Git doesn't always add files to a commit (amend)

Hi,

When intent to add a directory is made (`git add -N`), and then contents of any but the first file is staged, `git commit -v --amend` doesn't add it to the commit, see for yourself:

    #!/usr/bin/env bash
    set -eu
    rm -rf 1
    mkdir 1
    cd 1
    git init
    echo 1 > 1 && git add 1 && git commit -m 1
    mkdir 2
    echo 2/1 > 2/1
    echo 2/2 > 2/2
    git add -N 2
    # git add 2/1   # this file is added
    git add 2/2   # as opposed to this one
    git commit --amend -m 1
    git --no-pager log -p
    git reset
    git --no-pager status

I'm running git-2.9.0.

Regards, Yuri