I have my own gripes and struggles with Doxygen, but I think it's useful to realize that it's a documentation-generation toolkit that can serve many purposes.

I agree it's usually not the best tool for generating outward-facing API documentation for languages with native documentation tools (though mosra is demonstrating that it's not incapable).

With several different configs, however, Doxygen can generate different docsets that can be tailored to multiple audiences that need to understand different sections and facets of a sprawling codebase.