new layout and cli command

I changed the layout to src/... , updated all internal references and cleaned up some unused files. Since I had merged a django project with a python package, this was a mess that had caused trouble for over two years. This should be much cleaner now without changing the import and usage from outside. This also allowed me to add a "run_db_server" cli command. Applying the MR would require some changes in lab_adaption REAMDE.md. Does it cause any problems with Docker? I also updated the README