diff -u b/includes/bootstrap.inc b/includes/bootstrap.inc
--- b/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -835,6 +835,9 @@
 function drupal_get_filename($type, $name, $filename = NULL) {
   // The location of files will not change during the request, so do not use
   // drupal_static().
+  // The $files static variable will hold the locations of all requested files,
+  // and any file that gets added during the request will have been checked
+  // with a file_exists() at some point.
   static $files = array(), $dirs = array(), $files_scanned = array();
 
   // Profiles are a special case: they have a fixed location and naming.
@@ -850,13 +853,14 @@
     $files[$type][$name] = $filename;
   }
   elseif (isset($files[$type][$name])) {
-    // nothing
+    // This item had already been found earlier in the request. 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 location listed in the {system} table.
+    // 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.
     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();
@@ -865,6 +869,8 @@
             $files[$type][$name] = $file;
           }
           else {
+            // Flag that the filename in the database does not exist for the
+            // requested item, so we can figure out if it has moved.
             $database_file_exists = FALSE;
           }
         }
@@ -876,11 +882,9 @@
       // hide the error completely.
     }
     // Fallback to searching the filesystem if the database could not find the
-    // file or the file returned by the database is not found.
+    // file or the filename returned by the database is not found. We cache
+    // missing and moved files in order to prevent unnecessary file scans.
     if (!isset($files[$type][$name])) {
-      // We use drupal_static() for the missing records so we can test it.
-      $missing = &drupal_static('drupal_get_filename:missing');
-
       // We have a consistent directory naming: modules, themes...
       $dir = $type . 's';
       if ($type == 'theme_engine') {
@@ -894,19 +898,28 @@
         $extension = $type;
       }
 
-      // See if we have a cached list of files missing from the file system.
+      // This static variable will hold all missing and moved files, in order
+      // to prevent unnecessary file scans. It is an associative array with as
+      // keys the file type and name, and as value the boolean FALSE (if the
+      // module is missing) or a string (if the module has moved from the
+      // location listed in the {system} table) with the location that was
+      // found in a file scan.
+      $missing = &drupal_static('drupal_get_filename:missing');
       if (!isset($missing)) {
         $missing = array();
+      }
+      // Get the missing and moved files from persistent cache, if available.
+      if (!isset($missing['#cache_merge_done'])) {
         try {
           if (function_exists('cache_get')) {
             $cache = cache_get('drupal_get_filename:missing', 'cache_bootstrap');
             if (!empty($cache->data)) {
-              // Merge the changes already done in the current request (including
-              // the setting of missing records to NULL) into the values saved
-              // in persistent cache.
-              $missing = $cache->data + $missing;
-              // Set a flag so we know that we've already done a merge with values
-              // in cache_get().
+              // Merge the changes already done in the current request
+              // (including the setting of missing records to NULL) into the
+              // values saved in persistent cache.
+              $missing = drupal_array_merge_deep($cache->data, $missing);
+              // Set a flag so we know that we've already done a merge with
+              // the values in persistent cache.
               $missing['#cache_merge_done'] = TRUE;
             }
           }
@@ -916,19 +929,27 @@
         }
       }
 
+      // Check whether this file had previously moved from its location in
+      // the {system} table, and the result of a file scan had been cached.
       if (isset($missing[$type][$name]) && is_string($missing[$type][$name])) {
         // This file has moved and the result of a file scan had been cached.
         if (file_exists($missing[$type][$name])) {
+          // We found the file at the cached location.
           $files[$type][$name] = $missing[$type][$name];
         }
         else {
-          // File is not available anymore at its new location. Re-do file scan.
+          // File is not available anymore at the cached location. Remove the
+          // missing/moved file record so a new file scan will be performed.
           $missing[$type][$name] = NULL;
           $missing['#write_cache'] = TRUE;
         }
       }
 
+      // Check if we had already scanned this directory/extension combination,
+      // or if this file had been marked as missing/moved.
       if (!isset($dirs[$dir][$extension]) && !isset($missing[$type][$name])) {
+        // Log that we have now scanned this directory/extension combination
+        // into a static variable to prevent unnecessary scans.
         $dirs[$dir][$extension] = TRUE;
         if (!function_exists('drupal_system_listing')) {
           require_once DRUPAL_ROOT . '/includes/common.inc';
@@ -939,16 +960,24 @@
         // 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.
           $files_scanned[$type][$matched_name] = $file->uri;
         }
       }
 
+      // If current file had been found in a file scan earlier on in this
+      // request, use the new location that had been found in the file scan.
       if (isset($files_scanned[$type][$name])) {
+        // Use the location from the file scan earlier on in this request.
         $files[$type][$name] = $files_scanned[$type][$name];
+        // Check whether the current file was listed as being in another
+        // location in the {system} table.
         if (isset($database_file_exists) && $database_file_exists === FALSE) {
-          // This file has moved. Cache its new location into the missing files
-          // cache.
+          // This file has moved. Cache its new location into the missing and
+          // moved files list.
           $missing[$type][$name] = $files_scanned[$type][$name];
+          // Make sure our change to the missing and moved files list will be
+          // written to persistent cache.
           $missing['#write_cache'] = TRUE;
           trigger_error(format_string('The following @type has moved on the file system: @name. Clearing caches may help fix this. 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);
         }
@@ -957,15 +986,20 @@
   }
 
   if (isset($files[$type][$name])) {
+    // The requested file exists, return its filename.
     return $files[$type][$name];
   }
   else {
+    // The requested file does not exist in any location.
     if (!isset($missing[$type][$name])) {
-      // Add the missing file to a temporary cache and throw an alert.
-      // This cache will be cleared on module/theme rebuild.
+      // Mark the file as missing.
       $missing[$type][$name] = TRUE;
+      // Make sure our change to the missing files list will be written to
+      // persistent cache.
+      // This cache will be cleared on module/theme rebuild.
       $missing['#write_cache'] = TRUE;
     }
+    // Trigger a user-level warning on every request for the missing file.
     trigger_error(format_string('The following @type is missing from the file system: @name. 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);
   }
 }
@@ -977,15 +1011,18 @@
  *   The array of missing and moved files.
  */
 function drupal_missing_write_cache() {
+  // Only write to cache if we are fully bootstrapped.
   if (drupal_get_bootstrap_phase() != DRUPAL_BOOTSTRAP_FULL) {
     return;
   }
   $missing = &drupal_static('drupal_get_filename:missing');
   if (isset($missing['#write_cache'])) {
+    // Merge the newly found out missing and moved file data with
+    // the previously existing data, if we hadn't done so yet.
     if (!isset($missing['#cache_merge_done'])) {
       $cache = cache_get('drupal_get_filename:missing', 'cache_bootstrap');
       if (isset($cache->data)) {
-        $missing = $cache->data + $missing;
+        $missing = drupal_array_merge_deep($cache->data, $missing);
       }
     }
     $missing['#write_cache'] = NULL;