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.
