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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