code: private void processDirectories(final File[] networks) {
          phaseOutput(format("=== %s ===", getApplicationName()));
  
          ProtoNetwork network = stage1(networks);
          Set<EquivalenceDataIndex> eqs = stage2();
  
          if (!eqs.isEmpty()) {
              network = stage3(network, eqs);
          }
          stage4(network);
      }
docs: Starts phase two compilation of proto-networks.
  
  @param networks