This is an old question I posted when I was just experimenting with ways to document an API.
Eventually I switched to Apiary over MireDot, which makes this task trivial. The reason for this transition was mostly to decouple the JavaDoc from the actual API documentation, as I found coupling those two can create a very messy code-base for a sophisticated API that requires a lot of documentation.
Ideally would have built documentation using an all-encompassing API management platform like Mashery or the like, but at the time that was not an option.