This was the temporary development home for the WordPress Twenty Twelve theme until July 11, 2012. Now tracking back on WordPress core Trac.
See http://core.trac.wordpress.org/ticket/19978 as the original ticket there, and open new tickets for issues.
What's with the weird directory structure?
We used Forge during this stage of development to speed things up. When Twenty Twelve was checked back into WordPress core these development tools are no longer in use, and the directory structure is back to normal.