This corrects the order of operations in git reset so that the
checkout to reset the working directory content is done before
the HEAD is moved.  This allows us to use the HEAD and the index
content to know what files can / should safely be reset.

Unfortunately, there are still some cases where the behavior of
this revision differs from core git.  Notable, a file which has
been added to the index but is not present in the HEAD is
considered to be tracked by core git (and thus removable by a
reset command) whereas since this loads the target state into
the index prior to resetting, it will consider such a file to be
untracked and won't touch it.  That is a larger fix that I'll
defer to a future commit.

A number of diff APIs and the `git_checkout_index` API take a
`git_repository` object an operate on the index.  This updates
them to take a `git_index` pointer explicitly and only fall back
on the `git_repository` index if the index input is NULL.  This
makes it easier to operate on a temporary index.

This is a major reworking of checkout strategy options.  The
checkout code is now sensitive to the contents of the HEAD tree
and the new options allow you to update the working tree so that
it will match the index content only when it previously matched
the contents of the HEAD.  This allows you to, for example, to
distinguish between removing files that are in the HEAD but not
in the index, vs just removing all untracked files.

Because of various corner cases that arise, etc., this required
some additional capabilities in rmdir and other utility functions.

This includes the beginnings of an implementation of code to read
a partial tree into the index based on a pathspec, but that is
not enabled because of the possibility of creating conflicting
index entries.

git_index_read_tree() was exposing a parameter to provide the user with
a progress indicator. Unfortunately, due to the recursive nature of the
tree walk, the maximum number of items to process was unknown. Thus,
the indicator was only counting processed entries, without providing
any information how the number of remaining items.

This expands the types of peeling that `git_object_peel` knows
how to do to include TAG -> BLOB peeling, and makes the errors
slightly more consistent depending on the situation.  It also
adds a new special behavior where peeling to ANY will peel until
the object type changes (e.g. chases TAGs to a non-TAG).

Using this expanded peeling, this replaces peeling code that was
embedded in `git_tag_peel` and `git_reset`.

Replace with the contents of 
git_index_read_tree_with_stats() and improve
documentation comments.

Currently supports Soft and Mixed modes.