Program: 97819
Project: 97819
Buggy source:
@SuppressWarnings("String_Node_Str") private void stencilSave(final SnipeData v){
  final File file=new File("String_Node_Str" + this.filename + "String_Node_Str");
  try {
    this.x=(short)(Math.abs((this.firstPoint[0] - this.secondPoint[0])) + 1);
    this.z=(short)(Math.abs((this.firstPoint[1] - this.secondPoint[1])) + 1);
    this.y=(short)(Math.abs((this.firstPoint[2] - this.secondPoint[2])) + 1);
    this.xRef=(short)((this.firstPoint[0] > this.secondPoint[0]) ? (this.pastePoint[0] - this.secondPoint[0]) : (this.pastePoint[0] - this.firstPoint[0]));
    this.zRef=(short)((this.firstPoint[1] > this.secondPoint[1]) ? (this.pastePoint[1] - this.secondPoint[1]) : (this.pastePoint[1] - this.firstPoint[1]));
    this.yRef=(short)((this.firstPoint[2] > this.secondPoint[2]) ? (this.pastePoint[2] - this.secondPoint[2]) : (this.pastePoint[2] - this.firstPoint[2]));
    if ((this.x * this.y * this.z) > 50000) {
      v.sendMessage(ChatColor.AQUA + "String_Node_Str");
      return;
    }
    Files.createParentDirs(file);
    file.createNewFile();
    final DataOutputStream out=new DataOutputStream(new BufferedOutputStream(new FileOutputStream(file)));
    int blockPositionX=(this.firstPoint[0] > this.secondPoint[0]) ? this.secondPoint[0] : this.firstPoint[0];
    int blockPositionZ=(this.firstPoint[1] > this.secondPoint[1]) ? this.secondPoint[1] : this.firstPoint[1];
    int blockPositionY=(this.firstPoint[2] > this.secondPoint[2]) ? this.secondPoint[2] : this.firstPoint[2];
    out.writeShort(this.x);
    out.writeShort(this.z);
    out.writeShort(this.y);
    out.writeShort(this.xRef);
    out.writeShort(this.zRef);
    out.writeShort(this.yRef);
    v.sendMessage(ChatColor.AQUA + "String_Node_Str" + this.x * this.z * this.y + "String_Node_Str" + blockPositionX + "String_Node_Str" + blockPositionZ + "String_Node_Str" + blockPositionY);
    this.blockArray=new byte[this.x * this.z * this.y];
    this.dataArray=new byte[this.x * this.z * this.y];
    this.runSizeArray=new byte[this.x * this.z * this.y];
    byte lastId=(byte)(this.getWorld().getBlockTypeIdAt(blockPositionX,blockPositionY,blockPositionZ) - 128);
    byte lastData=(byte)(this.clampY(blockPositionX,blockPositionY,blockPositionZ).getData() - 128);
    byte thisId;
    byte thisData;
    int counter=0;
    int arrayIndex=0;
    for (int y=0; y < this.y; y++) {
      for (int z=0; z < this.z; z++) {
        for (int x=0; x < this.x; x++) {
          Block currentBlock=getWorld().getBlockAt(blockPositionX + x,blockPositionY + y,blockPositionZ + z);
          thisId=(byte)(currentBlock.getTypeId() - 128);
          thisData=(byte)(currentBlock.getData() - 128);
          if (thisId != lastId || thisData != lastData || counter == 255) {
            this.blockArray[arrayIndex]=lastId;
            this.dataArray[arrayIndex]=lastData;
            this.runSizeArray[arrayIndex]=(byte)(counter - 128);
            arrayIndex++;
            counter=1;
            lastId=thisId;
            lastData=thisData;
          }
 else {
            counter++;
            lastId=thisId;
            lastData=thisData;
          }
        }
      }
    }
    this.blockArray[arrayIndex]=lastId;
    this.dataArray[arrayIndex]=lastData;
    this.runSizeArray[arrayIndex]=(byte)(counter - 128);
    out.writeInt(arrayIndex);
    for (int i=0; i < arrayIndex + 1; i++) {
      if (this.runSizeArray[i] > -127) {
        out.writeBoolean(true);
        out.writeByte(this.runSizeArray[i]);
        out.writeByte(this.blockArray[i]);
        out.writeByte(this.dataArray[i]);
      }
 else {
        out.writeBoolean(false);
        out.writeByte(this.blockArray[i]);
        out.writeByte(this.dataArray[i]);
      }
    }
    v.sendMessage(ChatColor.BLUE + "String_Node_Str" + this.filename+ "String_Node_Str");
    out.close();
  }
 catch (  final Exception exception) {
    v.sendMessage(ChatColor.RED + "String_Node_Str");
    exception.printStackTrace();
  }
}

Fixed version (ground truth):
@SuppressWarnings("String_Node_Str") private void stencilSave(final SnipeData v){
  final File file=new File("String_Node_Str" + this.filename + "String_Node_Str");
  try {
    this.x=(short)(Math.abs((this.firstPoint[0] - this.secondPoint[0])) + 1);
    this.z=(short)(Math.abs((this.firstPoint[1] - this.secondPoint[1])) + 1);
    this.y=(short)(Math.abs((this.firstPoint[2] - this.secondPoint[2])) + 1);
    this.xRef=(short)((this.firstPoint[0] > this.secondPoint[0]) ? (this.pastePoint[0] - this.secondPoint[0]) : (this.pastePoint[0] - this.firstPoint[0]));
    this.zRef=(short)((this.firstPoint[1] > this.secondPoint[1]) ? (this.pastePoint[1] - this.secondPoint[1]) : (this.pastePoint[1] - this.firstPoint[1]));
    this.yRef=(short)((this.firstPoint[2] > this.secondPoint[2]) ? (this.pastePoint[2] - this.secondPoint[2]) : (this.pastePoint[2] - this.firstPoint[2]));
    if ((this.x * this.y * this.z) > 50000) {
      v.sendMessage(ChatColor.AQUA + "String_Node_Str");
      return;
    }
    Files.createParentDirs(file);
    file.createNewFile();
    final DataOutputStream out=new DataOutputStream(new BufferedOutputStream(new FileOutputStream(file)));
    int blockPositionX=(this.firstPoint[0] > this.secondPoint[0]) ? this.secondPoint[0] : this.firstPoint[0];
    int blockPositionZ=(this.firstPoint[1] > this.secondPoint[1]) ? this.secondPoint[1] : this.firstPoint[1];
    int blockPositionY=(this.firstPoint[2] > this.secondPoint[2]) ? this.secondPoint[2] : this.firstPoint[2];
    out.writeShort(this.x);
    out.writeShort(this.z);
    out.writeShort(this.y);
    out.writeShort(this.xRef);
    out.writeShort(this.zRef);
    out.writeShort(this.yRef);
    v.sendMessage(ChatColor.AQUA + "String_Node_Str" + this.x * this.z * this.y + "String_Node_Str" + blockPositionX + "String_Node_Str" + blockPositionZ + "String_Node_Str" + blockPositionY);
    this.blockArray=new byte[this.x * this.z * this.y];
    this.dataArray=new byte[this.x * this.z * this.y];
    this.runSizeArray=new byte[this.x * this.z * this.y];
    byte lastId=(byte)(this.getWorld().getBlockTypeIdAt(blockPositionX,blockPositionY,blockPositionZ) - 128);
    byte lastData=(byte)(this.clampY(blockPositionX,blockPositionY,blockPositionZ).getData() - 128);
    byte thisId;
    byte thisData;
    int counter=0;
    int arrayIndex=0;
    for (int y=0; y < this.y; y++) {
      for (int z=0; z < this.z; z++) {
        for (int x=0; x < this.x; x++) {
          Block currentBlock=getWorld().getBlockAt(blockPositionX + x,blockPositionY + y,blockPositionZ + z);
          thisId=(byte)(currentBlock.getTypeId() - 128);
          thisData=(byte)(currentBlock.getData() - 128);
          if (thisId != lastId || thisData != lastData || counter == 255) {
            this.blockArray[arrayIndex]=lastId;
            this.dataArray[arrayIndex]=lastData;
            this.runSizeArray[arrayIndex]=(byte)(counter - 128);
            arrayIndex++;
            counter=1;
            lastId=thisId;
            lastData=thisData;
          }
 else {
            counter++;
            lastId=thisId;
            lastData=thisData;
          }
        }
      }
    }
    this.blockArray[arrayIndex]=lastId;
    this.dataArray[arrayIndex]=lastData;
    this.runSizeArray[arrayIndex]=(byte)(counter - 128);
    out.writeInt(arrayIndex + 1);
    for (int i=0; i < arrayIndex + 1; i++) {
      if (this.runSizeArray[i] > -127) {
        out.writeBoolean(true);
        out.writeByte(this.runSizeArray[i]);
        out.writeByte(this.blockArray[i]);
        out.writeByte(this.dataArray[i]);
      }
 else {
        out.writeBoolean(false);
        out.writeByte(this.blockArray[i]);
        out.writeByte(this.dataArray[i]);
      }
    }
    v.sendMessage(ChatColor.BLUE + "String_Node_Str" + this.filename+ "String_Node_Str");
    out.close();
  }
 catch (  final Exception exception) {
    v.sendMessage(ChatColor.RED + "String_Node_Str");
    exception.printStackTrace();
  }
}