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I guess my main concern lies within breaking the catkin structure needed for proper compilation.

there is no such structure.

Catkin ~= CMake.

is [it] possible to structure the include folder for a ROS c++ package with subfolders?

yes, of course.

There is no magic here. It's all just regular C++ and CMake.

As long as you make sure everything which needs to be on the include path ends up there things will just work.

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