The processing.app.debug.AvrdudeUploader flushes the serial buffer on line 93. This is a call to the flushSerialBuffer() method in processing.app.debug.Uploader. As far as I can see, this method doesn't actually do anything. There is a while loop in it that reads data from the serial port while data is available. The problem with this loop is that the processing.app.Serial#available() method will always return 0, since the processing.app.Serial#serialEvent method never writes anything to the buffer: this method only reads data when either monitor == true or consumer != null (which both aren't the case). Even if either of them were true, the method still wouldn't write anything to the buffer.
Looks to me like a potential bug, or am I missing something?