For “core” ROS 2 repositories (rclcpp, rclpy, etc), we have a separate repository using the master branch for the most part. This makes sense since these repositories share no code with their ROS 1 counterparts.
Early on in the porting of some of the non-core repositories (pcl_conversions, depthimage_to_laserscan), we forked the repositories into the ros2 organization and did the ports there. But creating separate repositories means it is harder to port changes across, so our recommendation for new ports has been to make a ros2 branch on the upstream repository and do the port there.
We’d like to get to a place where you can host both the ROS 1 and ROS 2 ports of the code on the same branch, but I don’t think we have the documentation and/or pieces in place to do this quite yet. If someone is willing to work on this, though, it would be a great thing for the community to have.