diff --git a/includes/bootstrap.inc b/includes/bootstrap.inc
index e9665eb..5551699 100644
--- a/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -828,14 +828,21 @@ function drupal_settings_initialize() {
  * @param $filename
  *   The filename of the item if it is to be set explicitly rather
  *   than by consulting the database.
+ * @param bool $trigger_error
+ *   Whether to trigger an error when a file is missing or has unexpectedly
+ *   moved. This defaults to TRUE, but can be set to FALSE by calling code that
+ *   merely wants to check whether an item exists in the filesystem.
  *
  * @return
  *   The filename of the requested item or NULL if the item is not found.
  */
-function drupal_get_filename($type, $name, $filename = NULL) {
+function drupal_get_filename($type, $name, $filename = NULL, $trigger_error = TRUE) {
+  // The $files static variable will hold the locations of all requested files.
+  // We can be sure that any file listed in this static variable actually
+  // exists as all additions have gone through a file_exists() check.
   // The location of files will not change during the request, so do not use
   // drupal_static().
-  static $files = array(), $dirs = array();
+  static $files = array();
 
   // Profiles are a special case: they have a fixed location and naming.
   if ($type == 'profile') {
@@ -847,64 +854,252 @@ function drupal_get_filename($type, $name, $filename = NULL) {
   }
 
   if (!empty($filename) && file_exists($filename)) {
+    // Prime the static cache with the provided filename.
     $files[$type][$name] = $filename;
   }
   elseif (isset($files[$type][$name])) {
-    // nothing
+    // This item had already been found earlier in the request, either through
+    // priming of the static cache (for example, in system_list()), through a
+    // lookup in the {system} table, or through a file scan (cached or not). Do
+    // nothing.
   }
-  // Verify that we have an active database connection, before querying
-  // the database. This is required because this function is called both
-  // before we have a database connection (i.e. during installation) and
-  // when a database connection fails.
   else {
+    // Look for the filename listed in the {system} table. Verify that we have
+    // an active database connection before doing so, since this function is
+    // called both before we have a database connection (i.e. during
+    // installation) and when a database connection fails.
+    $database_unavailable = TRUE;
     try {
       if (function_exists('db_query')) {
         $file = db_query("SELECT filename FROM {system} WHERE name = :name AND type = :type", array(':name' => $name, ':type' => $type))->fetchField();
         if ($file !== FALSE && file_exists(DRUPAL_ROOT . '/' . $file)) {
           $files[$type][$name] = $file;
         }
+        $database_unavailable = FALSE;
       }
     }
     catch (Exception $e) {
       // The database table may not exist because Drupal is not yet installed,
-      // or the database might be down. We have a fallback for this case so we
-      // hide the error completely.
+      // the database might be down, or we may have done a non-database cache
+      // flush while $conf['page_cache_without_database'] = TRUE and
+      // $conf['page_cache_invoke_hooks'] = TRUE. We have a fallback for these
+      // cases so we hide the error completely.
     }
-    // Fallback to searching the filesystem if the database could not find the
-    // file or the file returned by the database is not found.
+    // Fall back to searching the filesystem if the database could not find the
+    // file or the file does not exist at the path returned by the database.
     if (!isset($files[$type][$name])) {
-      // We have a consistent directory naming: modules, themes...
-      $dir = $type . 's';
-      if ($type == 'theme_engine') {
-        $dir = 'themes/engines';
-        $extension = 'engine';
-      }
-      elseif ($type == 'theme') {
-        $extension = 'info';
-      }
-      else {
-        $extension = $type;
-      }
+      $files[$type][$name] = _drupal_get_filename_fallback($type, $name, $trigger_error, $database_unavailable);
+    }
+  }
 
-      if (!isset($dirs[$dir][$extension])) {
-        $dirs[$dir][$extension] = TRUE;
-        if (!function_exists('drupal_system_listing')) {
-          require_once DRUPAL_ROOT . '/includes/common.inc';
-        }
-        // Scan the appropriate directories for all files with the requested
-        // extension, not just the file we are currently looking for. This
-        // prevents unnecessary scans from being repeated when this function is
-        // called more than once in the same page request.
-        $matches = drupal_system_listing("/^" . DRUPAL_PHP_FUNCTION_PATTERN . "\.$extension$/", $dir, 'name', 0);
-        foreach ($matches as $matched_name => $file) {
-          $files[$type][$matched_name] = $file->uri;
+  if (isset($files[$type][$name])) {
+    return $files[$type][$name];
+  }
+}
+
+/**
+ * Performs a cached file system scan as a fallback when searching for a file.
+ *
+ * This function looks for the requested file by triggering a file scan,
+ * caching the new location if the file has moved and caching the miss
+ * if the file is missing. If a file had been marked as missing in a previous
+ * file scan, or if it has been marked as moved and is still in the last known
+ * location, no new file scan will be performed.
+ *
+ * @param string $type
+ *   The type of the item (theme, theme_engine, module, profile).
+ * @param string $name
+ *   The name of the item for which the filename is requested.
+ * @param bool $trigger_error
+ *   Whether to trigger an error when a file is missing or has unexpectedly
+ *   moved.
+ * @param bool $database_unavailable
+ *   Whether this function is being called because the Drupal database could
+ *   not be queried for the file's location.
+ *
+ * @return
+ *   The filename of the requested item or NULL if the item is not found.
+ *
+ * @see drupal_get_filename()
+ */
+function _drupal_get_filename_fallback($type, $name, $trigger_error, $database_unavailable) {
+  $file_scans = &_drupal_file_scan_cache();
+  $filename = NULL;
+
+  // If the cache indicates that the item is missing, or we can verify that the
+  // item exists in the location the cache says it exists in, use that.
+  if (isset($file_scans[$type][$name]) && ($file_scans[$type][$name] === FALSE || file_exists($file_scans[$type][$name]))) {
+    $filename = $file_scans[$type][$name];
+  }
+  // Otherwise, perform a new file scan to find the item.
+  else {
+    $filename = _drupal_get_filename_perform_file_scan($type, $name);
+    // Update the static cache, and mark the persistent cache for updating at
+    // the end of the page request. See drupal_file_scan_write_cache().
+    $file_scans[$type][$name] = $filename;
+    $file_scans['#write_cache'] = TRUE;
+  }
+
+  // If requested, trigger a user-level warning about the missing or
+  // unexpectedly moved file. If the database was unavailable, do not trigger a
+  // warning in the latter case, though, since if the {system} table could not
+  // be queried there is no way to know if the location found here was
+  // "unexpected" or not.
+  if ($trigger_error) {
+    $error_type = $filename === FALSE ? 'missing' : 'moved';
+    if ($error_type == 'missing' || !$database_unavailable) {
+      _drupal_get_filename_fallback_trigger_error($type, $name, $error_type);
+    }
+  }
+
+  // The cache stores FALSE for files that aren't found (to be able to
+  // distinguish them from files that have not yet been searched for), but
+  // drupal_get_filename() expects NULL for these instead, so convert to NULL
+  // before returning.
+  if ($filename === FALSE) {
+    $filename = NULL;
+  }
+  return $filename;
+}
+
+/**
+ * Returns the current list of cached file system scan results.
+ *
+ * @return
+ *   An associative array tracking the most recent file scan results for all
+ *   files that have had scans performed. The keys are the type and name of the
+ *   item that was searched for, and the values can be either:
+ *   - Boolean FALSE if the item was not found in the file system.
+ *   - A string pointing to the location where the item was found.
+ */
+function &_drupal_file_scan_cache() {
+  $file_scans = &drupal_static(__FUNCTION__, array());
+
+  // The file scan results are stored in a persistent cache (in addition to the
+  // static cache) but because this function can be called before the
+  // persistent cache is available, we must merge any items that were found
+  // earlier in the page request into the results from the persistent cache.
+  if (!isset($file_scans['#cache_merge_done'])) {
+    try {
+      if (function_exists('cache_get')) {
+        $cache = cache_get('_drupal_file_scan_cache', 'cache_bootstrap');
+        if (!empty($cache->data)) {
+          // File scan results from the current request should take precedence
+          // over the results from the persistent cache, since they are newer.
+          $file_scans = drupal_array_merge_deep($cache->data, $file_scans);
         }
+        // Set a flag to indicate that the persistent cache does not need to be
+        // merged again.
+        $file_scans['#cache_merge_done'] = TRUE;
       }
     }
+    catch (Exception $e) {
+      // Hide the error.
+    }
   }
 
-  if (isset($files[$type][$name])) {
-    return $files[$type][$name];
+  return $file_scans;
+}
+
+/**
+ * Performs a file system scan to search for a system resource.
+ *
+ * @param $type
+ *   The type of the item (theme, theme_engine, module, profile).
+ * @param $name
+ *   The name of the item for which the filename is requested.
+ *
+ * @return
+ *   The filename of the requested item or FALSE if the item is not found.
+ *
+ * @see drupal_get_filename()
+ * @see _drupal_get_filename_fallback()
+ */
+function _drupal_get_filename_perform_file_scan($type, $name) {
+  // The location of files will not change during the request, so do not use
+  // drupal_static().
+  static $dirs = array(), $files = array();
+
+  // We have a consistent directory naming: modules, themes...
+  $dir = $type . 's';
+  if ($type == 'theme_engine') {
+    $dir = 'themes/engines';
+    $extension = 'engine';
+  }
+  elseif ($type == 'theme') {
+    $extension = 'info';
+  }
+  else {
+    $extension = $type;
+  }
+
+  // Check if we had already scanned this directory/extension combination.
+  if (!isset($dirs[$dir][$extension])) {
+    // Log that we have now scanned this directory/extension combination
+    // into a static variable so as to prevent unnecessary file scans.
+    $dirs[$dir][$extension] = TRUE;
+    if (!function_exists('drupal_system_listing')) {
+      require_once DRUPAL_ROOT . '/includes/common.inc';
+    }
+    // Scan the appropriate directories for all files with the requested
+    // extension, not just the file we are currently looking for. This
+    // prevents unnecessary scans from being repeated when this function is
+    // called more than once in the same page request.
+    $matches = drupal_system_listing("/^" . DRUPAL_PHP_FUNCTION_PATTERN . "\.$extension$/", $dir, 'name', 0);
+    foreach ($matches as $matched_name => $file) {
+      // Log the locations found in the file scan into a static variable.
+      $files[$type][$matched_name] = $file->uri;
+    }
+  }
+
+  // Return the results of the file system scan, or FALSE to indicate the file
+  // was not found.
+  return isset($files[$type][$name]) ? $files[$type][$name] : FALSE;
+}
+
+/**
+ * Triggers a user-level warning for missing or unexpectedly moved files.
+ *
+ * @param $type
+ *   The type of the item (theme, theme_engine, module, profile).
+ * @param $name
+ *   The name of the item for which the filename is requested.
+ * @param $error_type
+ *   The type of the error ('missing' or 'moved').
+ *
+ * @see drupal_get_filename()
+ * @see _drupal_get_filename_fallback()
+ */
+function _drupal_get_filename_fallback_trigger_error($type, $name, $error_type) {
+  // Make sure we only show any missing or moved file errors only once per
+  // request.
+  static $errors_triggered = array();
+  if (empty($errors_triggered[$type][$name][$error_type])) {
+    if ($error_type == 'missing') {
+      trigger_error(format_string('The following @type is missing from the file system: %name. In order to fix this, put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
+    }
+    elseif ($error_type == 'moved') {
+      trigger_error(format_string('The following @type has moved within the file system: %name. In order to fix this, clear caches or put the @type back in its original location. For more information, see <a href="@documentation">the documentation page</a>.', array('@type' => $type, '%name' => $name, '@documentation' => 'https://www.drupal.org/node/2487215')), E_USER_WARNING);
+    }
+    $errors_triggered[$type][$name][$error_type] = TRUE;
+  }
+}
+
+/**
+ * Writes the file scan cache to the persistent cache.
+ *
+ * This cache stores all files marked as missing or moved after a file scan
+ * to prevent unnecessary file scans in subsequent requests. This cache is
+ * cleared in system_list_reset() (i.e. after a module/theme rebuild).
+ */
+function drupal_file_scan_write_cache() {
+  // Only write to the persistent cache if requested, and if we know that any
+  // data previously in the cache was successfully loaded and merged in by
+  // _drupal_file_scan_cache().
+  $file_scans = &_drupal_file_scan_cache();
+  if (isset($file_scans['#write_cache']) && isset($file_scans['#cache_merge_done'])) {
+    unset($file_scans['#write_cache']);
+    cache_set('_drupal_file_scan_cache', $file_scans, 'cache_bootstrap');
   }
 }
 
diff --git a/includes/common.inc b/includes/common.inc
index 34fa9b9..5c41932 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -2757,6 +2757,7 @@ function drupal_page_footer() {
   _registry_check_code(REGISTRY_WRITE_LOOKUP_CACHE);
   drupal_cache_system_paths();
   module_implements_write_cache();
+  drupal_file_scan_write_cache();
   system_run_automated_cron();
 }
 
diff --git a/includes/install.inc b/includes/install.inc
index 2b55589..a41bc88 100644
--- a/includes/install.inc
+++ b/includes/install.inc
@@ -1177,6 +1177,10 @@ function drupal_check_profile($profile) {
     throw new Exception(install_no_profile_error());
   }
 
+  // Prime the cache to find our profile file.
+  // This is the same record as inserted into the system table after install.
+  drupal_get_filename('module', $profile, "profiles/$profile/$profile.profile");
+
   $info = install_profile_info($profile);
 
   // Collect requirement testing results.
diff --git a/includes/module.inc b/includes/module.inc
index 7bf619b..cbc44a5 100644
--- a/includes/module.inc
+++ b/includes/module.inc
@@ -227,6 +227,10 @@ function system_list_reset() {
   drupal_static_reset('list_themes');
   cache_clear_all('bootstrap_modules', 'cache_bootstrap');
   cache_clear_all('system_list', 'cache_bootstrap');
+
+  // Clean up the bootstrap file scan cache.
+  drupal_static_reset('_drupal_file_scan_cache');
+  cache_clear_all('_drupal_file_scan_cache', 'cache_bootstrap');
 }
 
 /**
diff --git a/includes/update.inc b/includes/update.inc
index 35a73c3..2167db7 100644
--- a/includes/update.inc
+++ b/includes/update.inc
@@ -795,6 +795,14 @@ function update_fix_d7_requirements() {
 function update_fix_d7_install_profile() {
   $profile = drupal_get_profile();
 
+  // 'Default' profile has been renamed to 'Standard' in D7.
+  // We change the profile here to prevent a broken record in the system table.
+  // See system_update_7049().
+  if ($profile == 'default') {
+    $profile = 'standard';
+    variable_set('install_profile', $profile);
+  }
+
   $results = db_select('system', 's')
     ->fields('s', array('name', 'schema_version'))
     ->condition('name', $profile)
diff --git a/modules/simpletest/simpletest.module b/modules/simpletest/simpletest.module
index 29a20bb..cf83047 100644
--- a/modules/simpletest/simpletest.module
+++ b/modules/simpletest/simpletest.module
@@ -374,7 +374,10 @@ function simpletest_test_get_all() {
           // If this test class requires a non-existing module, skip it.
           if (!empty($info['dependencies'])) {
             foreach ($info['dependencies'] as $module) {
-              if (!drupal_get_filename('module', $module)) {
+              // Pass FALSE as fourth argument so no error gets created for
+              // the missing file.
+              $found_module = drupal_get_filename('module', $module, NULL, FALSE);
+              if (!$found_module) {
                 continue 2;
               }
             }
diff --git a/modules/simpletest/tests/bootstrap.test b/modules/simpletest/tests/bootstrap.test
index d46c6ec..4626b33 100644
--- a/modules/simpletest/tests/bootstrap.test
+++ b/modules/simpletest/tests/bootstrap.test
@@ -379,13 +379,20 @@ class BootstrapGetFilenameTestCase extends DrupalUnitTestCase {
 
   public static function getInfo() {
     return array(
-      'name' => 'Get filename test',
-      'description' => 'Test that drupal_get_filename() works correctly when the file is not found in the database.',
+      'name' => 'Get filename test (without the system table)',
+      'description' => 'Test that drupal_get_filename() works correctly when the database is not available.',
       'group' => 'Bootstrap',
     );
   }
 
   /**
+   * The last file-related error message triggered by the filename test.
+   *
+   * Used by BootstrapGetFilenameTestCase::testDrupalGetFilename().
+   */
+  protected $getFilenameTestTriggeredError;
+
+  /**
    * Test that drupal_get_filename() works correctly when the file is not found in the database.
    */
   function testDrupalGetFilename() {
@@ -414,6 +421,148 @@ class BootstrapGetFilenameTestCase extends DrupalUnitTestCase {
     // automatically check there for 'script' files, just as it does for (e.g.)
     // 'module' files in modules.
     $this->assertIdentical(drupal_get_filename('script', 'test'), 'scripts/test.script', t('Retrieve test script location.'));
+
+    // When searching for a module that does not exist, drupal_get_filename()
+    // should return NULL and trigger an appropriate error message.
+    $this->getFilenameTestTriggeredError = NULL;
+    set_error_handler(array($this, 'fileNotFoundErrorHandler'));
+    $non_existing_module = $this->randomName();
+    $this->assertNull(drupal_get_filename('module', $non_existing_module), 'Searching for a module that does not exist returns NULL.');
+    $this->assertTrue(strpos($this->getFilenameTestTriggeredError, format_string('The following module is missing from the file system: %name', array('%name' => $non_existing_module))) === 0, 'Searching for an item that does not exist triggers the correct error.');
+    restore_error_handler();
+
+    // Check that the result is stored in the file system scan cache.
+    $file_scans = _drupal_file_scan_cache();
+    $this->assertIdentical($file_scans['module'][$non_existing_module], FALSE, 'Searching for a module that does not exist creates a record in the missing and moved files static variable.');
+
+    // Performing the search again in the same request still should not find
+    // the file, but the error message should not be repeated (therefore we do
+    // not override the error handler here).
+    $this->assertNull(drupal_get_filename('module', $non_existing_module), 'Searching for a module that does not exist returns NULL during the second search.');
+  }
+
+  /**
+   * Skips handling of "file not found" errors.
+   */
+  public function fileNotFoundErrorHandler($error_level, $message, $filename, $line, $context) {
+    // Skip error handling if this is a "file not found" error.
+    if (strpos($message, 'is missing from the file system:') !== FALSE || strpos($message, 'has moved within the file system:') !== FALSE) {
+      $this->getFilenameTestTriggeredError = $message;
+      return;
+    }
+    _drupal_error_handler($error_level, $message, $filename, $line, $context);
+  }
+}
+
+/**
+ * Test drupal_get_filename() in the context of a full Drupal installation.
+ */
+class BootstrapGetFilenameWebTestCase extends DrupalWebTestCase {
+
+  public static function getInfo() {
+    return array(
+      'name' => 'Get filename test (full installation)',
+      'description' => 'Test that drupal_get_filename() works correctly in the context of a full Drupal installation.',
+      'group' => 'Bootstrap',
+    );
+  }
+
+  /**
+   * The last file-related error message triggered by the filename test.
+   *
+   * Used by BootstrapGetFilenameWebTestCase::testDrupalGetFilename().
+   */
+  protected $getFilenameTestTriggeredError;
+
+  /**
+   * Test that drupal_get_filename() works correctly with a full Drupal site.
+   */
+  function testDrupalGetFilename() {
+    // Search for a module that exists in the file system and the {system}
+    // table and make sure that it is found.
+    $this->assertIdentical(drupal_get_filename('module', 'node'), 'modules/node/node.module', 'Module found at expected location.');
+
+    // Search for a module that does not exist in either the file system or the
+    // {system} table. Make sure that an appropriate error is triggered and
+    // that the module winds up in the static and persistent cache.
+    $this->getFilenameTestTriggeredError = NULL;
+    set_error_handler(array($this, 'fileNotFoundErrorHandler'));
+    $non_existing_module = $this->randomName();
+    $this->assertNull(drupal_get_filename('module', $non_existing_module), 'Searching for a module that does not exist returns NULL.');
+    $this->assertTrue(strpos($this->getFilenameTestTriggeredError, format_string('The following module is missing from the file system: %name', array('%name' => $non_existing_module))) === 0, 'Searching for a module that does not exist triggers the correct error.');
+    restore_error_handler();
+    $file_scans = _drupal_file_scan_cache();
+    $this->assertIdentical($file_scans['module'][$non_existing_module], FALSE, 'Searching for a module that does not exist creates a record in the missing and moved files static variable.');
+    drupal_file_scan_write_cache();
+    $cache = cache_get('_drupal_file_scan_cache', 'cache_bootstrap');
+    $this->assertIdentical($cache->data['module'][$non_existing_module], FALSE, 'Searching for a module that does not exist creates a record in the missing and moved files persistent cache.');
+
+    // Simulate moving a module to a location that does not match the location
+    // in the {system} table and perform similar tests as above.
+    db_update('system')
+      ->fields(array('filename' => 'modules/simpletest/tests/fake_location/module_test.module'))
+      ->condition('name', 'module_test')
+      ->condition('type', 'module')
+      ->execute();
+    $this->getFilenameTestTriggeredError = NULL;
+    set_error_handler(array($this, 'fileNotFoundErrorHandler'));
+    $this->assertIdentical(drupal_get_filename('module', 'module_test'), 'modules/simpletest/tests/module_test.module', 'Searching for a module that has moved finds the module at its new location.');
+    $this->assertTrue(strpos($this->getFilenameTestTriggeredError, format_string('The following module has moved within the file system: %name', array('%name' => 'module_test'))) === 0, 'Searching for a module that has moved triggers the correct error.');
+    restore_error_handler();
+    $file_scans = _drupal_file_scan_cache();
+    $this->assertIdentical($file_scans['module']['module_test'], 'modules/simpletest/tests/module_test.module', 'Searching for a module that has moved creates a record in the missing and moved files static variable.');
+    drupal_file_scan_write_cache();
+    $cache = cache_get('_drupal_file_scan_cache', 'cache_bootstrap');
+    $this->assertIdentical($cache->data['module']['module_test'], 'modules/simpletest/tests/module_test.module', 'Searching for a module that has moved creates a record in the missing and moved files persistent cache.');
+
+    // Simulate a module that exists in the {system} table but does not exist
+    // in the file system and perform similar tests as above.
+    $non_existing_module = $this->randomName();
+    db_update('system')
+      ->fields(array('name' => $non_existing_module))
+      ->condition('name', 'module_test')
+      ->condition('type', 'module')
+      ->execute();
+    $this->getFilenameTestTriggeredError = NULL;
+    set_error_handler(array($this, 'fileNotFoundErrorHandler'));
+    $this->assertNull(drupal_get_filename('module', $non_existing_module), 'Searching for a module that exists in the system table but not in the file system returns NULL.');
+    $this->assertTrue(strpos($this->getFilenameTestTriggeredError, format_string('The following module is missing from the file system: %name', array('%name' => $non_existing_module))) === 0, 'Searching for a module that exists in the system table but not in the file system triggers the correct error.');
+    restore_error_handler();
+    $file_scans = _drupal_file_scan_cache();
+    $this->assertIdentical($file_scans['module'][$non_existing_module], FALSE, 'Searching for a module that exists in the system table but not in the file system creates a record in the missing and moved files static variable.');
+    drupal_file_scan_write_cache();
+    $cache = cache_get('_drupal_file_scan_cache', 'cache_bootstrap');
+    $this->assertIdentical($cache->data['module'][$non_existing_module], FALSE, 'Searching for a module that exists in the system table but not in the file system creates a record in the missing and moved files persistent cache.');
+
+    // Simulate a module that exists in the file system but not in the {system}
+    // table and perform similar tests as above.
+    db_delete('system')
+      ->condition('name', 'common_test')
+      ->condition('type', 'module')
+      ->execute();
+    system_list_reset();
+    $this->getFilenameTestTriggeredError = NULL;
+    set_error_handler(array($this, 'fileNotFoundErrorHandler'));
+    $this->assertIdentical(drupal_get_filename('module', 'common_test'), 'modules/simpletest/tests/common_test.module', 'Searching for a module that does not exist in the system table finds the module at its actual location.');
+    $this->assertTrue(strpos($this->getFilenameTestTriggeredError, format_string('The following module has moved within the file system: %name', array('%name' => 'common_test'))) === 0, 'Searching for a module that does not exist in the system table triggers the correct error.');
+    restore_error_handler();
+    $file_scans = _drupal_file_scan_cache();
+    $this->assertIdentical($file_scans['module']['common_test'], 'modules/simpletest/tests/common_test.module', 'Searching for a module that does not exist in the system table creates a record in the missing and moved files static variable.');
+    drupal_file_scan_write_cache();
+    $cache = cache_get('_drupal_file_scan_cache', 'cache_bootstrap');
+    $this->assertIdentical($cache->data['module']['common_test'], 'modules/simpletest/tests/common_test.module', 'Searching for a module that does not exist in the system table creates a record in the missing and moved files persistent cache.');
+  }
+
+  /**
+   * Skips handling of "file not found" errors.
+   */
+  public function fileNotFoundErrorHandler($error_level, $message, $filename, $line, $context) {
+    // Skip error handling if this is a "file not found" error.
+    if (strpos($message, 'is missing from the file system:') !== FALSE || strpos($message, 'has moved within the file system:') !== FALSE) {
+      $this->getFilenameTestTriggeredError = $message;
+      return;
+    }
+    _drupal_error_handler($error_level, $message, $filename, $line, $context);
   }
 }
 
diff --git a/modules/system/system.updater.inc b/modules/system/system.updater.inc
index a14d788..2a32c4b 100644
--- a/modules/system/system.updater.inc
+++ b/modules/system/system.updater.inc
@@ -24,7 +24,7 @@ class ModuleUpdater extends Updater implements DrupalUpdaterInterface {
    * found on your system, and if there was a copy in sites/all, we'd see it.
    */
   public function getInstallDirectory() {
-    if ($relative_path = drupal_get_path('module', $this->name)) {
+    if ($this->isInstalled() && ($relative_path = drupal_get_path('module', $this->name))) {
       $relative_path = dirname($relative_path);
     }
     else {
@@ -34,7 +34,7 @@ class ModuleUpdater extends Updater implements DrupalUpdaterInterface {
   }
 
   public function isInstalled() {
-    return (bool) drupal_get_path('module', $this->name);
+    return (bool) drupal_get_filename('module', $this->name, NULL, FALSE);
   }
 
   public static function canUpdateDirectory($directory) {
@@ -109,7 +109,7 @@ class ThemeUpdater extends Updater implements DrupalUpdaterInterface {
    * found on your system, and if there was a copy in sites/all, we'd see it.
    */
   public function getInstallDirectory() {
-    if ($relative_path = drupal_get_path('theme', $this->name)) {
+    if ($this->isInstalled() && ($relative_path = drupal_get_path('theme', $this->name))) {
       $relative_path = dirname($relative_path);
     }
     else {
@@ -119,7 +119,7 @@ class ThemeUpdater extends Updater implements DrupalUpdaterInterface {
   }
 
   public function isInstalled() {
-    return (bool) drupal_get_path('theme', $this->name);
+    return (bool) drupal_get_filename('theme', $this->name, NULL, FALSE);
   }
 
   static function canUpdateDirectory($directory) {