[project @ Bypass pipe lock mystery bug for configure step]

[project @ Bypass pipe lock mystery bug for configure step]
 * There was a weird bug where certain failures of the pipeline could
   leave the configure_run.py configure code waiting for output from the
   configuration pipe, but where the program has already finished... leaving
   the configure step stuck in a perminate state of waiting.
 * This patch bypasses this problem by passing subprocess.Popen file
   descriptors instead of subproccess.PIPE and then processing the
   output after the program has terminated. I have never seen the
   mystery bug when using this approach. This is how the run pipeline
   step already handles running the pipeline and is also where I first
   encountered this problem.