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Ros groovy is the first release that can use both catkin and rosbuild. If i'm not wrong, in the stacks folder there are the packages that are under rosbuild, while in the share folder the packages that use catkin. In ros hydro the stacks folder has been removed and there is only /ros/hydro/share. Anyway, answering your second question, when you create a package, you should put it in a workspace in your home directory and never in the /ros/groovy/... directory!