Installing the Arduino IDE on the Raspberry Pi allows you to program your Arduino fro the Pi. The normal instructions require you to use apt- get, but this installs an old version. Whitewitch has uploaded a script on GitHub to upload the latest Arduino IDE (August 2014).
Once you have finished installation you are asked if you want to add a desktop shortcut, the Arduino Is connected to the Raspberry Pi via the USB lead. I found that i had to set the port to /dev/ttyACMO in the Tools/Serial Port tab. To try the system out compile and upload Blink.
Many thanks to whitewitch for this.