Refactor location of scripts

[agstephens]

• Move the command-line scripts are located in a cli directory, from script.
• Move nappy/utils/compare_na.py to cli/ - but remember that compare is imported in tests and other code, so the underlying functions need to remain in a library rather than a script.
• Maybe compare_na.py and compare.py are the same!?

[agstephens]

And make them install with setup.py