Proper Markdown parsing

MSP-11356

# Verification Steps

## Before
- [ ] `git checkout 55b8d7f`
- [ ] `bundle install`
- [ ] `rake yard`
- [ ] `open doc/index.html`
- [ ] VERIFY Markdown links aren't rendered correctly: 
![screen shot 2014-09-12 at 3 19 38 pm](https://cloud.githubusercontent.com/assets/2230482/4256689/d132a8d2-3aba-11e4-8f0c-7f1a23322532.png)

## After
- [ ] `git checkout 58c3197 `
- [ ] `bundle install`
- [ ] `rake yard`
- [ ] `open doc/index.html`
- [ ] VERIFY Markdown link are rendered correctly:
![screen shot 2014-09-12 at 3 25 51 pm](https://cloud.githubusercontent.com/assets/2230482/4256703/04029362-3abb-11e4-886d-e16da1c38e8e.png)