Fix formatting of some code blocks in pdf docs

I was reading through the tutorial and manual pdfs and noticed some of the code blocks have glitches in their formatting:

![](http://i.imgur.com/9HXZ4dW.png)
![](http://i.imgur.com/Ds2By6j.png)

Putting empty lines around the blocks fixes this. I did a search through the other markdown files and made the change there as well.