code: private void processOutputDirectory() {
          final String root = outputDirectory.getAbsolutePath();
          final String leaf = PhaseOneApplication.DIR_ARTIFACT;
          final String path = asPath(root, leaf);
          final File phaseIPath = new File(path);
  
          // Fail if the working path doesn't contain a phase I artifact
          if (!phaseIPath.isDirectory()) {
              error(NOT_A_PHASE1_DIR + ": " + phaseIPath);
              failUsage();
          }
  
          // Fail if the working path doesn't contain any proto-networks
          final File[] networks = phaseIPath.listFiles(new ProtonetworkFilter());
          if (networks.length == 0) {
              error(NO_PROTO_NETWORKS + " found in " + phaseIPath);
              failUsage();
          }
  
          // Create the directory artifact or fail
          artifactPath = createDirectoryArtifact(outputDirectory, DIR_ARTIFACT);
  
          processDirectories(networks);
      }
docs: Processes the output directory.