Suggestion: Make example commands runable

[de-code]

The example commands in the documentation refer to files like my_script.py. It would be good if all of the example commands were runable, as in copy and paste, provided they are run from the r2t2 directory. i.e. we could refer to docs/examples/....

[rgaiacs]

Is this for documentation or test?

[de-code]

It is for the documentation, so that someone could reproduce results with minimal effort.