Merge pull request #9 from twitch153/gsoc2014

This merge includes updates to the documentation and the configuration file to reflect the new features added.
Various syntax fixes

Fixes to docstring indentation, output messages, and function
definition syntax.
Replaces "subpath" with "branch"

In favor of a more widely used varaible, the subpath variable has
been replaced with branch. In preparation for branch support in
overlay.xml files.