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We're using the object manipulation stack with our robots. If you want to have a look at how we did that it is available on Launchpad (still in development so it's quite hard to install it etc...).

Regarding changing the IK for object manipulator, you should have a look at the file manipulator.launch. The object_manipulator node is commented out as we're not using it anymore (we replaced it by a simpler node in sr_pick_and_place), but the syntax for calling the IK for our arm is there (all the remaps). The IK solver was generated using the arm_navigation wizard.

Hope this helps.