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You can have subfolders in your catkin_ws/src folder which are not valid ros packages without any problem. I think you future catkin workspace structure could be like this:
/catkin_ws
/src
-CmakeList.txt [symlink by catkin to toplevel cmake]
/quadrotor [this is my github repro]
/controllers
/controller_1
-CMakeLists.txt
-package.xml
/src
/controller_2
-CMakeLists.txt
-package.xml
/src
/experiments
/user_1
/what_evernode_1
-CMakeLists.txt
-package.xml
/src
/devel
/build