Fix fingerprinting test and add a new test to command-test

This fixes the fingerprinting test failure (referenced [here](https://github.com/stefanpenner/ember-cli/pull/563)), by switching the order when parsing command arguments (so that command-line args take precedence over config files). Also removed serve-settings-test.js as command-test seemed more like the place for that.

(This also includes a semi-recent rebase)