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I finally managed to get this working. I had put many packages in the same catkin workspace, so I started over and included only some basic packages in my initial catkin workspace that contains non-catkin packages. I then created another catkin workspace that contains only catkin packages. By overlaying these workspaces I get "normal" environment variables and I can add new packages using catkin_make. I am not sure how I got into a mess in the first place, but I hope this helps anyone that might have a similar problem!