Hey Eric, Here are the commands I used to program my arduino.

 avr-gcc -Os -DF_CPU=16000000UL -mmcu=atmega2560 -o blink.out blink.c
 avr-objcopy -O ihex -R .eeprom blink.out blink.hex
 sudo avrdude -c stk500v2 -p m2560 -P /dev/tty.usbmodem621 -U flash:w:blink.hex
 

 -Dan