JSObject win =  (JSObject) webEngine.executeScript("window");
 win.setMember("app", new JavaApp());

<p><a href="about:blank" onclick="app.exit()">Exit the Application</a></p>  

(function (G, U) {
    "use strict";
    var UI = G.java || {};

    function getOptionsJson(key) {
        alert("window.app is undefined " + (G.app == undefined));
        G.app.getOptionsJson(key);
    }

    UI.getOptionsJson = getOptionsJson;
    G.java = UI;

}(window, undefined));

$(function () {
    initUI();
});


function initUI() {
    app.exit(); 
}