fixed error in strcuture of document
added scripts directory and script rst files
added text to index page
removed py extension from within documentation

the current version of this script assumes that all scripts should end with .py. for now just manually changing but in the future, when this script is re-factored as discussed in #14, we'll drop that assumption.
linked to script documentation
Merge pull request #20 from gregcaporaso/doc-updates

doc updates: added script documentation, and fixed an issue with the structure of the script testing doc