ls-files: excludes should not impact tracked files

In all parts of git, .gitignore and other exclude files
impact only how we treat untracked files; they should have
no effect on files listed in the index.

This behavior was originally implemented very early on in
9ff768e, but only for --exclude-from. Later, commit 63d285c
accidentally caused us to trigger the behavior for
--exclude-per-directory.

This patch totally ignores excludes for files found in the
index. This means we are reversing the original intent of
9ff768e, while at the same time fixing the accidental
behavior of 63d285c. This is a good thing, though, as the
way that 9ff768e behaved does not really make sense with the
way exclusions are used in modern git.

Signed-off-by: Jeff King <peff@peff.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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