The idea was that when they check code into their continuous integration system (see defunkt/CI Joe) the stoplight would turn yellow while the code was building, red if the build failed because of failing tests, and green if the build succeeded. It would give them a large unmissable indicator in their office for the status of their current code.
One of the GitHub founders, PJ Hyett played around with using an Arduino to integrate with the continuous integration server. He wrote a ruby script that polled the server and then sent a serial message to an Arduino which turned on an appropriate green, yellow, or red LED.
This worked, but had a couple of downsides: first it required a laptop to be connected to the Arduino to talk to the CI server; second it only lit up little LEDs rather than the big beautiful stoplight. For good reason, as a beginner PJ balked at the idea of controlling the AC power needed by the stoplight.