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If you source the workspace containing your modified controller_manager package, it should prefer your modified version over the system version.

You can verify that it's set up properly by inspecting the LD_LIBRARY_PATH variable, and running ldd on your node to see the exact paths of the dynamic libraries that it's using.

If something isn't right, DON'T MODIFY LD_LIBRARY_PATH directly; instead, check to make sure that you've built and sourced your catkin workspace properly.

The reason that you shouldn't modify LD_LIBRARY_PATH is because it's only one of the many variables that are set by the setup scripts, and if isn't set correctly, chances are the other environment variables aren't set correctly either. Sorting out your workspace and which setup file to use will be a far more robust solution.