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You can still set individual link padding using the yaml method - just make sure it's getting loaded in the private namespace when you launch the environment server (or wherever else you are creating a planning_environment::CollisionModels class". The default_robot_padding value is taken from the global namespace under /robot_description_planning/default_robot_padding - if you put it in your <your_robot>_planning_description.yaml using the auto-generated arm navigation app than things should happen correctly.