public static  void sort(List modules) 
{
    final HashMap moduleMap = new HashMap();
    final ArrayList errorModules = new ArrayList();
    final ArrayList weightModules = new ArrayList();
    for (int i = 0; i <  modules.size(); i++)
    {
      final PackageState state = (PackageState) modules.get(i);
      if (state.getState() == PackageState.STATE_ERROR)
      {
        errorModules.add (state);
      }
      else
      {
        final SortModule mod = new SortModule(state);
        weightModules.add (mod);
        moduleMap.put(state.getModule().getModuleClass(), mod);
      }
    }
    final SortModule[] weigths = (SortModule[])
        weightModules.toArray(new SortModule[weightModules.size()]);
    for (int i = 0; i <  weigths.length; i++)
    {
      final SortModule sortMod = weigths[i];
      sortMod.setDependSubsystems
          (collectSubsystemModules(sortMod.getState().getModule(),
              moduleMap));
    }
    // repeat the computation until all modules have a matching
    // position. This is not the best algorithm, but it works
    // and is relativly simple. It will need some optimizations
    // in the future, but as this is only executed once, we don't
    // have to care much about it.
    boolean doneWork = true;
    while (doneWork)
    {
      doneWork = false;
      for (int i = 0; i <  weigths.length; i++)
      {
        final SortModule mod = weigths[i];
        final int position = searchModulePosition(mod, moduleMap);
        if (position != mod.getPosition())
        {
          mod.setPosition(position);
          doneWork = true;
        }
      }
    }
    Arrays.sort(weigths);
    modules.clear();
    for (int i = 0; i <  weigths.length; i++)
    {
      modules.add (weigths[i].getState());
    }
    for (int i = 0; i <  errorModules.size(); i++)
    {
      modules.add (errorModules.get(i));
    }
}

Sorts the given list of package states. ToDo: The algorithm used is simple and not optimized, we could write something better in a near future.