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Ok,

I found my problem. This is linked to this thread :

https://answers.ros.org/question/224698/what-causes-a-library-so-to-be-copied-to-devellib/

Along with this :

http://wiki.ros.org/catkin/CMakeLists.txt#Overall_Structure_and_Ordering

The problem is not based on the change from catkin_make to catkin build, but the order in which the element of my CMakeLists were writing. By following the CMakeLists rules from the second link, my plugin.so was generated in devel/lib and everything is working fine.