Pre-merge code cleanup

src/opticalcontroller/OpticalController.py

src/opticalcontroller/RSA.py

src/opticalcontroller/json_files/nodes.json

src/opticalcontroller/json_files/optical_TFSworking.json

src/opticalcontroller/json_files/optical_topoTFS.json

src/opticalcontroller/json_files/tfs.json

src/opticalcontroller/json_files/tfs_dict.json

src/opticalcontroller/json_files/tfs_dict_modified.json

src/opticalcontroller/json_files/topo_2_links.json

src/opticalcontroller/json_files/topology-optical.json

src/opticalcontroller/json_files/topology-optical2.json

src/opticalcontroller/variables.py