Restructuring of quantum-circuit to quantum-device configuration files

The current structure was made very ad-hoc and is not well defined. During the quantum-control-design meetings, we had extensive discussions on how to redesign this. This is triggered once again because we are now including acquisition protocols #36 (closed). The ad-hoc nature of the current compilation steps (involving many if-statements) is also a consequence of the format of these files #64 (closed) .

This issue tracks the proposals for a new structure of this config file. #64 (closed) relates to improving the compilation steps based on this new proposal.