Tourmaline initial set-up in v2

[ksilnoaa]

Instead of cloning the github directory every time to start a brand new Tourmaline run, have a Bash script that will generate all of the required input config files.

[lukenoaa]

The script initialize_dir_from_existing_tourmaline_dir.sh already does a lot of this. Maybe it can be adapted to copy the entire directory from an existing run? Alternatively, the Docker container can be constructed such that that GitHub repo is already there.