update-index: refresh should rewrite index in case of racy timestamps

'git update-index --refresh' and '--really-refresh' should force writing
of the index file if racy timestamps have been encountered, as
'git status' already does [1].

Note that calling 'git update-index --refresh' still does not guarantee
that there will be no more racy timestamps afterwards (the same holds
true for 'git status'):

- calling 'git update-index --refresh' immediately after touching and
  adding a file may still leave racy timestamps if all three operations
  occur within the racy-tolerance (usually 1 second unless USE_NSEC has
  been defined)

- calling 'git update-index --refresh' for timestamps which are set into
  the future will leave them racy

To guarantee that such racy timestamps will be resolved would require to
wait until the system clock has passed beyond these timestamps and only
then write the index file. Especially for future timestamps, this does
not seem feasible because of possibly long delays/hangs.

[1] https://lore.kernel.org/git/d3dd805c-7c1d-30a9-6574-a7bfcb7fc013@syntevo.com/

Signed-off-by: Marc Strapetz <marc.strapetz@syntevo.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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