Improvements to Application docs

Described some things that are not obvious from the docblocks.

I'm confused, what is supposed to come into README.md's. Now we have
- There is an [API documentation](http://api.joomla.org/framework-1.0/index.html)
- Framework [GitHub page](http://joomla.github.io/joomla-framework/) with obsolete documentation
- [Experimental developer documentation](https://github.com/joomla/joomla-developer-docs) which is aggregating the README's and adding the Recipes