I am now updating these at https://github.com/oobrien/vis/tree/master/tube/data - specifically https://github.com/oobrien/vis/tree/master/tube/data/tfl_lines.json and https://github.com/oobrien/vis/tree/master/tube/data/tfl_stations.json
TfL lines and stations. Includes, Tube, DLR, Overground, Tramlink, Emirates Air Line and Crossrail. All as currently running/aligned, except Crossrail. Original data source: OpenStreetMap, which is Copyright OpenStreetMap contributors and available under the Open Database Licence.