Improved CLI logging

This PR improves logging across the board by using treating the logger as something you can access by grabbing the logger at a module-level, rather than passing it around as a variable. Since it's a singleton, you can avoid doing this and this allows one to use the logging module within classifiers as well. This also tweaks the default logging level for lots of logs to avoid excessive output.

Finally, as an aside, add some CLI tests to verify that the logging changes didn't break anything.