There is a whole lot of information on the internet about using the Arduino with Eclipse on Xubuntu 10.04 LTS, much of it out of date. Here I document my experience in the hope that this process becomes more smooth.
I followed documentation from a couple of very key people, which helped a lot. Still, there are certain issues that threw me off. I have added my experiences where I had issues. The Arduino IDE is the standard method to connect to and program the Arduino. It is simple to use. If you want a more rich programming environment you can also use Eclipse, with the Arduino plugin. Either method can be used to program and run the Arduino. Here are the steps: