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If you want to use CATKIN_IGNORE for this, just create a file with that name in each of the package directories that you want catkin to ignore. You can use touch for that, ie:
touch /path/to/catkin_ws/your/package/CATKIN_IGNORE
If you now run catkin_make (or any of the other catkin variants), it should ignore any package in that directory (and also in all subdirectories). Note that if you already built your workspace before adding CATKIN_IGNORE, the pkgs might still be picked up by catkin, as it then uses some of the information in the build directory. Simply removing build/ and devel/ and rebuilding should fix that.
The new catkin_tools package supports so called profiles, which allow you to configure the black and whitelists in a more comfortable way (and also makes switching between them very easy).
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