Added new option to create_stops_shp_file_combined_from_existing() to
auto-create new GTFS stop IDs.

And set this to be used in hte script
create_network_topology_extended_from_existing_gtfs.py .

The reason this is necessary is the whole per-time period speeds model is
currently still somewhat tied to GTFS, so each stop needs to have a GTFS id as
well as a regular one.