Update Protocol documentation
Update Protocol documentation

- Re-wrap a few long lines.
- Remove documentation for `Ref` and `Protocol.refify`, as they are
	internal-use only.
- Update documentation for `Protocol`, to highlight the helper methods and
	remove reference to the fact that you can pass in a list of instructions to
	the constructor.

transcripticpll/autoprotocol-python,merrywhether/autoprotocol-python,dotsilverman/autoprotocol-python,therzka/autoprotocol-python