opts/command line args precedence over config is inconsistent

[lloydcotten]

While doing pull request #163, I noticed that nyc will take config from package.json over command line args and/or opts passed into the NYC constructor for some cases, but will take opts over config for other values (namely cwd). See these lines:
https://github.com/bcoe/nyc/blob/master/index.js#L34
https://github.com/bcoe/nyc/blob/master/index.js#L64

I patterned the new extension config after the require config where config from package.json is preferred:
https://github.com/bcoe/nyc/blob/master/index.js#L54

To me (and @novemberborn seems to agree) this is not intuitive. The only way command line args or opts are used for these properties, is if no package.json config exists. If we switched it around, it would make testing a bit easier, and would be more intuitive for usage when mixing package.json config and command line usage.

[bcoe]

@lloydcotten my plan is to moving to having yargs load the configuration:

#156

Command-line arguments will take precedence over package.json configuration when I make this change 👍 Mind adding a note to #156

[lloydcotten]

Sounds good.