Remove mention of protected() because it's not very useful

[tbooth]

Comment from Ezra:

Lesson “Cleaning up” – protected files. I’ve never used this functionality before and found it difficult to explain why it would be useful, as it stops the execution of the workflow. Maybe a better option would be to use an ancient() function, which means snakemake does not check the timestamp of the file.

[tbooth]

I'm not sure about this. Stopping the workflow is exactly the point of the functionality, and I have found it somewhat useful in the past.
I agree that ancient() is a good thing to cover, but the semantics are not that simple - if an ancient file is used as an input to a rule AND there is no known rule to make that file then Snakemake will ignore the timestamp. However, if Snakemake sees a rule to make the ancient file, and any inputs to that rule are newer, it will re-run the rule and regenerate the file.

I'll come back to this one.