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It seems like you have installed the packages ros-fuerte-arm-navigation and ros-fuerte-moveit-msgs on your computer. The former provides the version in /opt/ros/fuerte/stacks/arm_navigation while the latter provides /opt/ros/fuerte/include/kinematics_msgs.

I would consider this as a bug in the ROS packages and to solve it, I guess you will have to remove one of the two packages from your system. Also, consider filing it at the moveit bug tracker.

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