This guide will show you how to program an Arduino connected to your Raspberry PI from the Arduino IDE on your local computer. Linux and OS X for now
On your Raspberry PI
First install avrdude
Install avrdude-rpi using the installation tips from https://github.com/deanmao/avrdude-rpi they boil down to this:
Next open the file /usr/bin/autoreset and change the reset pin to the pin you connected the Arduino reset to. The GPIO pin number corresponds to the number of the pin of the header.
On your computer
Download and install Arduino IDE go to the folder containing avrdude On OS X this most likely is /Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/bin