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I would suggest following the Industrial Ros tutorial for creating a Moveit pkg, linked below. http://wiki.ros.org/Industrial/Tutorials/Create_a_MoveIt_Pkg_for_an_Industrial_Robot

It has you add a Kin. chain for the arms instead of adding joint. This seems to solve the issue of the missing markers. This method is the same way the arms are descriped in the kinematics.yaml that you can download through "sudo apt-get install ros-hydro-moveit-pr2".

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