nios2: Use read_persistent_clock64() instead of read_persistent_clock()

Since struct timespec is not y2038 safe on 32bit machines, this patch
converts read_persistent_clock() to read_persistent_clock64() using
struct timespec64, as well as converting mktime() to mktime64().

Signed-off-by: Baolin Wang <baolin.wang@linaro.org>
Signed-off-by: Ley Foon Tan <ley.foon.tan@intel.com>