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Isn't it the job of ros dependencies system to add the includes ? for example in the <export> section of the manifest.xml ?

It most certainly is! However, the manifest.xml file is actually where dependencies are specified, not in the CMakeLists.txt file. rosbuild only pulls in the <export> section of manifest.xml files for packages that you list a dependency on (or dependencies of your dependencies).

Your package should automatically have the correct includes for Eigen if you edit your manifest.xml file and add a line like <depend package="eigen" />. This manifest.xml line would make the stuff you did in your CMakeLists to find and include Eigen unnecessary.

Try adding the dependency to your manifest.xml file and removing anything related to finding the Eigen includes from your CMakeLists and see if that fixes things.