You can clone with
HTTPS or Subversion.
in the standard wp instructions for calling wp from a subdirectory http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory the 2 files you need to move are index.php and .htcaccess into the root.
Since Roots uses it's own way to generate the .htaccess and it resides in a different directory within the thme files, is there a specific way to do it, or do I just move the index.php file and leave htaccess alone?
Thanks for clarifying.
This isn't really just a subdirectory install. It's actually a custom core file location which isn't supported in Roots due to a WordPress bug. See #54.
Bummer. even though it isn't a standard installation, it is a very useful one for development.
Ran headlong into this - glad I noticed the issue before attempting to go live on this project. Reading the trac ticket looks like the priority isn't very high.