Yard updates

I'm trying to slowly improve the documentation and iron out some of the kinks with our YARD setup.

I noticed recently that YARD can't differentiate between identical file names in different directories. As a result, our documentation site has three README files in the menu, but each links to the same file, which happened to (luckily) be the top-level README. This PR preprends to the names of markdown files in subdirectories. 

Before:
![Screen Shot 2013-04-05 at 12 30 52 PM](https://f.cloud.github.com/assets/1626547/344873/3fe8c414-9e0e-11e2-953b-8baa6532af8f.png)
(3 README links triggered by 3 distinct files but pointing to only 1 of them)

After:
![Screen Shot 2013-04-05 at 12 31 32 PM](https://f.cloud.github.com/assets/1626547/344877/5492392c-9e0e-11e2-8ded-effbfaab4adc.png)

Now, we may want to cleanup, merge, or exclude some of these, but that can be another issue.