punybench: remove readdir_r

`readdir_r` is deprecated in glibc 2.24.
It is advised to use the readdir instead.

BUG=chromium:859528
TEST=emerge-samus punybench passes with glibc 2.27

Change-Id: I108c37eb3509137e72839727e6f2bc759e215deb
Reviewed-on: https://chromium-review.googlesource.com/1122844
Commit-Ready: Yunlian Jiang <yunlian@chromium.org>
Tested-by: Yunlian Jiang <yunlian@chromium.org>
Reviewed-by: Sonny Rao <sonnyrao@chromium.org>