This should fix#490, at least in the case that I've been able to
verify.
The issue is that reset was setting the skip-worktree bit more
frequently than it should have. The previous fix in #494 was focused on
the case where a file is added or removed across the diff. However, when
the file exists on both sides but still needs to be staged in a mixed
reset then we should avoid the skip-worktree bit.
Signed-off-by: Derrick Stolee <dstolee@microsoft.com>