Thanks!

rem This will create the API for  application
rem YOU MUST EDIT THE SETTINGS IN THIS FILE TO MATCH YOUR CONFIGURATION

rem Save old classpath
set OLD_CP=%CLASSPATH%

rem Output directory
rem CHANGE THIS TO THE FOLDER YOU WISH TO CREATE THE API DOCUMENTATION
set OUTPUT_FOLDER=..\doc\api

rem Application top-level directory
rem CHANGE THIS TO MATCH YOUR CONFIGURATION
set APP_HOME=.

rem CLASSPATH
set CLASSPATH=.;%APP_HOME%;

javadoc -d "%OUTPUT_FOLDER%" -windowtitle " - Copyright @ 2006-2007" -doctitle " API Specification" -bottom  "©, ” -classpath %classpath%  -package -author -version @packages.txt

rem Restore old classpath
set CLASSPATH=%OLD_CP%

Save the above to a .bat or .cmd or .sh file in the top directory of your application, e.g. where folder app is, if app is the name of the root package of your application.

You also need a packages.txt file in the same directory which contains the names of all the packages of your application one per line, i.e. in the form:
app
app.db
app.io
app.io.ui
app.help
etc.

Inside each package you must have a package.html file with the following ingredients:

Application package

bla bla bla description of the package bla bla bla

Here you modify the title and the body. You must add a package.html to every package and sub-package of your application.

I know it is a lot of work, but Voila.