Make default output root path folder configurable in settings.toml

[alexdewar]

Currently MUSE2 uses muse2_results/{model_name} as the output path whenever a model is run. We should make the muse2_results part configurable, as users may not want their output files saved in the CWD (e.g. they might want "C:\Users\Alice\My Documents\muse2_results" or something). I think it makes most sense to add an option for this in settings.toml.

I think we should also let users output files for a specific run of a model to a different directory (e.g. with a command-line argument), but that's a separate issue (#371).