Replace HardwareSerial.cpp in the Arduino installation folder with the modified version you downloaded. In older versions of the Arduino IDE(1.0.x) this is located at {Arduino IDE installation folder}/hardware/arduino/cores/arduino, in newer versions of the Arduino IDE(1.5 and greater) it is located at {Arduino IDE installation folder}/hardware/arduino/avr/cores/arduino
The modified file is 2 years old so there's a possibility it won't work with newer versions of the Arduino IDE so give it a try and then if there's an issue you can try it with older IDE versions or merge Buoni's modifications(https://github.com/Bouni/Arduino/commit/c555624cb8138c4b4e0cce2820e21bf6e9326d5f) with the current HardwareSerial.cpp.
Thanks for your advice; with your help I sorted it out.
The new files works well for 1.6.9
I thought I was smart putting some old and the original library files in a subfolder to the libraryfolder.
This messed up everything when trying to compile the sketch.
After moving the subfolder to another location away from arduino folders every worked fine.