Feature/3 nile workflow

[LouiseABowler]

Covers most of #3:

• Introduce command line arguments for most parameters so that the user doesn't have to change the script
• Print error metrics used in Table 1 of the paper
• General tidy up of main script and paper pictured script (remove repeated code etc.)

I'll leave the issue open as we may still want to make changes to the plotting section, but the intended work on the script that manages the CP detection process is now finished.