diff --git a/modules/system/system.install b/modules/system/system.install
index ad15851..903137e 100644
--- a/modules/system/system.install
+++ b/modules/system/system.install
@@ -233,10 +233,18 @@ function system_requirements($phase) {
     }
   }
 
-  // Test settings.php file writability
+  // Test settings.php file writability.
   if ($phase == 'runtime') {
-    $conf_dir = drupal_verify_install_file(conf_path(), FILE_NOT_WRITABLE, 'dir');
-    $conf_file = drupal_verify_install_file(conf_path() . '/settings.php', FILE_EXIST|FILE_READABLE|FILE_NOT_WRITABLE);
+    // Allow system administrators to ignore permissions hardening for the site
+    // directory. This allows additional files in the site directory to be
+    // updated when they are managed in a version control system.
+    if (!variable_get("ignore_site_directory_permissions", FALSE)) {
+      $conf_dir = drupal_verify_install_file(conf_path(), FILE_NOT_WRITABLE, 'dir');
+      $conf_file = drupal_verify_install_file(conf_path() . '/settings.php', FILE_EXIST|FILE_READABLE|FILE_NOT_WRITABLE);
+    }
+    else {
+      $conf_dir = FALSE;
+    }
     if (!$conf_dir || !$conf_file) {
       $requirements['settings.php'] = array(
         'value' => $t('Not protected'),
diff --git a/sites/default/default.settings.php b/sites/default/default.settings.php
index 30699a0..a81ae70 100644
--- a/sites/default/default.settings.php
+++ b/sites/default/default.settings.php
@@ -510,3 +510,18 @@ $conf['404_fast_html'] = '<html xmlns="http://www.w3.org/1999/xhtml"><head><titl
  * Remove the leading hash signs to disable.
  */
 # $conf['allow_authorize_operations'] = FALSE;
+
+/**
+ * Override file system permissions hardening.
+ *
+ * The system module will periodically check the permissions of your site
+ * site directory to ensure that they are not writable by the website user.
+ * For sites that are managed with a version control system, this can cause
+ * problems when files in that directory (such as a "settings.inc" containing
+ * additional configuration) when the files are updated, as the user pulling
+ * in the changes won't have permissions to modify files in the directory.
+ *
+ * Remove the leading hash sign to disable permissions hardening.
+ */
+# $conf['ignore_site_directory_permissions'] = TRUE;
+