Help with the new SAMTools website

Hi there,

I saw the new SAMTools / HTSlib website today and thought that I might be able to help out a little. You've used a great setup for the website (github hosting + jekyll + bootstrap :+1: ) but were missing out on much of the stuff that these tools give you for free.

I've had a quick whip through and done some redesigning. Specifically:
* Convert most of the pages from HTML to markdown
 * Markdown makes updating much easier, plus styling more consistent. There was quite a lot of broken HTML in these pages (unclosed tags etc) and using Markdown avoids all of this.
* Structure rewrite using bootstrap styles
 * I rewrote the display of the header and homepage using some of the bootstrap components designed for this purpose. _eg._ using glyphicon icons instead of home-written SVG files; navbar component instead of submenu navigation pills.
* One or two new features
 * Highlighting the current page in the navigation
 * Direct call to action (download button) on the homepage
 * Responsive features of bootstrap now work - pages should look good on all screen sizes (_eg._ mobile phones)

Feel free to use as much or as little as you like - creating these pages is one of those things that is "easy when you know how" and can be very frustrating when you don't, so thought that I might be able to save some stress.

The man pages are longer so I thought I'd hold off restructuring these until you'd seen this PR - I'm happy to give them similar treatment if you'd like though. Same goes for making a logo for the home page and actually styling the website - this is fairly trivial if you're interested and don't mind shortcuts using one of the many [free](http://bootswatch.com/) [themes](http://startbootstrap.com/) which are available.

Cheers,

Phil

![screen shot 2014-09-08 at 15 10 35](https://cloud.githubusercontent.com/assets/465550/4185722/4209257c-375a-11e4-896b-036d180e72cc.png)
![screen shot 2014-09-08 at 15 11 01](https://cloud.githubusercontent.com/assets/465550/4185723/420c67e6-375a-11e4-9c6d-d3926c662b6f.png)