You can clone with
HTTPS or Subversion.
During 0.6.4 setup and install, you are prompted for the "name" and "URL" of your website.
After completing setup, if you go to Settings > Websites, you will find the URL has been set as example.com.
reported in: http://forum.piwik.org/index.php?showtopic=12421
(In ) fixes #1503