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

apt-get install avrdude

Install avrdude-rpi using the installation tips from https://github.com/deanmao/avrdude-rpi they boil down to this:

wget https://raw.githubusercontent.com/deanmao/avrdude-rpi/master/autoreset
wget https://raw.githubusercontent.com/deanmao/avrdude-rpi/master/avrdude-autoreset
sudo cp autoreset /usr/bin
sudo cp avrdude-autoreset /usr/bin
sudo mv /usr/bin/avrdude /usr/bin/avrdude-original
sudo ln -s /usr/bin/avrdude-autoreset /usr/bin/avrdude

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.

vim /usr/bin/autoreset

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

cd /Applications/Arduino.app/Contents/Resources/Java/hardware/tools/avr/bin
mv avrdude avrdude-original
wget https://gist.githubusercontent.com/erikkallen/11153072/raw/3e1cdfdef6aee12b9f0f47b50bc33849612f2a0d/avrdude
chmod +x avrdude