Updated the configuration file documentation

Updated the documentation of the configuration file documentation. Now it
accounts for the changes I made to support oulining and environment variables.
Split up parsing and configuration representation.

This is the first step towards a more modular design. I waited only to get some feedback.
I split up the represenation of a confiuration file and generating it and parsing it
into three different entities.
This is also a first step towards replacing this version of the configuration file format
with an XML based version, which will be the next step.
Started with documentation

I started with a small piece of documentation. It is meant as motivation, documentation and reference.