You can't clone a site.
You can create some config files that will determine initial pages and what features are on them when a new site is created.
http://www.mojoportal.com/configuring-initial-content.aspx
By default I only package a config file to create a home page in new installations, but for example on demo.mojoportal.com I use a set of custom files so that every time the demo site is recreated its gets the same set of pages with features on them. It is fairly limited in that for most features all it can do is put the feature on the page, only for the main Html feature does it also allow you to configure some initial html content.
Hope it helps,
Joe