diff -u b/core/includes/bootstrap.inc b/core/includes/bootstrap.inc
--- b/core/includes/bootstrap.inc
+++ b/core/includes/bootstrap.inc
@@ -264,10 +264,10 @@
     }
     // If still unknown, perform a filesystem scan.
     if (!isset($files[$type][$name])) {
-      if (is_null($missing)) {
+      if (!isset($missing)) {
         $missing = array();
         if (\Drupal::hasService('cache.bootstrap')) {
-          $cache = \Drupal::cache('bootstrap')->get('drupal_get_filename:missing', TRUE);
+          $cache = \Drupal::cache('bootstrap')->get('drupal_get_filename:missing');
           if ($cache && $cache->data) {
             $missing = $cache->data;
           }
@@ -295,7 +295,7 @@
     // theme list pages.
     $missing[$type][$name] = TRUE;
     if (\Drupal::hasService('cache.bootstrap')) {
-      \Drupal::cache('bootstrap')->set('drupal_get_filename:missing', $missing, REQUEST_TIME);
+      \Drupal::cache('bootstrap')->set('drupal_get_filename:missing', $missing, REQUEST_TIME + 24 * 60 * 60);
     }
     trigger_error(SafeMarkup::format('The following @type is missing from the file system: @name', array('@type' => $type, '@name' => $name)), E_USER_WARNING);
   }
diff -u b/core/modules/system/src/Controller/SystemController.php b/core/modules/system/src/Controller/SystemController.php
--- b/core/modules/system/src/Controller/SystemController.php
+++ b/core/modules/system/src/Controller/SystemController.php
@@ -15,6 +15,7 @@
 use Drupal\Core\Menu\MenuLinkTreeInterface;
 use Drupal\Core\Menu\MenuTreeParameters;
 use Drupal\Core\Theme\ThemeAccessCheck;
+use Drupal\Core\Cache\CacheBackendInterface;
 use Drupal\Core\Url;
 use Drupal\system\SystemManager;
 use Symfony\Component\DependencyInjection\ContainerInterface;
@@ -67,6 +68,13 @@
   protected $menuLinkTree;
 
   /**
+   * The bootstrap cache service.
+   *
+   * @var \Drupal\Core\Cache\CacheBackendInterface
+   */
+  protected $bootstrapCache;
+
+  /**
    * Constructs a new SystemController.
    *
    * @param \Drupal\system\SystemManager $systemManager
@@ -81,14 +89,17 @@
    *   The theme handler.
    * @param \Drupal\Core\Menu\MenuLinkTreeInterface
    *   The menu link tree service.
+   * @parm \Drupal\Core\Cache\CacheBackendInterface
+   *   The bootstrap cache service.
    */
-  public function __construct(SystemManager $systemManager, QueryFactory $queryFactory, ThemeAccessCheck $theme_access, FormBuilderInterface $form_builder, ThemeHandlerInterface $theme_handler, MenuLinkTreeInterface $menu_link_tree) {
+  public function __construct(SystemManager $systemManager, QueryFactory $queryFactory, ThemeAccessCheck $theme_access, FormBuilderInterface $form_builder, ThemeHandlerInterface $theme_handler, MenuLinkTreeInterface $menu_link_tree, CacheBackendInterface $bootstrap_cache) {
     $this->systemManager = $systemManager;
     $this->queryFactory = $queryFactory;
     $this->themeAccess = $theme_access;
     $this->formBuilder = $form_builder;
     $this->themeHandler = $theme_handler;
     $this->menuLinkTree = $menu_link_tree;
+    $this->bootstrapCache = $bootstrap_cache;
   }
 
   /**
@@ -101,7 +112,8 @@
       $container->get('access_check.theme'),
       $container->get('form_builder'),
       $container->get('theme_handler'),
-      $container->get('menu.link_tree')
+      $container->get('menu.link_tree'),
+      $container->get('cache.bootstrap')
     );
   }
 
@@ -187,10 +199,8 @@
    */
   public function themesPage() {
     //  Clean up the bootstrap "missing files" cache when listing themes.
-    if (\Drupal::hasService('cache.bootstrap')) {
-      \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
-      drupal_static_reset('drupal_get_filename:missing');
-    }
+    $this->bootstrapCache->delete('drupal_get_filename:missing');
+    drupal_static_reset('drupal_get_filename:missing');
 
     $config = $this->config('system.theme');
     // Get all available themes.
diff -u b/core/modules/system/src/Form/ModulesListForm.php b/core/modules/system/src/Form/ModulesListForm.php
--- b/core/modules/system/src/Form/ModulesListForm.php
+++ b/core/modules/system/src/Form/ModulesListForm.php
@@ -175,10 +175,8 @@
     $this->moduleHandler->loadInclude('system', 'inc', 'system.admin');
 
     //  Clean up the "missing files" cache when listing modules.
-    if (\Drupal::hasService('cache.bootstrap')) {
-      \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
-      drupal_static_reset('drupal_get_filename:missing');
-    }
+    \Drupal::cache('bootstrap')->delete('drupal_get_filename:missing');
+    drupal_static_reset('drupal_get_filename:missing');
 
     $form['filters'] = array(
       '#type' => 'container',
diff -u b/core/modules/system/src/Tests/Bootstrap/GetFilenameUnitTest.php b/core/modules/system/src/Tests/Bootstrap/GetFilenameUnitTest.php
--- b/core/modules/system/src/Tests/Bootstrap/GetFilenameUnitTest.php
+++ b/core/modules/system/src/Tests/Bootstrap/GetFilenameUnitTest.php
@@ -73,8 +73,18 @@
     // Generate a non-existing module name.
     $non_existing_module = uniqid("", TRUE);
 
+    // Set a custom error handler so we can ignore the file not found error.
+    set_error_handler(function($severity, $message, $file, $line) {
+      // Skip error handling if this is a "file not found" error.
+      if (!(error_reporting() & $severity) || strstr($message, 'is missing from the file system:')) {
+        return;
+      }
+      throw new ErrorException($message, 0, $severity, $file, $line);
+    });
     // Searching for an item that does not exist returns NULL.
     $this->assertNull(drupal_get_filename('module', $non_existing_module), 'Searching for an item that does not exist returns NULL.');
+    // Restore the original error handler.
+    restore_error_handler();
 
     // Get the missing records static from drupal_get_filename.
     $missing = &drupal_static('drupal_get_filename:missing');
reverted:
--- b/core/modules/system/system.module
+++ a/core/modules/system/system.module
@@ -1201,12 +1201,6 @@
     $cache_backend->garbageCollection();
   }
 
-  // Clean up the bootstrap "missing files" cache when running cron.
-  if (\Drupal::hasService('cache.bootstrap')) {
-    \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
-    drupal_static_reset('drupal_get_filename:missing');
-  }
-
   // Clean up the expirable key value database store.
   if (\Drupal::service('keyvalue.expirable.database') instanceof KeyValueDatabaseExpirableFactory) {
     \Drupal::service('keyvalue.expirable.database')->garbageCollection();
only in patch2:
unchanged:
--- a/core/modules/comment/src/Tests/CommentStringIdEntitiesTest.php
+++ b/core/modules/comment/src/Tests/CommentStringIdEntitiesTest.php
@@ -27,7 +27,6 @@ class CommentStringIdEntitiesTest extends KernelTestBase {
     'user',
     'field',
     'field_ui',
-    'entity',
     'entity_test',
     'text',
   );
only in patch2:
unchanged:
--- a/core/modules/system/src/Tests/Common/AttachedAssetsTest.php
+++ b/core/modules/system/src/Tests/Common/AttachedAssetsTest.php
@@ -74,10 +74,20 @@ function testDefault() {
    * Tests non-existing libraries.
    */
   function testLibraryUnknown() {
+    // Set a custom error handler so we can ignore the file not found error.
+    set_error_handler(function($severity, $message, $file, $line) {
+      // Skip error handling if this is a "file not found" error.
+      if (!(error_reporting() & $severity) || strstr($message, 'is missing from the file system:')) {
+        return;
+      }
+      throw new ErrorException($message, 0, $severity, $file, $line);
+    });
     $build['#attached']['library'][] = 'unknown/unknown';
     $assets = AttachedAssets::createFromRenderArray($build);
 
     $this->assertIdentical([], $this->assetResolver->getJsAssets($assets, FALSE)[0], 'Unknown library was not added to the page.');
+    // Restore the original error handler.
+    restore_error_handler();
   }
 
   /**
only in patch2:
unchanged:
--- a/core/modules/system/src/Tests/Entity/EntitySchemaTest.php
+++ b/core/modules/system/src/Tests/Entity/EntitySchemaTest.php
@@ -28,7 +28,7 @@ class EntitySchemaTest extends EntityUnitTestBase  {
    *
    * @var array
    */
-  public static $modules = array('menu_link');
+  public static $modules = array('menu_link_content');
 
   /**
    * {@inheritdoc}
only in patch2:
unchanged:
--- a/core/modules/taxonomy/src/Tests/TermKernelTest.php
+++ b/core/modules/taxonomy/src/Tests/TermKernelTest.php
@@ -23,7 +23,7 @@ class TermKernelTest extends KernelTestBase {
   /**
    * {@inheritdoc}
    */
-  public static $modules = array( 'filter', 'taxonomy', 'taxonomy_term', 'text', 'user' );
+  public static $modules = array( 'filter', 'taxonomy', 'text', 'user' );
 
   /**
    * {@inheritdoc}
only in patch2:
unchanged:
--- a/core/modules/views/src/Tests/Plugin/RowEntityTest.php
+++ b/core/modules/views/src/Tests/Plugin/RowEntityTest.php
@@ -24,7 +24,7 @@ class RowEntityTest extends ViewUnitTestBase {
    *
    * @var array
    */
-  public static $modules = ['taxonomy', 'text', 'filter', 'field', 'entity', 'system', 'node', 'user'];
+  public static $modules = ['taxonomy', 'text', 'filter', 'field', 'system', 'node', 'user'];
 
   /**
    * Views used by this test.