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There is no "wrong order" here.

The ros_controllers/JointStateController puts joint names and handles in a C++ hash map, which sorts alpabetically.

I am not sure if just the names are switched or the data as well.

Everything is correct.

This code has been in use for the past 6 years at least. I'm going to make an assumption here (which is not always the best idea), but if there would be such a problem as you hint at (ie: names not matching with indices in the other vectors), we would probably have seen countless of bug reports about it.

Can somebody tell me where the publisher for this is defined so I can check?

You may find the code for the JointStateController here: ros-controls/ros_controllers/joint_state_controller/src/joint_state_controller.cpp.

There is no "wrong order" here.

The ros_controllers/JointStateController puts retrieves joint names and handles in from a C++ hash map, which sorts alpabetically.

I am not sure if just the names are switched or the data as well.

Everything is correct.

This code has been in use for the past 6 years at least. I'm going to make an assumption here (which is not always the best idea), but if there would be such a problem as you hint at (ie: names not matching with indices in the other vectors), we would probably have seen countless of bug reports about it.

Can somebody tell me where the publisher for this is defined so I can check?

You may find the code for the JointStateController here: ros-controls/ros_controllers/joint_state_controller/src/joint_state_controller.cpp.