diff --git a/setup/cli/modules/deploy.php b/setup/cli/modules/deploy.php
index 97d3e1abb7b02f4bd3c51284f0d128d88aacd7bb..aa123bfcb1de9524ddb3b9bf3d291450eb866d62 100644
--- a/setup/cli/modules/deploy.php
+++ b/setup/cli/modules/deploy.php
@@ -127,7 +127,9 @@ class Deployment extends Unpacker {
             // Clean everything but include folder first
             $this->clean($root, $this->destination, -1,
                 array($include, "setup/"));
-            $this->clean("$root/include", $include, -1);
+            $this->clean("$root/include", $include, -1,
+                array("ost-config.php","settings.php","plugins/",
+                "*/.htaccess"));
         }
     }
 }