Squirrels have fuzzy tails.
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Why not just skip the bootloader and use AVRStudio to upload the hex file?
# Arduino 0011 Makefile# Arduino adaptation by mellis, eighthave, oli.keller## This makefile allows you to build sketches from the command line# without the Arduino environment (or Java).## Detailed instructions for using the makefile:## 1. Copy this file into the folder with your sketch. There should be a# file with the extension .pde (e.g. foo.pde)## 2. Below, modify the line containing "TARGET" to refer to the name of# of your program's file without an extension (e.g. TARGET = foo).## 3. Modify the line containg "INSTALL_DIR" to point to the directory that# contains the Arduino installation (for example, under Mac OS X, this# might be /Applications/arduino-0011).## 4. Modify the line containing "PORT" to refer to the filename# representing the USB or serial connection to your Arduino board# (e.g. PORT = /dev/tty.USB0). If the exact name of this file# changes, you can use * as a wildcard (e.g. PORT = /dev/tty.USB*).## 5. Set the line containing "MCU" to match your board's processor. # Older one's are atmega8 based, newer ones like Arduino Mini, Bluetooth# or Diecimila have the atmega168. If you're using a LilyPad Arduino,# change F_CPU to 8000000.## 6. At the command line, change to the directory containing your# program's file and the makefile.## 7. Type "make" and press enter to compile/verify your program.## 8. Type "make upload", reset your Arduino board, and press enter to# upload your program to the Arduino board.## $Id$