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rosdeps are indeed for system dependencies (libraries), while the <depend package=.../> tags in the manifest are for ROS dependencies. Unfortunately, they do not automatically get resolved to Debian packages if you installed ROS through apt (though that would be nice to have).

Once your package / stack is released its stack dependencies will get mapped to dependencies on ROS Debian packages, so that if you install it all stacks it depends on will get installed as well.