You can clone with
HTTPS or Subversion.
I get confused every time I try to look up the sitemap specs, but it sounds like if the sitemap files are in /sitemaps, then they can only report urls under /sitemaps.
Does symlinking the sitemap index file to the root of the site solve this? I don't think it would?
Sitemaps are now generated in the root directory by default, as of version 1.0.0. Please see the README for details and the new syntax.