Just discovered this great piece of work. One of the things that I think would be great would be to change the format of the warnings you get from the command line in to something Xcode can parse.
I'm not sure if there's an exact format, but if I run doxygen and it returns warnings about undocumented parameters and whatever, XCode can parse those messages and link you to the methods they're referring to.
It's a neat feature and it'd make this tool fit very nicely in to the Xcode workflow.
Does --logformat xcode work good enough? Read http://gentlebytes.com/appledoc-docs-examples-xcode/ for details.
Thanks! Can't believe I missed that.