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The order of sourcing multiple setup files does not matter. Since the last one will overwrite all environment variables anyway.

What does matter is the environment you used when creating these workspaces. At the initial configure time the current environment (basically the CMAKE_PREFIX_PATH defining the already sourced workspaces which you want to overlay) is extended with the environment for this new workspace.

You can not overlay my_catkin_ws and my_other_catkin_ws by just sourcing both setup files if they been created independently in the first place.