lib: Fix calls that naively set F_SETFD.

With the recent inclusion of the FD_CLOFORK and FD_RESOLVE_BENEATH flags,
we must avoid clearing them when setting only FD_CLOEXEC.

Signed-off-by: Ricardo Branco <rbranco@suse.de>

Reviewed by: kib, markj
MFC after: 1 month
Pull Request: https://github.com/freebsd/freebsd-src/pull/1766