feat: refactored config to fix precedence of config vs. args

[bcoe]

see #379

• refactors config to simplify logic and fix order that args vs. config is applied.
• should improve performance since yargs is only applied once now.

@mourner I will be landing your performance fixes to lib-instrument along with these other fixes, in the next nyc release.

reviewers: @addaleax, @JaKXz, @mourner

[mourner]

@bcoe the config refactor looks good, the only thing that doesn't fit usual JS conventions is the Config object, which is both a factory and a namespace, although typically capitalized names in JS are classes which are instantiated with new. For clarity, I'd turn the factory into another function (exports.makeConfig), and make the namespace lowercase (or maybe rename to config-util?).