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Usually one does not write new nodes or code in the /opt/ros/<distro_release>/stacks/ area, but rather somewhere on the system when permissions are not an issue, e.g in the /home/<user>/, then you can let ros know of these packages but just doing export ROS_PACKAGE_PATH=$ROS_PACKAGE_PATH:<path_to_own_packages>. For version control, say git one can then easily set up using git init in the say /home/<user>/packages directory.