[project @ Method 2 for monitoring pipeline run (based on config_pipeline.py]

[project @ Method 2 for monitoring pipeline run (based on config_pipeline.py]
 * Since the first version stalled in a mysterious way,
   I am trying a new method.
 * Now writes out standard out and standard error to file using
   file descriptors.
 * Also uses inotify to detect "finished" files.
   * FIXME: Need to do something about all other files (currently
     printed to stdout).
 * FIXME: Double check the run_dir exists in configure step.
 * FIXME: Upon run completion, read and process stderr output.