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The easiest way is to do a local (in ~/ros, for example) checkout of a the source code for a particular package, and then (as noted above) make sure it appears before /opt/ros/... in your ROS_PACKAGE_PATH.

But this is not going to generalize well, particularly if you want to distribute your code, because then everybody's going to need your patched version of move_base (or whatever).

If you're finding bugs, send them to the maintainers. Otherwise, a formal fork is going to be a better choice.