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There already have docs about customize API doc for Java SE: Doclet Overview. How about JavaFX doclet?

Actually, most of part in that Java SE doc can be applied to JavaFX's. You need download JavaFX sdk from JavaFX website. There have a file whose name is javafxdoc.jar. You need compile and run your customized doclet class with that library. You can use that simple example doclet provided in Doclet Overview and take a try to compile your doclet class:

javac -classpath javafxdoc.jar ListClass.java 

And then write some javafx code MyClass.fx and run it with your doclet:

javafxdoc -doclet ListClass -docletpath .  MyClass.fx

It will create output for MyClass.fx according to your doclet class.