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Looking at wiki/genmsg, it would seem that it invokes github/gencpp, github/genpy and any other message generators based on parameters supplied by some catkin / cmake macro wrappers.
I haven't done this myself, but I can imagine those generators can be invoked from a command line as well, provided you provide the proper arguments. The genpy readme even seems to give some hints about how to do that:
$ ./scripts/genmsg_py.py -p geometry_msgs -Istd_msgs:`rospack find std_msgs`/msg -Igeometry_msgs:`rospack find geometry_msgs`/msg -o gen `rospack find geometry_msgs`/msg/PoseStamped.msg
This can probably be integrated into a Scons build, by declaring the correct dependencies?
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