ModSorter sorter = new ModSorter(getActiveModList(), namedMods);
try
{
FMLLog.finer("Sorting mods into an ordered list");
List<ModContainer> sortedMods = sorter.sort();
// Reset active list to the sorted list
modController.getActiveModList().clear();
modController.getActiveModList().addAll(sortedMods);
// And inject the sorted list into the overall list
mods.removeAll(sortedMods);