diff --git a/core/includes/install.core.inc b/core/includes/install.core.inc
index f798392..ba11eca 100644
--- a/core/includes/install.core.inc
+++ b/core/includes/install.core.inc
@@ -273,7 +273,12 @@ function install_begin_request(&$install_state) {
   // This primes the site path to be used during installation. By not requiring
   // settings.php, a bare site folder can be prepared in the /sites directory,
   // which will be used for installing Drupal.
-  conf_path(FALSE);
+  $conf_path = conf_path(FALSE);
+
+  // Make a record of the original permissions in the install state. These are
+  // checked again in install_configure_form(), which determines if Drupal will
+  // attempt to modify the permissions to read-only automatically.
+  $install_state['conf_permissions'] = fileperms(DRUPAL_ROOT . '/' . $conf_path);
 
   drupal_bootstrap(DRUPAL_BOOTSTRAP_CONFIGURATION);
 
@@ -1846,15 +1851,18 @@ function install_configure_form($form, &$form_state, &$install_state) {
   // Warn about settings.php permissions risk
   $settings_dir = conf_path();
   $settings_file = $settings_dir . '/settings.php';
-  // Check that $_POST is empty so we only show this message when the form is
-  // first displayed, not on the next page after it is submitted. (We do not
-  // want to repeat it multiple times because it is a general warning that is
-  // not related to the rest of the installation process; it would also be
-  // especially out of place on the last page of the installer, where it would
-  // distract from the message that the Drupal installation has completed
-  // successfully.)
-  if (empty($_POST) && (!drupal_verify_install_file(DRUPAL_ROOT . '/' . $settings_file, FILE_EXIST|FILE_READABLE|FILE_NOT_WRITABLE) || !drupal_verify_install_file(DRUPAL_ROOT . '/' . $settings_dir, FILE_NOT_WRITABLE, 'dir'))) {
-    drupal_set_message(st('All necessary changes to %dir and %file have been made, so you should remove write permissions to them now in order to avoid security risks. If you are unsure how to do so, consult the <a href="@handbook_url">online handbook</a>.', array('%dir' => $settings_dir, '%file' => $settings_file, '@handbook_url' => 'http://drupal.org/server-permissions')), 'warning');
+  // Check that $form_state['input'] is empty so we only show this message when
+  // the form is first displayed, not on the next page after it is submitted.
+  if (empty($form_state['input'])) {
+    $permissions_changed = ($install_state['conf_permissions'] !== fileperms(DRUPAL_ROOT . '/' . $settings_dir));
+    if ($permissions_changed) {
+      $permissions_set_readonly = (!drupal_verify_install_file(DRUPAL_ROOT . '/' . $settings_file, FILE_EXIST|FILE_READABLE|FILE_NOT_WRITABLE) || !drupal_verify_install_file(DRUPAL_ROOT . '/' . $settings_dir, FILE_NOT_WRITABLE, 'dir'));
+    }
+    // Show the message if we didn't set permissions automatically for the user,
+    // or if we couldn't set the permissions back to read-only.
+    if (!$permissions_changed || !$permissions_set_readonly) {
+      drupal_set_message(st('All necessary changes to %dir and %file have been made, so you should remove write permissions to them now in order to avoid security risks. If you are unsure how to do so, consult the <a href="@handbook_url">online handbook</a>.', array('%dir' => $settings_dir, '%file' => $settings_file, '@handbook_url' => 'http://drupal.org/server-permissions')), 'warning');
+    }
   }
 
   drupal_add_library('system', 'drupal.system');
diff --git a/sites/README.txt b/sites/README.txt
deleted file mode 100644
index 0372902..0000000
--- a/sites/README.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-This directory structure contains the settings and configuration files specific
-to your site or sites and is an integral part of multisite configurations.
-
-It is now recommended to place your custom and downloaded extensions in the
-/modules, /themes, and /profiles directories located in the Drupal root. The
-sites/all/ subdirectory structure, which was recommended in previous versions
-of Drupal, is still supported.
-
-See core/INSTALL.txt for information about single-site installation or
-multisite configuration.