Use MarkDown for help documentation

[briantoby]

The help files would also benefit from being created from a Markdown precursor rather than edited in Word, as implemented for the tutorials in #93.

This would require a few things:

1. The existing help files would need to be translated to markdown.
2. A CSS format appropriate for help is needed.
3. A mechanism would be needed to create .html files, similar to before
4. The workflow would be needed to create .html files that would be placed both in the distribution files and the on-line documentation