Don't clean plugins/ folder or config files

Also, if any non-shipped .htaccess files exist, don't clean those either

Fixes #60

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"));
         }
     }
 }