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It is advised not to do this because every update to the ROS stacks will wipe your changes. If you need to make modifications to the ROS stacks, it's generally advised that you check out the source from SVN so that you have control over all updates to the stack.
For the pr2_mechanism_model, you could check out the stack with:
hg clone https://kforge.ros.org/pr2mechanism/hg
(you must have Mercurial installed to do this. sudo apt-get install mercurial).
This is the generally accepted method for making modifications to ROS stacks.
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