popen: fix close-on-exec flag setting

fcntl(2) lists flags that can be set using F_SETFL: O_CLOEXEC is not
included there. F_SETFD should be used to set close-on-exec.

Parent's end of pipes are closed explicitly in a child process anyway.
However this change fixes closing of the copy of a logger fd. See commit
07a07b3c ('popen: decouple logger fd
from stderr') for more information why this file descriptor was
introduced.

Part of #4031.

Acked-by: Cyrill Gorcunov <gorcunov@gmail.com>