dir: add a usage note to exclude_per_dir

As evidenced by the fix a couple commits ago, places in the code using
exclude_per_dir are likely buggy and should be adapted to call
setup_standard_excludes() instead.  Unfortunately, the usage of
exclude_per_dir has been hardcoded into the arguments ls-files accepts,
so we cannot actually remove it.  Add a note that it is deprecated and
no other callers should use it directly.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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