Add comments with inline documentation

[jorinvo]

We tried writing the code as simple, modular and straight-forward as possible, but it would be still better to have some explanation about what certain modules and functions do.
I think it wouldn't even be necessary to just an official documentation style and document every parameter.
I'm more thinking about having some introduction at the to of each file. It should be simpler for new contributors to see what the different parts of the project do.