Since the Raspberry Pi lacks a DTR pin that makes it oh-so-easy to upload your hex files into the avr, we need this hack to make it just as easy. When you wire up your atmega chip, be sure to connect one of the digital gpio pins to the reset pin, and then you'll be able to use avrdude as if your serial cable actually had a dtr pin.
Copy both files into your /usr/bin directory, then rename the original avrdude to avrdude-original and symlink avrdude-autoreset to become avrdude.
cp autoreset /usr/bin
cp avrdude-autoreset /usr/bin
mv /usr/bin/avrdude /usr/bin/avrdude-original
ln -s /usr/bin/avrdude-autoreset /usr/bin/avrdude
Modify the autoreset script to use the pin that you wired up to the reset pin. See the line in autoreset where we do "pin = 11" and change the 11 to your gpio pin number.
Now when you run avrdude from anywhere (including via arduino's normal UI) it will flag dtr when it is about to upload hex data.