/Drupal/Core/Menu/MenuLinkInterface.php b/core/lib/Drupal/Core/Menu/MenuLinkInterface.php
index 36d8520..64f99a2 100644
--- a/core/lib/Drupal/Core/Menu/MenuLinkInterface.php
+++ b/core/lib/Drupal/Core/Menu/MenuLinkInterface.php
@@ -68,14 +68,6 @@ public function isHidden();
   public function isExpanded();
 
   /**
-   * Returns whether this link was discovered.
-   *
-   * @return bool
-   *    TRUE if it is a discovered link, FALSE otherwise.
-   */
-  public function isDiscovered();
-
-  /**
    * Returns whether this link can be reset.
    *
    * In general, only links that store overrides using the
diff --git a/core/lib/Drupal/Core/Menu/MenuLinkManager.php b/core/lib/Drupal/Core/Menu/MenuLinkManager.php
index ed51745..33521fc 100644
--- a/core/lib/Drupal/Core/Menu/MenuLinkManager.php
+++ b/core/lib/Drupal/Core/Menu/MenuLinkManager.php
@@ -50,9 +50,7 @@ class MenuLinkManager implements MenuLinkManagerInterface {
     'options' => array(),
     'expanded' => 0,
     'hidden' => 0,
-    // Flag for whether this plugin was discovered. Should be set to 0 or NULL
-    // for definitions that are added via a direct save.
-    'discovered' => 0,
+    // The name of the module providing this link.
     'provider' => '',
     'metadata' => array(),
     // Default class for local task implementations.
@@ -150,7 +148,7 @@ public function getDefinitions() {
     // Since this function is called rarely, instantiate the discovery here.
     $definitions = $this->getDiscovery()->getDefinitions();
 
-    $this->moduleHandler->alter('menu_links', $definitions);
+    $this->moduleHandler->alter('menu_links_discovered', $definitions);
 
     foreach ($definitions as $plugin_id => &$definition) {
       $definition['id'] = $plugin_id;
@@ -163,11 +161,6 @@ public function getDefinitions() {
       if (!empty($plugin_definition['provider']) && !$this->moduleHandler->moduleExists($plugin_definition['provider'])) {
         unset($definitions[$plugin_id]);
       }
-      else {
-        // Any link found here is flagged as discovered, so it can be purged
-        // if it does not exist in the future.
-        $definitions[$plugin_id]['discovered'] = 1;
-      }
     }
     return $definitions;
   }
diff --git a/core/lib/Drupal/Core/Menu/MenuTreeStorage.php b/core/lib/Drupal/Core/Menu/MenuTreeStorage.php
index 89e0c80..003356c 100644
--- a/core/lib/Drupal/Core/Menu/MenuTreeStorage.php
+++ b/core/lib/Drupal/Core/Menu/MenuTreeStorage.php
@@ -87,7 +87,6 @@ class MenuTreeStorage implements MenuTreeStorageInterface {
     'options',
     'expanded',
     'hidden',
-    'discovered',
     'provider',
     'metadata',
     'class',
@@ -140,6 +139,8 @@ public function rebuild(array $definitions) {
     $before_menus = $this->getMenuNames();
     if ($definitions) {
       foreach ($definitions as $id => $link) {
+        // Flag this link as discovered, i.e. saved via rebuild().
+        $link['discovered'] = 1;
         if (!empty($link['parent'])) {
           $children[$link['parent']][$id] = $id;
         }
diff --git a/core/lib/Drupal/Core/Menu/MenuTreeStorageInterface.php b/core/lib/Drupal/Core/Menu/MenuTreeStorageInterface.php
index 5e7232d..0de1fe6 100644
--- a/core/lib/Drupal/Core/Menu/MenuTreeStorageInterface.php
+++ b/core/lib/Drupal/Core/Menu/MenuTreeStorageInterface.php
@@ -25,6 +25,10 @@ public function resetDefinitions();
   /**
    * Rebuilds the stored menu link definitions.
    *
+   * Links that saved by passing definitions into this method must be included
+   * on all future calls, or they will be purged. This allows for automatic
+   * cleanup e.g. when modules are uninstalled.
+   *
    * @param array $definitions
    *   The new menu link definitions.
    *
diff --git a/core/modules/content_translation/content_translation.module b/core/modules/content_translation/content_translation.module
index 466b561..a738ddb 100644
--- a/core/modules/content_translation/content_translation.module
+++ b/core/modules/content_translation/content_translation.module
@@ -203,9 +203,9 @@ function content_translation_entity_operation_alter(array &$operations, \Drupal\
 }
 
 /**
- * Implements hook_menu_links_alter().
+ * Implements hook_menu_links_discovered_alter().
  */
-function content_translation_menu_links_alter(array &$links) {
+function content_translation_menu_links_discovered_alter(array &$links) {
   // Clarify where translation settings are located.
   $links['language.content_settings_page']['title'] = 'Content language and translation';
   $links['language.content_settings_page']['description'] = 'Configure language and translation support for content.';
diff --git a/core/modules/dblog/dblog.module b/core/modules/dblog/dblog.module
index 3e18f0e..50b09e1 100644
--- a/core/modules/dblog/dblog.module
+++ b/core/modules/dblog/dblog.module
@@ -37,9 +37,9 @@ function dblog_help($route_name, RouteMatchInterface $route_match) {
 }
 
 /**
- * Implements hook_menu_links_alter().
+ * Implements hook_menu_links_discovered_alter().
  */
-function dblog_menu_links_alter(&$links) {
+function dblog_menu_links_discovered_alter(&$links) {
   if (\Drupal::moduleHandler()->moduleExists('search')) {
     $links['dblog.search'] = array(
       'title' => 'Top search phrases',
diff --git a/core/modules/editor/editor.module b/core/modules/editor/editor.module
index 86fb63b..40c1eb7 100644
--- a/core/modules/editor/editor.module
+++ b/core/modules/editor/editor.module
@@ -40,12 +40,12 @@ function editor_help($route_name, RouteMatchInterface $route_match) {
 }
 
 /**
- * Implements hook_menu_links_alter().
+ * Implements hook_menu_links_discovered_alter().
  *
  * Rewrites the menu entries for filter module that relate to the configuration
  * of text editors.
  */
-function editor_menu_links_alter(array &$links) {
+function editor_menu_links_discovered_alter(array &$links) {
   $links['filter.admin_overview']['title'] = 'Text formats and editors';
   $links['filter.admin_overview']['description'] = 'Configure how user-contributed content is filtered and formatted, as well as the text editor user interface (WYSIWYGs or toolbars).';
 }
diff --git a/core/modules/menu_ui/menu_ui.module b/core/modules/menu_ui/menu_ui.module
index 0b57ffe..13596e3 100644
--- a/core/modules/menu_ui/menu_ui.module
+++ b/core/modules/menu_ui/menu_ui.module
@@ -100,23 +100,6 @@ function menu_ui_menu_insert(Menu $menu) {
   if (\Drupal::moduleHandler()->moduleExists('block')) {
     \Drupal::service('plugin.manager.block')->clearCachedDefinitions();
   }
-
-  if ($menu->isSyncing()) {
-    return;
-  }
-
-  // Make sure the menu is present in the active menus variable so that its
-  // items may appear in the menu active trail.
-  // See menu_set_active_menu_names().
-  $config = \Drupal::config('system.menu');
-
-  $active_menus = $config->get('active_menus_default') ?: array_keys(menu_ui_get_menus());
-  if (!in_array($menu->id(), $active_menus)) {
-    $active_menus[] = $menu->id();
-    $config
-      ->set('active_menus_default', $active_menus)
-      ->save();
-  }
 }
 
 /**
@@ -138,19 +121,6 @@ function menu_ui_menu_predelete(Menu $menu) {
   /** @var \Drupal\Core\Menu\MenuLinkManagerInterface $menu_link_manager */
   $menu_link_manager = \Drupal::service('plugin.manager.menu.link');
   $menu_link_manager->deleteLinksInMenu($menu->id());
-
-  // Remove menu from active menus variable.
-  $config = \Drupal::config('system.menu');
-  $active_menus = $config->get('active_menus_default') ?: array_keys(menu_ui_get_menus());
-  if (in_array($menu->id(), $active_menus)) {
-    $active_menus = array_diff($active_menus, array($menu->id()));
-    // Prevent the gap left by the removed menu from causing array indices to
-    // be saved.
-    $active_menus = array_values($active_menus);
-    $config
-      ->set('active_menus_default', $active_menus)
-      ->save();
-  }
 }
 
 /**
diff --git a/core/modules/system/config/install/system.menu.yml b/core/modules/system/config/install/system.menu.yml
deleted file mode 100644
index e73636c..0000000
--- a/core/modules/system/config/install/system.menu.yml
+++ /dev/null
@@ -1 +0,0 @@
-active_menus_default: []
diff --git a/core/modules/system/config/schema/system.schema.yml b/core/modules/system/config/schema/system.schema.yml
index 77e1382..f524376 100644
--- a/core/modules/system/config/schema/system.schema.yml
+++ b/core/modules/system/config/schema/system.schema.yml
@@ -168,17 +168,6 @@ system.logging:
       type: string
       label: 'Error messages to display'
 
-system.menu:
-  type: mapping
-  label: 'Menu settings'
-  mapping:
-    active_menus_default:
-      type: sequence
-      label: 'Active menus'
-      sequence:
-        - type: string
-          label: 'Menu'
-
 system.performance:
   type: mapping
   label: 'Performance settings'
diff --git a/core/modules/system/system.api.php b/core/modules/system/system.api.php
index cd3e79d..ef02d89 100644
--- a/core/modules/system/system.api.php
+++ b/core/modules/system/system.api.php
@@ -397,13 +397,13 @@ function hook_page_build(&$page) {
 }
 
 /**
- * Alter links for menus.
+ * Alter all the menu links discovered by the menu link plugin manager.
  *
  * @param array $links
  *   The link definitions to be altered.
  *
  * @return array
- *   An array of default menu links. Each link has a key that is the machine
+ *   An array of discovered menu links. Each link has a key that is the machine
  *   name, which must be unique. By default, use the route name as the
  *   machine name. In cases where multiple links use the same route name, such
  *   as two links to the same page in different menus, or two links using the
@@ -440,7 +440,7 @@ function hook_page_build(&$page) {
  *
  * @ingroup menu
  */
-function hook_menu_links_alter(&$links) {
+function hook_menu_links_discovered_alter(&$links) {
   // Change the weight and title of the user.logout link.
   $links['user.logout']['weight'] = -10;
   $links['user.logout']['title'] = 'Logout';
diff --git a/core/modules/system/tests/modules/menu_test/menu_test.module b/core/modules/system/tests/modules/menu_test/menu_test.module
index 5299b0d..b4f76a2 100644
--- a/core/modules/system/tests/modules/menu_test/menu_test.module
+++ b/core/modules/system/tests/modules/menu_test/menu_test.module
@@ -6,9 +6,9 @@
  */
 
 /**
- * Implements hook_menu_links_alter().
+ * Implements hook_menu_links_discovered_alter().
  */
-function menu_test_menu_links_alter(&$links) {
+function menu_test_menu_links_discovered_alter(&$links) {
   // Many of the machine names here are slightly different from the route name.
   // Since the machine name is arbitrary, this helps ensure that core does not
   // add mistaken assumptions about the correlation.