tutorial/ user guide work

[punkpony]

• as we go through testing - note down key points for the tutorial
• work through setup of various clays, write the example input files

[punkpony]

• Tutorials as a separate folder, including example input for various clays
• git Pages in the readthedoc style https://erastova-group.github.io/ClayCode
• structure the Pages
• write the user manual on the Pages
• write tutorials on the Pages
• write developer guide (not priority)