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avrdude

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danselmi:
As obf suggested, you can use the following tool to program the flash:

--- Code: ---Name: AVRDUDE write flash
Executable: C:\tools\avrdude\avrdude.exe
Parameters: -p ${MCU} -c avrftdi -v -U flash:w:$(TARGET_OUTPUT_BASENAME).hex:i
Working direcotry: $(TARGET_OUTPUT_DIR)

--- End code ---
and similar calls to program the eeprom and the fuses.

This is a bad idea:

--- Quote ---burn the controller, each time a AVR project is compiled successfully.
--- End quote ---
Since you are wasting write/erase cycles this way.

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