Personally I cannot stand the arduino IDE for multiple reasons that I could write an essay on and be here for days. However I purchased an Arduino Mega 2560 to do development on a current project of mine that will use an ATmega2560 and plan to program it in C like most MCUs. At first I thought Eclipse CDT was being weird but when I went into cmd and started mucking around with avrdude directly, I found that I cannot get my computer to talk to my arduino board.
Reguardless if I don't specify the baud rate, or use stk500v2 instead of arduino, I cannot get it to even acknowledge the device. The arduino IDE will write sketches no problem.
In the terminal if I try:
avrdude -p atmega2560 -b115200 -c arduino -P COM3
Error: stk500-getsync(): not in sync
<avrdude -p atmega2560 -b115200 -c stk500v2 -P COM3>
Leaving the baud rate out on both lines makes no difference. The Rx on the board will occasionally blink but not like when a sketch from the arduino IDE is being uploaded. I have no clue what I am doing wrong.