Looks like an interesting project. I may be missing something, but I think in terms of math especially it would be hard to use Markdown instead of something more robust like LaTeX which supports proper mathematical notation.

Edit: yes, I was missing something. Scholdoc supports MathJax (which has browser, Office, and LaTeX support).

Small issue: The title isn't showing up in Firefox (or Chrome) because there are two title elements and the first one is blank.