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if I stick a CATKIN_IGNORE file into a specific ROS package in my src/ directory, will rosdep respect that file and not install dependencies needed by the ignored package?

Yes, rosdep will not "see" the directory (or any sub directories) in which the CATKIN_IGNORE file is located and thus will not consider it when looking for and parsing package manifests.

I'm currently developing on ROS Kinetic and Melodic on Ubuntu 16.04 and 18.04 respectively. In order to make it easy for people to install my ROS packages, I have been taking advantage of the rosdep tool to automatically install dependencies.

I'm not exactly sure how you intend to use CATKIN_IGNORE with rosdep in the context of developing for multiple ROS versions. Are you maintaining two versions of the same package as siblings (ie: in the same workspace and/or repository)?

Common practice is to use branches in a VCS for this, and checking out the correct branch with the version compatible with the ROS version (and/or operating system) you target.