Update: Factor ignores out of Config

Fixes #958.

I thought that using the term "ignores" everywhere and never "exclusions" would make things more consistent and less confusing. The only confusing part now is where `isExcluded` is changed to `ignores.isIncluded`, but I think `ignores.isIncluded` makes sense by itself, it's just an odd difference. Open to suggestions.

All of the logic remains the same, but now instead of calling Config.getExclusions for an exclusions array and doing the matching logic in cli.js, you load up Ignores with a config object and then call Ignores.isIncluded which encapsulates the matching logic. (By the way, it's kind of confusing how the Config object is called "configHelper" in some places in cli.js.)