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The easiest way to provide custom CMake logic with a catkin package is using an extras file:

http://docs.ros.org/api/catkin/html/dev_guide/generated_cmake_api.html#catkin_package

This allows you to specify a cmake file for catkin to include(...) anytime that package is find_package'ed.

Related:

http://answers.ros.org/question/93266/how-to-export-non-standard-include-directories-in-catkin/