Don't assume the file system has sub-second precision timestamp

For example, FreeBSD doesn't have that
(see http://lists.freebsd.org/pipermail/freebsd-fs/2012-February/013677.html).

Docker-DCO-1.1-Signed-off-by: Kato Kazuyoshi <kato.kazuyoshi@gmail.com> (github: kzys)
Merge pull request #5039 from kzys/freebsd-timestamp

Don't assume the file system has sub-second precision timestamp