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Thank you for your answers, they brought me on the right track.

I solved it in via the creation of a secondary workspace, just for my code and augmenting the turtlebot code before using it in my application. With this i have two working workspaces and can source them independently, also I can have my workspace tidy by applying structure. Now I have sub-packages in parallel as required but I have one my_sim_bringup, for the applications start sequence and in the same style my_sim_gazebo, my_sim_robots, my_sim_slam for each aspect of the project.