diff --git a/commands/core/site_install.drush.inc b/commands/core/site_install.drush.inc
index fc1300e..2c9e290 100644
--- a/commands/core/site_install.drush.inc
+++ b/commands/core/site_install.drush.inc
@@ -30,7 +30,7 @@ function drush_core_pre_site_install($profile = NULL) {
   $files = "$conf_path/files";
   $settingsfile = "$conf_path/settings.php";
   $sitesfile = "sites/sites.php";
-  $sitesfile_write = drush_drupal_major_version() >= 8 && !file_exists($sitesfile);
+  $sitesfile_write = drush_drupal_major_version() >= 8 && !file_exists($sitesfile) && $sites_subdir != 'default';
   if (!file_exists($files)) {
     $msg[] = dt('create a @files directory', array('@files' => $files));
   }
@@ -46,6 +46,9 @@ function drush_core_pre_site_install($profile = NULL) {
   else {
     $msg[] = dt("CREATE  the '@db' database.", array('@db' => $db_spec['database']));
   }
+  if (glob("$files/*")) {
+    $msg[] = dt("Remove all files in the '@files' directory", array('@files' => $files));
+  }
 
   if (!drush_confirm(dt('You are about to ') . implode(dt(' and '), $msg) . ' Do you want to continue?')) {
     return drush_user_abort();
@@ -141,18 +144,9 @@ function drush_core_pre_site_install($profile = NULL) {
     drush_sql_empty_db($db_spec);
   }
 
-  // Empty out any existing config directories.
+  // Empty out files completely.
   if (drush_drupal_major_version() >= 8) {
-    try {
-      // Exception in line below when config dirs don't exist.
-      $active = config_get_config_directory();
-      $staging = config_get_config_directory(CONFIG_STAGING_DIRECTORY);
-      drush_delete_dir_contents(config_get_config_directory(CONFIG_ACTIVE_DIRECTORY), TRUE);
-      drush_delete_dir_contents(config_get_config_directory(CONFIG_STAGING_DIRECTORY), TRUE);
-    }
-    catch (Exception $e) {
-      // Nothing to do.
-    }
+    drush_delete_dir_contents($files, TRUE);
   }
 
   return TRUE;
diff --git a/includes/filesystem.inc b/includes/filesystem.inc
index 1f88a6b..ef58b27 100644
--- a/includes/filesystem.inc
+++ b/includes/filesystem.inc
@@ -151,7 +151,7 @@ function drush_delete_dir_contents($dir, $force = FALSE) {
       continue;
     }
     if ($force) {
-      @chmod($dir, 0777);
+      @chmod($item, 0777);
     }
     if (!drush_delete_dir($dir . '/' . $item, $force)) {
       return FALSE;