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When you update your source based ROS installation it won't overwrite your changes, at worst you would have to merge the changed files manually if there are any conflicts. But things like CMakeList doesn't change very often. Another thing to do is submit patches to package maintainers, so that your changes can be integrated and whenever next version is released it will just work out of the box.

When you update your source based ROS installation it won't overwrite your changes, at worst you would have to merge the changed files manually if there are any conflicts. conflicts (see rosinstall documentation). But things like CMakeList doesn't change very often. Another thing to do is submit patches to package maintainers, so that your changes can be integrated and whenever next version is released it will just work out of the box.