shell_directive: fix race condition when running commands
    
    Even though some commands exited with non-zero exit code, we sometimes
    believed it exited with zero code due to a race condition. This patch
    fixes that and also moves the code to a separate function
    `os_utils.popen_rt()`.
    
    Differential Revision: https://phab.qadevel.cloud.fedoraproject.org/D983