Program: 134255
Project: 134255
Buggy source:
@Override public void transformBlock(World world,Random random,Phase phase,BlockCoord coord,Block sourceBlock,int sourceMetadata){
  BiomeGenBase biome=world.getBiomeGenForCoords(coord.x,coord.z);
  Block topBlock=biome.topBlock;
  Block fillerBlock=biome.fillerBlock;
  Block mainBlock=world.provider.dimensionId == -1 ? Blocks.netherrack : (world.provider.dimensionId == 1 ? Blocks.end_stone : Blocks.stone);
  boolean useStoneBlock=hasBlockAbove(world,coord.x,coord.y,coord.z,mainBlock);
  if (phase == Phase.BEFORE) {
    int currentY=coord.y;
    List<int[]> currentList=new ArrayList<>();
    List<int[]> nextList=new ArrayList<>();
    nextList.add(new int[]{coord.x,coord.z});
    while (nextList.size() > 0 && currentY > 1) {
      List<int[]> cachedList=currentList;
      currentList=nextList;
      nextList=cachedList;
      while (currentList.size() > 0) {
        int[] currentPos=currentList.remove(0);
        int currentX=currentPos[0];
        int currentZ=currentPos[1];
        Block curBlock=world.getBlock(currentX,currentY,currentZ);
        boolean replaceable=currentY == coord.y || curBlock.isReplaceable(world,currentX,currentY,currentZ);
        if (replaceable) {
          Block setBlock=useStoneBlock ? mainBlock : (isTopBlock(world,currentX,currentY,currentZ) ? topBlock : fillerBlock);
          world.setBlock(currentX,currentY,currentZ,setBlock);
        }
        if (replaceable) {
          double yForDistance=coord.y * 0.3 + currentY * 0.7;
          double distToOrigSQ=IvVecMathHelper.distanceSQ(new double[]{coord.x,coord.y,coord.z},new double[]{currentX,yForDistance,currentZ});
          double add=(random.nextDouble() - random.nextDouble()) * NATURAL_DISTANCE_RANDOMIZATION;
          distToOrigSQ+=add < 0 ? -(add * add) : (add * add);
          if (distToOrigSQ < NATURAL_EXPANSION_DISTANCE * NATURAL_EXPANSION_DISTANCE) {
            addIfNew(nextList,currentX,currentZ);
            addIfNew(nextList,currentX - 1,currentZ);
            addIfNew(nextList,currentX + 1,currentZ);
            addIfNew(nextList,currentX,currentZ - 1);
            addIfNew(nextList,currentX,currentZ + 1);
          }
        }
      }
      currentY--;
    }
  }
 else {
    Block setBlock=useStoneBlock ? mainBlock : (isTopBlock(world,coord.x,coord.y,coord.z) ? topBlock : fillerBlock);
    world.setBlock(coord.x,coord.y,coord.z,setBlock);
  }
}

Fixed version (ground truth):
@Override public void transformBlock(World world,Random random,Phase phase,BlockCoord coord,Block sourceBlock,int sourceMetadata){
  BiomeGenBase biome=world.getBiomeGenForCoords(coord.x,coord.z);
  Block topBlock=biome.topBlock != null ? biome.topBlock : Blocks.air;
  Block fillerBlock=biome.fillerBlock != null ? biome.fillerBlock : Blocks.air;
  Block mainBlock=world.provider.dimensionId == -1 ? Blocks.netherrack : (world.provider.dimensionId == 1 ? Blocks.end_stone : Blocks.stone);
  boolean useStoneBlock=hasBlockAbove(world,coord.x,coord.y,coord.z,mainBlock);
  if (phase == Phase.BEFORE) {
    int currentY=coord.y;
    List<int[]> currentList=new ArrayList<>();
    List<int[]> nextList=new ArrayList<>();
    nextList.add(new int[]{coord.x,coord.z});
    while (nextList.size() > 0 && currentY > 1) {
      List<int[]> cachedList=currentList;
      currentList=nextList;
      nextList=cachedList;
      while (currentList.size() > 0) {
        int[] currentPos=currentList.remove(0);
        int currentX=currentPos[0];
        int currentZ=currentPos[1];
        Block curBlock=world.getBlock(currentX,currentY,currentZ);
        boolean replaceable=currentY == coord.y || curBlock.isReplaceable(world,currentX,currentY,currentZ);
        if (replaceable) {
          Block setBlock=useStoneBlock ? mainBlock : (isTopBlock(world,currentX,currentY,currentZ) ? topBlock : fillerBlock);
          world.setBlock(currentX,currentY,currentZ,setBlock);
        }
        if (replaceable) {
          double yForDistance=coord.y * 0.3 + currentY * 0.7;
          double distToOrigSQ=IvVecMathHelper.distanceSQ(new double[]{coord.x,coord.y,coord.z},new double[]{currentX,yForDistance,currentZ});
          double add=(random.nextDouble() - random.nextDouble()) * NATURAL_DISTANCE_RANDOMIZATION;
          distToOrigSQ+=add < 0 ? -(add * add) : (add * add);
          if (distToOrigSQ < NATURAL_EXPANSION_DISTANCE * NATURAL_EXPANSION_DISTANCE) {
            addIfNew(nextList,currentX,currentZ);
            addIfNew(nextList,currentX - 1,currentZ);
            addIfNew(nextList,currentX + 1,currentZ);
            addIfNew(nextList,currentX,currentZ - 1);
            addIfNew(nextList,currentX,currentZ + 1);
          }
        }
      }
      currentY--;
    }
  }
 else {
    Block setBlock=useStoneBlock ? mainBlock : (isTopBlock(world,coord.x,coord.y,coord.z) ? topBlock : fillerBlock);
    world.setBlock(coord.x,coord.y,coord.z,setBlock);
  }
}