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Do your packages still contain manifest.xml? If yes you need to port them all to Catkin.

http://wiki.ros.org/catkin/migrating_from_rosbuild

If they are already Catkin packages, you just need to build them even when in a subfolder of src it should directly build them.

Do your packages still contain manifest.xml? If yes you need to port them all to Catkin.

http://wiki.ros.org/catkin/migrating_from_rosbuild

If they are already Catkin packages, you just need to build them with catkin_make, even when in a subfolder of src it should directly build them.