Shutting down a running app

How does IntelliJ Shutdown a running app? I have a web app running that
I've created a plugin for. The app starts up fine and when our web app
starts it registers with Runtime.addShutdownHook(Thread) which should be
called when the application is shutting down. However when I click the red
box to stop the web app it does not get called? Is there a reason and can
it be changed?