Allow users to choose results folder with command-line argument

[alexdewar]

Currently the simulation results are written to muse2_results/{model_name}, but users may want to output the files for a particular run somewhere else. Let's add a command-line argument (--output, -o or something) to do this.

All the command-line parsing magic lives in commands.rs. I think you'll need to add fields to Commands::Run and ExampleSubcommands::Run, maybe of type Option<PathBuf>.