Apart from "private", I need to add two more folders. Is there any GUI to modify the new website default folder structure? If no, which script should I hack? Thanks!
There is no template for that. If you want to mofify the layout, then you have to modify the apache and nginx plugin. This will work if you add folders, if you want to rename folders, then you might have to change all serverside plugins and the cron scripts as tehy all depend on the layout.