This adds an option to checkout a la the diff option to turn off
fnmatch evaluation for pathspec entries.  This can be useful to
make sure your "pattern" in really interpretted as an exact file
match only.

This moves a lot of the detailed checkout documentation into a new
file (docs/checkout-internals.md) and simplifies the public docs
for the checkout API.

Make checkout update entries in the index for all files that are
updated and/or removed, unless flag GIT_CHECKOUT_DONT_UPDATE_INDEX
is given.  To do this, iterators were extended to allow a little
more introspection into the index being iterated over, etc.

This flips checkout back to be driven off the changes between
the baseline and the target trees.  This reinstates the complex
code for tracking the contents of the working directory, but
overall, I think the resulting logic is easier to follow.

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.

Conflicts:
	src/branch.c
	tests-clar/refs/branches/create.c