Ensure unused fds are closed when calling subprocesses via Popen

When sos communicates with a child process using Popen all IO
takes place on stdin/stdout/stderr (or a subset). No other open
file descriptors should be inherited by the child.

Make all calls to Popen set close_fds=True.

Signed-off-by: Bryn M. Reeves <bmr@redhat.com>