Windup 3.0 will be a web application. It can still be used as command line application, but on top of that, you can deploy Windup to a JBoss WildFly (or EAP) and scan your applications from a nice web UI.

Look at Windup Migration Platform and try migrating your application to the newest Java EE.

From the developers perspective, the frontend stack is Angular 2, TypeScript, ReactJS, Keycloak for security, and few other libraries. It's a bit pain for me to learn the new paradigm and to leave the very comfortable Java ecosystem, but on the other hand, looks like all the JavaScript-centered craziness is going to stay around for a couple of decades and eventually settle down, so why not embrace it (thinking, "Banzaaaii!!" )

Look at GitHub - windup/windup-web: Windup as a Web Service  if interested in code.

Enjoy!