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The documentation generated by rosdoc_lite should be the same as the documentation generated locally. I think the reason that you're getting the "srv" and "cfg" namespaces to show up is because you're running rosdoc_lite on a package that has been built. As such, there are a bunch of auto-generated header files that Doxygen is processing that aren't run by the automated doc system.

Do you have a specific package in mind that you're seeing this for? If I know what you're trying to replicate, I can double check that this is, indeed the case.