update $GIT_INDEX_FILE when there are racily clean entries

Traditional "opportunistic index update" done by read-only "diff" and
"status" was about updating cached lstat(2) information in the index for
the next round.  We missed another obvious optimization opportunity: when
there are racily clean entries that will cease to be racily clean by
updating $GIT_INDEX_FILE.  Detect that case and write $GIT_INDEX_FILE out
to give it a newer timestamp.

Noticed by Lasse Makholm by stracing "git status" in a fresh checkout and
counting the number of open(2) calls.

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

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