Patch JGit FS class to prevent classloader memory leak (#2544)

When using the rewrite-gradle-plugin, JGit's FS class adds a Runtime shutdown hook that inadvertently creates a shadow reference to the RewriteClassLoader of the plugin's classpath isolation feature. This expands to effectively mean that each time the rewrite configuration is modified and a new RewriteClassLoader is created, the previous one is leaked on the heap without ever being able to be reclaimed by the garbage collector. The included patch here removes just the shutdown hook, so that we can stop leaking the classloader