Refactoring index.html and using bower for client side dependencies

I hope this change isn't too big for a single PR.  It's mostly copy and paste, to break the css and js out of index.html into separate files.  I also fixed the structure of index.html so it's a valid document.

When I setup bower I grabbed the current version of d3 and jquery.  The d3 bump is minimal, but jquery is a full version increase, as long as no one cares about old versions of IE it should be fine.

Let me know what you think, I'm happy to make changes.