Integrate documentation

* Clean unused files
* Integrate documentation

![screen shot 2014-07-07 at 16 38 45](https://cloud.githubusercontent.com/assets/615085/3497567/e9261102-05ec-11e4-9e61-8a49ce2c13fe.png)
![screen shot 2014-07-07 at 16 38 57](https://cloud.githubusercontent.com/assets/615085/3497569/e92690e6-05ec-11e4-8b6e-68e641057deb.png)
![screen shot 2014-07-07 at 16 39 07](https://cloud.githubusercontent.com/assets/615085/3497568/e926462c-05ec-11e4-9558-9fbaff0f565e.png)
![screen shot 2014-07-07 at 16 39 17](https://cloud.githubusercontent.com/assets/615085/3497570/e9272272-05ec-11e4-9bc6-445ae48acd6f.png)

The content in the documentation may not be perfect, but it will be easier to update once this pull request has been merged. 
@gidsg what are the licensing issues?