I've tried to map out the detailed behaviors of checkout and make
sure that we're handling the various cases correctly, along with
providing options to allow us to emulate "git checkout" and "git
checkout-index" with the various flags.  I've thrown away flags
in the checkout API that seemed like clutter and added some new
ones.  Also, I've converted the conflict callback to a general
notification callback so we can emulate "git checkout" output and
display "dirty" files.

As of this commit, the new behavior is not working 100% but some
of that is probably baked into tests that are not testing the
right thing.  This is a decent snapshot point, I think, along the
way to getting the update done.