Read .gitignore from index if it is skip-worktree

Read .gitignore from index if it is skip-worktree

This adds index as a prerequisite for directory listing (with
exclude).  At the moment directory listing is used by "git clean",
"git add", "git ls-files" and "git status"/"git commit" and
unpack_trees()-related commands.  These commands have been
checked/modified to populate index before doing directory listing.

add_excludes_from_file() does not enable this feature, because it
is used to read .git/info/exclude and some explicit files specified
by "git ls-files".

Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>