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In most cases, you should keep the run_depends on the message packages.

If you're building a ROS node in C++ that subscribes or publishes messages of a particular type, you should have a run_depend on that type so that it's available to debugging tools like rostopic that are written in python.

If you're building a C++ library that publishes or subscribes to messages, the same idea applies.

In either case, don't assume that another package will provide the dependency for you; that package may not need it.