Merge handbook into doxygen
In order to have all documentation in one place, I suggest to merge the handbook into doxygen. This also allows to easily view everything online and improve searchability and cross-linking capabilities.
As far as I can see the handbook content is up-to-date and useful documentation. Currently, we have some sections doubled like the installation instructions. But also the advanced topic make sense for me in the doxygen documentation in the respective group, linked from the high-level documentation.
In case some people prefer PDF it is also possible to look into generating PDFs which doxygen from which the class docs could be excluded. Another possibility since all doc will be in markdown is to generate latex from selected markdown documents via pandoc. That way the sources are not doubled and the documentation will be easier to maintain and find.