How do I update from the Fuerte Gazebo release to version 1.3

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You can still follow the instructions, it won't change your ROS files. The only reason why ROS users are told to use the ROS package is that Gazebo itself is standalone and hence does not offer all the ROS plugins that are part of the simulator_gazebo stack and you might run into issues when trying to run old code/models.

Updated plugins that work with Gazebo 1.3 are part of the drcsim package which you can install additionally (i.e. simply follow the full drcsim install instructions). For launching gazebo within your launch file you'll then have to switch to the standalone executable instead of the gazebo inside the ros package (e.g. use the run_gazebo script in atlas_utils which starts gazebo with the ros api plugin loaded).