Resurrect "git apply --flags -" to read from the standard input

Resurrect "git apply --flags -" to read from the standard input

The previous "parse-opt"ification broke git-apply reading from the
standard input.  "git apply A - C <B" is supposed to read patches from
files A, B and C in this order.

Before "parse-opt"ification, we used be able to:

	git apply --stat - --apply <A B

to read the patch from file A, showing only the diffstat, and then read the
patch from file B, showing the diffstat and actually applying it.  Even
with this fix we cannot do that anymore, but that is so crazy use case I
do not think anybody sane relied on such a broken behaviour.

Signed-off-by: Junio C Hamano <gitster@pobox.com>