[PYOPENMS] setup.py as minimal as possible + other improvements

I moved code generation and moving of files  to new script create_cpp_extension.py.
This includes running autowrap and Cython.

setup.py is now as minimal as possible, which prevents errors when using pip and its dependency resolution mechanism.

I updated the cmake files, and cleaned up the targets. Now we have a target pyopenms which builds pyopenms in place which is suited for running tests, and a target pyopenms_dist which builds binary installers for pyopenms.