Leonardo: after burning a sketch, remove the magic baud rate to avoid future unwanted board resets #103
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An example of such an unwanted board reset happens if you burn ArduinoISP into a leonardo and subsequently want to use the leonardo to burn a bootloader into another avr chip.
See also: http://arduino.cc/forum/index.php/topic,108270.msg838797.html#msg838797
This is what happens, withou this modification:
It does not use avrdude to do this.
Then you decide to burn a bootloader to your target:
3.The ide makes its first call to avrdude. Again, when avrdude is done, just before it closes the port it sets the speed back to what it was: 1200 baud. Closing the port toggles DTR and the leoardo reboots!