Program: 166000
Project: 166000
Buggy source:
@Override public void constructDimension(List<Pair<DimletKey,List<DimletKey>>> dimlets,Random random,DimensionInformation dimensionInformation){
  Set<DimletKey> biomeKeys=new HashSet<DimletKey>();
  List<Pair<DimletKey,List<DimletKey>>> biomeDimlets=DimensionInformation.extractType(DimletType.DIMLET_BIOME,dimlets);
  List<Pair<DimletKey,List<DimletKey>>> controllerDimlets=DimensionInformation.extractType(DimletType.DIMLET_CONTROLLER,dimlets);
  ControllerType controllerType;
  if (controllerDimlets.isEmpty()) {
    if (random.nextFloat() < DimletConfiguration.randomControllerChance) {
      List<DimletKey> keys=new ArrayList<DimletKey>(DimletObjectMapping.idToControllerType.keySet());
      DimletKey key=keys.get(random.nextInt(keys.size()));
      controllerType=DimletObjectMapping.idToControllerType.get(key);
    }
 else {
      if (biomeDimlets.isEmpty()) {
        controllerType=ControllerType.CONTROLLER_DEFAULT;
      }
 else       if (biomeDimlets.size() > 1) {
        controllerType=ControllerType.CONTROLLER_FILTERED;
      }
 else {
        controllerType=ControllerType.CONTROLLER_SINGLE;
      }
    }
  }
 else {
    DimletKey key=controllerDimlets.get(random.nextInt(controllerDimlets.size())).getLeft();
    controllerType=DimletObjectMapping.idToControllerType.get(key);
  }
  for (  Pair<DimletKey,List<DimletKey>> dimletWithModifiers : biomeDimlets) {
    DimletKey key=dimletWithModifiers.getKey();
    biomeKeys.add(key);
  }
  int neededBiomes=controllerType.getNeededBiomes();
  if (neededBiomes == -1) {
    if (biomeKeys.size() >= 2) {
      neededBiomes=biomeKeys.size();
    }
 else {
      neededBiomes=random.nextInt(10) + 3;
    }
  }
  while (biomeKeys.size() < neededBiomes) {
    DimletKey key;
    List<DimletKey> keys=new ArrayList<DimletKey>(DimletObjectMapping.idToBiome.keySet());
    key=keys.get(random.nextInt(keys.size()));
    while (biomeKeys.contains(key)) {
      key=keys.get(random.nextInt(keys.size()));
    }
    biomeKeys.add(key);
  }
  List<BiomeGenBase> biomes=dimensionInformation.getBiomes();
  biomes.clear();
  for (  DimletKey key : biomeKeys) {
    biomes.add(DimletObjectMapping.idToBiome.get(key));
  }
}

Fixed version (ground truth):
@Override public void constructDimension(List<Pair<DimletKey,List<DimletKey>>> dimlets,Random random,DimensionInformation dimensionInformation){
  Set<DimletKey> biomeKeys=new HashSet<DimletKey>();
  List<Pair<DimletKey,List<DimletKey>>> biomeDimlets=DimensionInformation.extractType(DimletType.DIMLET_BIOME,dimlets);
  List<Pair<DimletKey,List<DimletKey>>> controllerDimlets=DimensionInformation.extractType(DimletType.DIMLET_CONTROLLER,dimlets);
  ControllerType controllerType;
  if (controllerDimlets.isEmpty()) {
    if (random.nextFloat() < DimletConfiguration.randomControllerChance) {
      List<DimletKey> keys=new ArrayList<DimletKey>(DimletObjectMapping.idToControllerType.keySet());
      DimletKey key=keys.get(random.nextInt(keys.size()));
      controllerType=DimletObjectMapping.idToControllerType.get(key);
    }
 else {
      if (biomeDimlets.isEmpty()) {
        controllerType=ControllerType.CONTROLLER_DEFAULT;
      }
 else       if (biomeDimlets.size() > 1) {
        controllerType=ControllerType.CONTROLLER_FILTERED;
      }
 else {
        controllerType=ControllerType.CONTROLLER_SINGLE;
      }
    }
  }
 else {
    DimletKey key=controllerDimlets.get(random.nextInt(controllerDimlets.size())).getLeft();
    controllerType=DimletObjectMapping.idToControllerType.get(key);
  }
  dimensionInformation.setControllerType(controllerType);
  for (  Pair<DimletKey,List<DimletKey>> dimletWithModifiers : biomeDimlets) {
    DimletKey key=dimletWithModifiers.getKey();
    biomeKeys.add(key);
  }
  int neededBiomes=controllerType.getNeededBiomes();
  if (neededBiomes == -1) {
    if (biomeKeys.size() >= 2) {
      neededBiomes=biomeKeys.size();
    }
 else {
      neededBiomes=random.nextInt(10) + 3;
    }
  }
  while (biomeKeys.size() < neededBiomes) {
    DimletKey key;
    List<DimletKey> keys=new ArrayList<DimletKey>(DimletObjectMapping.idToBiome.keySet());
    key=keys.get(random.nextInt(keys.size()));
    while (biomeKeys.contains(key)) {
      key=keys.get(random.nextInt(keys.size()));
    }
    biomeKeys.add(key);
  }
  List<BiomeGenBase> biomes=dimensionInformation.getBiomes();
  biomes.clear();
  for (  DimletKey key : biomeKeys) {
    biomes.add(DimletObjectMapping.idToBiome.get(key));
  }
}