Add some logging to let the users know what's happening. Minor PEP-8.
Update `cli` to use the new `MergeConfigMixIn`.

The purpose of the above MixIn is to override the options on the configuration file with the options passed from the console.
Merge pull request #51 from s0undt3ch/hotfix/make-logfile-logging-work

Hotfix/make logfile logging work