Update makefile and readme

I tried to harmonize the .gitlab-ci and the README and the Makefile, so that they use the same make scripts. Hopefully the README has become more coherent now.

Also I deleted several files (e.g. the docs) and other utilities (e.g. the Python linting scripts since Python code is only generated) which came from the cookiecutter template. The project has now not much more to do with the original template, because it has a special setting with the LinkML and was in retrospective not a good candidate to try out the template.