When stashing the workdir tree, examine the index as well.  Using
a mechanism similar to `git_diff_tree_to_workdir_with_index`
allows us to determine that a file was added in the index and
subsequently modified in the working directory.  Without examining
the index, we would erroneously believe that this file was
untracked and fail to include it in the working directory tree.

Use a slightly modified `git_diff_tree_to_workdir_with_index` in
order to avoid some of the behavior custom to `git diff`.  In
particular, be sure to include the working directory side of a
file when it was deleted in the index.