Added breathe documentation

Currently as it seems `breathe` is quite broken. 
The `autodoxygen` directive don't work, so we will have to write a script to get this done by parsing each file.
See [this issue](https://github.com/michaeljones/breathe/issues/83) for more details.

I've updated the `Doxyfile`. Earlier the paths were fixed, changed them to relative. So should work for each user. 

The sphinx `conf.py` is quite extensive. We can remove some stuff from it. 
@certik I might need some inputs from your side regarding this.

The theme is `default`. We can shift it to someting else.

Building instructions.
In the `doc` directory:

    doxygen Doxyfile
    make html

In the `_build/html` is the breathe html output. In `html` folder is the Doxygen output. We can supress it once we are sure about using breathe.