Program: 11773
Project: 11773
Buggy source:
public void paint(){
  if (terrainPopulated == 0x01) {
    return;
  }
  for (int i=location.x() - 1; i < location.x() + 1; i++) {
    for (int j=location.z() - 1; j < location.z() + 1; j++) {
      rawChunk(ChunkLocation.create(i,j));
    }
  }
  List<AbstractOverlayBrush> brushes=world.loader().brushes();
  AbstractOverlayBrush.ChunkManipulator manipulator=new AbstractOverlayBrush.ChunkManipulator(){
    private final MassChange change=new ThreadSafeChange(world);
    @Override public void manipulate(    int relX,    int y,    int relZ,    Substance substance,    byte data){
      if (relX >= 0 && relX <= 15 && relZ >= 0 && relZ <= 15) {
        setAt(relX,y,relZ,substance,data,(byte)255,(byte)15);
        return;
      }
      int cx=location.x();
      int cz=location.z();
      int xMinDiff=Math.max(relX,0) - Math.min(relX,0);
      int xMaxDiff=Math.max(relX,15) - Math.min(relX,15);
      int zMinDiff=Math.max(relZ,0) - Math.min(relZ,0);
      int zMaxDiff=Math.max(relZ,15) - Math.min(relZ,15);
      if (relX < 0 && relZ > 15) {
        ChunkLocation loc=ChunkLocation.create(cx - up(xMinDiff / 16),cz + up(zMaxDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        TridentLogger.get().debug(relX + "String_Node_Str" + relZ+ "String_Node_Str"+ xMinDiff+ "String_Node_Str"+ xMaxDiff+ "String_Node_Str"+ zMinDiff+ "String_Node_Str"+ zMaxDiff+ "String_Node_Str"+ (16 - xMinDiff)+ "String_Node_Str"+ (zMaxDiff - 1));
        chunk.setAndSend(16 - xMinDiff,y,zMaxDiff - 1,substance,data,(byte)255,(byte)15,change);
      }
 else       if (relX > 15 && relZ > 15) {
        ChunkLocation loc=ChunkLocation.create(cx + up(xMaxDiff / 16),cz + up(zMaxDiff / 16));
        TridentLogger.get().debug(relX + "String_Node_Str" + relZ+ "String_Node_Str"+ xMinDiff+ "String_Node_Str"+ xMaxDiff+ "String_Node_Str"+ zMinDiff+ "String_Node_Str"+ zMaxDiff+ "String_Node_Str"+ (xMaxDiff - 1)+ "String_Node_Str"+ (zMaxDiff - 1));
        TridentChunk chunk=rawChunk(loc);
        chunk.setAndSend(xMaxDiff - 1,y,zMaxDiff - 1,substance,data,(byte)255,(byte)15,change);
      }
 else       if (relX < 0 && relZ < 0) {
        ChunkLocation loc=ChunkLocation.create(cx - up(xMinDiff / 16),cz - up(zMinDiff / 16));
        TridentLogger.get().debug(relX + "String_Node_Str" + relZ+ "String_Node_Str"+ xMinDiff+ "String_Node_Str"+ xMaxDiff+ "String_Node_Str"+ zMinDiff+ "String_Node_Str"+ zMaxDiff+ "String_Node_Str"+ (16 - xMinDiff)+ "String_Node_Str"+ (16 - zMinDiff));
        TridentChunk chunk=rawChunk(loc);
        chunk.setAndSend(16 - xMinDiff,y,16 - zMinDiff,substance,data,(byte)255,(byte)15,change);
      }
 else       if (relX > 15 && relZ < 0) {
        ChunkLocation loc=ChunkLocation.create(cx + up(xMaxDiff / 16),cz - up(zMinDiff / 16));
        TridentLogger.get().debug(relX + "String_Node_Str" + relZ+ "String_Node_Str"+ xMinDiff+ "String_Node_Str"+ xMaxDiff+ "String_Node_Str"+ zMinDiff+ "String_Node_Str"+ zMaxDiff+ "String_Node_Str"+ (xMaxDiff - 1)+ "String_Node_Str"+ (16 - zMinDiff));
        TridentChunk chunk=rawChunk(loc);
        chunk.setAndSend(xMaxDiff - 1,y,16 - zMinDiff,substance,data,(byte)255,(byte)15,change);
      }
    }
    @Override public Block blockAt(    int relX,    int y,    int relZ){
      if (y == Integer.MAX_VALUE) {
        change.commitChanges();
        return null;
      }
      if (relX >= 0 && relX <= 15 && relZ >= 0 && relZ <= 15) {
        return TridentChunk.this.blockAt(relX,y,relZ);
      }
      int cx=location.x();
      int cz=location.z();
      int xMinDiff=Math.max(relX,0) - Math.min(relX,0);
      int xMaxDiff=Math.max(relX,15) - Math.min(relX,15);
      int zMinDiff=Math.max(relZ,0) - Math.min(relZ,0);
      int zMaxDiff=Math.max(relZ,15) - Math.min(relZ,15);
      if (relX < 0 && relZ > 15) {
        ChunkLocation loc=ChunkLocation.create(cx - up(xMinDiff / 16),cz + up(zMaxDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        return chunk.blockAt(16 - xMinDiff,y,zMaxDiff - 1);
      }
 else       if (relX > 15 && relZ > 15) {
        ChunkLocation loc=ChunkLocation.create(cx + up(xMaxDiff / 16),cz + up(zMaxDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        return chunk.blockAt(xMaxDiff - 1,y,zMaxDiff - 1);
      }
 else       if (relX < 0 && relZ < 0) {
        ChunkLocation loc=ChunkLocation.create(cx - up(xMinDiff / 16),cz - up(zMinDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        return chunk.blockAt(16 - xMinDiff,y,16 - zMinDiff);
      }
 else       if (relX > 15 && relZ < 0) {
        ChunkLocation loc=ChunkLocation.create(cx + up(xMaxDiff / 16),cz - up(zMinDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        return chunk.blockAt(xMaxDiff - 1,y,16 - zMinDiff);
      }
      return null;
    }
  }
;
  CountDownLatch latch=new CountDownLatch(256);
  for (int i=0; i < 16; i++) {
    final int finalI=i;
    executor.execute(() -> {
      for (int j=0; j < 16; j++) {
        for (        AbstractOverlayBrush brush : brushes) {
          brush.brush(location,finalI,j,world.random(),heights,manipulator);
          latch.countDown();
        }
      }
    }
);
  }
  manipulator.blockAt(0,Integer.MAX_VALUE,0);
  terrainPopulated=0x01;
  try {
    latch.await();
  }
 catch (  InterruptedException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
public void paint(){
  if (terrainPopulated == 0x01) {
    return;
  }
  for (int i=location.x() - 1; i <= location.x() + 1; i++) {
    for (int j=location.z() - 1; j <= location.z() + 1; j++) {
      rawChunk(ChunkLocation.create(i,j));
    }
  }
  List<AbstractOverlayBrush> brushes=world.loader().brushes();
  AbstractOverlayBrush.ChunkManipulator manipulator=new AbstractOverlayBrush.ChunkManipulator(){
    private final MassChange change=new ThreadSafeChange(world);
    @Override public void manipulate(    int relX,    int y,    int relZ,    Substance substance,    byte data){
      if (relX >= 0 && relX <= 15 && relZ >= 0 && relZ <= 15) {
        setAt(relX,y,relZ,substance,data,(byte)255,(byte)15);
        return;
      }
      int cx=location.x();
      int cz=location.z();
      int xMinDiff=Math.max(relX,0) - Math.min(relX,0);
      int xMaxDiff=Math.max(relX,15) - Math.min(relX,15);
      int zMinDiff=Math.max(relZ,0) - Math.min(relZ,0);
      int zMaxDiff=Math.max(relZ,15) - Math.min(relZ,15);
      int chunkX=location.x();
      int chunkZ=location.z();
      int newX=relX;
      int newZ=relZ;
      if (relX < 0) {
        newX=16 - xMinDiff;
        chunkX=cx - up(xMinDiff / 16) - 1;
      }
 else       if (relX > 15) {
        newX=xMaxDiff - 1;
        chunkX=cx + up(xMaxDiff / 16) + 1;
      }
      if (relZ < 0) {
        newZ=16 - zMinDiff;
        chunkZ=cz - up(zMinDiff / 16) - 1;
      }
 else       if (relZ > 15) {
        newZ=zMaxDiff - 1;
        chunkZ=cz + up(zMaxDiff / 16) + 1;
      }
      ChunkLocation loc=ChunkLocation.create(chunkX,chunkZ);
      TridentChunk chunk=rawChunk(loc);
      TridentLogger.get().debug(relX + "String_Node_Str" + relZ+ "String_Node_Str"+ xMinDiff+ "String_Node_Str"+ xMaxDiff+ "String_Node_Str"+ zMinDiff+ "String_Node_Str"+ zMaxDiff+ "String_Node_Str"+ newX+ "String_Node_Str"+ newZ);
      chunk.setAndSend(newX,y,newZ,substance,data,(byte)255,(byte)15,change);
    }
    @Override public Block blockAt(    int relX,    int y,    int relZ){
      if (y == Integer.MAX_VALUE) {
        change.commitChanges();
        return null;
      }
      if (relX >= 0 && relX <= 15 && relZ >= 0 && relZ <= 15) {
        return TridentChunk.this.blockAt(relX,y,relZ);
      }
      int cx=location.x();
      int cz=location.z();
      int xMinDiff=Math.max(relX,0) - Math.min(relX,0);
      int xMaxDiff=Math.max(relX,15) - Math.min(relX,15);
      int zMinDiff=Math.max(relZ,0) - Math.min(relZ,0);
      int zMaxDiff=Math.max(relZ,15) - Math.min(relZ,15);
      if (relX < 0 && relZ > 15) {
        ChunkLocation loc=ChunkLocation.create(cx - up(xMinDiff / 16),cz + up(zMaxDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        return chunk.blockAt(16 - xMinDiff,y,zMaxDiff - 1);
      }
 else       if (relX > 15 && relZ > 15) {
        ChunkLocation loc=ChunkLocation.create(cx + up(xMaxDiff / 16),cz + up(zMaxDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        return chunk.blockAt(xMaxDiff - 1,y,zMaxDiff - 1);
      }
 else       if (relX < 0 && relZ < 0) {
        ChunkLocation loc=ChunkLocation.create(cx - up(xMinDiff / 16),cz - up(zMinDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        return chunk.blockAt(16 - xMinDiff,y,16 - zMinDiff);
      }
 else       if (relX > 15 && relZ < 0) {
        ChunkLocation loc=ChunkLocation.create(cx + up(xMaxDiff / 16),cz - up(zMinDiff / 16));
        TridentChunk chunk=rawChunk(loc);
        return chunk.blockAt(xMaxDiff - 1,y,16 - zMinDiff);
      }
      return null;
    }
  }
;
  CountDownLatch latch=new CountDownLatch(256);
  for (int i=0; i < 16; i++) {
    final int finalI=i;
    executor.execute(() -> {
      for (int j=0; j < 16; j++) {
        for (        AbstractOverlayBrush brush : brushes) {
          brush.brush(location,finalI,j,world.random(),heights,manipulator);
          latch.countDown();
        }
      }
    }
);
  }
  manipulator.blockAt(0,Integer.MAX_VALUE,0);
  terrainPopulated=0x01;
  try {
    latch.await();
  }
 catch (  InterruptedException e) {
    e.printStackTrace();
  }
}