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No idea what caused this, but does a sudo apt-get install --reinstall ros-kinetic-catkin resolve it?

No idea what caused this, Not sure, but does it could be that apt did not remove ros-kinetic-catkin with the autoremove, and then when you installed everything the second time, dependency resolution determined that the package ros-kinetic-catkin was already installed, so it skipped it.

But because you rm- fr /opt/ros before, the files are not actually there anymore.

Can you check whether a sudo apt-get install --reinstall ros-kinetic-catkin resolve it?gets the files back?

sudo apt-get remove ros-kinetic-desktop-full
...
sudo rm -fr /opt/ros
...
sudo apt-get autoremove

Not sure, but it could be that apt did not remove ros-kinetic-catkin with the autoremove, and then when you installed everything the second time, dependency resolution determined that the package ros-kinetic-catkin was already installed, so it skipped it.

But because you rm- fr rm -fr /opt/ros before, the files are not actually there anymore.

Can you check whether a sudo apt-get install --reinstall ros-kinetic-catkin gets the files back?

Btw: I would never (well, never ..) rm -rf files or directories that were installed by a package manager. Use apt-get remove or apt-get purge with a regex or a package list. If there are still files left after running that, then removing them manually could be acceptable.