Update site generation with dependencies (#129) and jxr (#128)

Resolves issue #128 and #129.

In addition to solving the issues, I added a prefix to make the base URL absolute. This is needed if you want to run mvn site:stage. Andy, can you check that this won't break deployment of site to Github?

I also removed the doxia-module-markdown definition for the maven-site-plugin. Is there a specific reason for why it was there? It is automatically included, but the definition specified an older version of doxia-module-markdown. I couldn't find any problems after removing it.