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I have this same problem. No clue WHICH packages are "non-catkin". Looks like many other people have had this SAME PROBLEM over the years. Why hasn't this bug been fixed??

What finally worked (after two days of cargo-cult "programming") was eliminating the build/devel/install folders, doing catkin_make_isolated --install (in the catkin_ws folder), then source devel_isolated/setup.bash.

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