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Hmm... I just did a rosinstall update. My changes seems to be intact so far.
I thought my changes are erased, because my changes to setup.sh were gone after an update. The documentation does indicate that setup.sh is re-generated...

Most of the changes I am making are to make ROS packages compile with gcc-4.6. I have submitted patches to https://code.ros.org/trac/ros-pkg/, though nothing seems to be happening with them.

Other changes I had to make are due to locations of header files, which are system specific, so I doubt the package maintainers would want them.

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