Doxygen generated documentation

As I read trough the sources of the project, I figured I could also extract some ideas for the doxygen generated documentation. I also plan to improve the comments in the source code and make them visible to doxygen, if required.

This patch adds a main page and some basic pages as a proof-of-concept and adds a python script to manage the tree structure of the pages (update-links.py).

Things to be done in the near future:
- integrate update-links.py with cmake files (maybe a dedicated CMakeLists.txt in doc directory)
- transfer content from readme files (we can do better than README_to_doxygen.sh)