My HTML pages are grouped and have a collapsible menu.
Use doxygen to generate the files from the Java sources. Doxygen really has some nice features to build an index on those files (static!).
You will have to read the manual, but it's free and has very good results. At least for me, it was great.
You can even take out the generated files and include them in your own javadoc (if you do not like the style, which you can configure, btw).
Doxy rules !
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