Added Docs directory wth expanded documentation as a start

git-svn-id: svn+ssh://civmxsrv2.duhs.duke.edu/Users/civmsvn/svn/repos/mat_recon_pipe/trunk@2092 d41079a3-eaa1-4f09-8506-b324c47726bb
Merge branch 'master' of github.com:jamesjcook/mat_recon_pipe