NaturalDocsGreg

For languages that have a custom parser written for it (currently only C#) you can absolutely omit the first line. For all other languages it needs the line to know what its documenting and how to include the prototype since it's relying on a more generic parser. This lets it work with almost any language, and you can even add support for new languages just by editing a text file, but it admittedly makes it more verbose.

Hi, I'm the author. That language was intended to specifically say that Natural Docs' license doesn't affect the rest of the documentation, let alone the project it's documenting, but without forfeiting my copyright to those particular files. If there's language that I could include to make this even clearer I'd be happy to.

In my opinion shipping code plus documentation generated by Natural Docs does not cause the code to fall under the AGPL, as you are bundling it rather than making a derivation of it. You could argue that the documentation is a derivation of it, but that's what I try to explicitly disavow above.