Program: 107690
Project: 107690
Buggy source:
/** 
 * Uploads a binary file to a device on background process.
 * @param board board profile e.g. Boards.ARDUINO_UNO
 * @param filePath a binary file path e.g. /sdcard/arduino/Blink.hex
 * @param callback
 * @return true: success, false: fail
 * @throws RuntimeException
 */
public void upload(Boards board,String filePath,UploadCallBack callback) throws RuntimeException {
  mUploader=new Uploader();
  mCallBack=callback;
  mFilePath=filePath;
  mBoard=board;
  new Thread(new Runnable(){
    @Override public void run(){
      boolean cleanAfter=false;
      UartConfig tmpUartConfig=new UartConfig();
      if (mSerial == null) {
        mSerial=new AutoCommunicator().getSerialCommunicator(mContext);
        if (!mSerial.open()) {
          if (mCallBack != null) {
            mCallBack.onError(UploadErrors.OPEN_DEVICE);
          }
          mBoard=null;
          mFilePath=null;
          mCallBack=null;
          mUploader=null;
          mSerial=null;
          return;
        }
 else {
          cleanAfter=true;
        }
      }
 else {
synchronized (mSerial) {
          tmpUartConfig=mSerial.getUartConfig();
        }
      }
synchronized (mSerial) {
        mUploader.upload(mFilePath,mBoard,mSerial,mCallBack);
        mSerial.setUartConfig(tmpUartConfig);
        if (cleanAfter) {
          mSerial.close();
          mSerial=null;
        }
      }
      mBoard=null;
      mFilePath=null;
      mCallBack=null;
      mUploader=null;
    }
  }
).start();
}

Fixed version (ground truth):
/** 
 * Uploads a binary file to a device on background process.
 * @param board board profile e.g. Boards.ARDUINO_UNO
 * @param filePath a binary file path e.g. /sdcard/arduino/Blink.hex
 * @param callback
 * @return true: success, false: fail
 * @throws RuntimeException
 */
public void upload(Boards board,String filePath,UploadCallBack callback) throws RuntimeException {
  mUploader=new Uploader();
  mCallBack=callback;
  mFilePath=filePath;
  mBoard=board;
  new Thread(new Runnable(){
    @Override public void run(){
      boolean cleanAfter=false;
      UartConfig tmpUartConfig=new UartConfig();
      if (mSerial == null) {
        mSerial=new AutoCommunicator().getSerialCommunicator(mContext);
        if (!mSerial.open()) {
          if (mCallBack != null) {
            mCallBack.onError(UploadErrors.OPEN_DEVICE);
          }
          mBoard=null;
          mFilePath=null;
          mCallBack=null;
          mUploader=null;
          mSerial=null;
          return;
        }
 else {
          cleanAfter=true;
        }
      }
 else {
synchronized (mSerial) {
          UartConfig origUartConfig=mSerial.getUartConfig();
          tmpUartConfig.baudrate=origUartConfig.baudrate;
          tmpUartConfig.dataBits=origUartConfig.dataBits;
          tmpUartConfig.stopBits=origUartConfig.stopBits;
          tmpUartConfig.parity=origUartConfig.parity;
          tmpUartConfig.dtrOn=origUartConfig.dtrOn;
          tmpUartConfig.rtsOn=origUartConfig.rtsOn;
        }
      }
synchronized (mSerial) {
        mSerial.clearBuffer();
        mUploader.upload(mFilePath,mBoard,mSerial,mCallBack);
        mSerial.setUartConfig(tmpUartConfig);
        mSerial.clearBuffer();
        if (cleanAfter) {
          mSerial.close();
          mSerial=null;
        }
      }
      mBoard=null;
      mFilePath=null;
      mCallBack=null;
      mUploader=null;
    }
  }
).start();
}