Standardize function use off axe, axe.utils, and axe.commons

The root `axe` should only have functions for configuring and running axe, and plugins. `axe.utils` should have functions that are safe to use outside of an `axe.run` (no reliance on the virtual tree being set up). `axe.commons` should be functions that rely on the virtual tree and thus could be unsafe to run outside of `axe.run`.