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These setup.bash files setup your environment variables and paths. When first setting up your workspace, you need to have sourced /opt/ros/distro/setup.bash. After you have a workspace and have run catkin_make, there will be a new setup file found in <workspace>/devel/setup.bash or, if you ran catkin_make with install, <workspace>/install/setup.bash. To have your workspace be part of your paths/environment, you need to use these new setup.bash files (which will effectively already include all the paths and environment variables found in the one in /opt/ros since they were part of the environment when you created the workspace)