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The Boot loader for the arduino is simply a program that is on the arduino micro controller that allows us to flash the chip without having to use an external flashing device.

You can not overwrite the boot loader with your program because it it is stored in a special section of memory where you can only access with an external flasher.

The bootl oader pulses a signal on pin 13, so to see if there is a boot loader on the chip and it is working, all you have to do is hook an LED up to pin 13 and see if it flashes. If it does, it is already on the chip.