Include cli options into loaded config dictionary.

The merge with cli mix in, only merges option keys which exist in both places, cli options and loaded config. Since neither `profile` not `parallel` existed in any of the default config dictionary, not the loaded config files, that info was not getting included.
Now `parsers.MergeConfigMixIn` actually does it's job.
Logging can now be instantiated at module level.
Minor formatting changes.
Merge pull request #293 from s0undt3ch/develop

Include cli options into loaded config dictionary.