Could resolve the same by bypassing the verification.
Though on running the windup report. I am getting
java.lang.IllegalArgumentException: Application path must not be null.
Can you let me know what am I missing.
I would recommend to use already built update site from JBoss Tools - Windup - Update Site: 3.1.0.Alpha (Alpha)
That error shows there is not set/configured the input option like what PROJECT/APPLICATION in eclipse you would like to run Windup on.