Update src/docco.coffee to support .md output as an option

Added support to optionally produce markdown files in addition to html.
Update resources/docco.jst

Adding an optional second output type required the destionation()
method to have a second argument for the extension.
Update test/tests.coffee

Added a new test case for markdown_output and adjusted the expected var
in the testDoccoRun method to account for the extra file in this test
case.