updated settings cleanup to prevent issue with the update process

Former-commit-id: 07122c535d47f3f414659013555fa826ce0e9b9c

dependency-check-cli/src/main/java/org/owasp/dependencycheck/App.java

@@ -62,7 +62,7 @@ public class App {
             final App app = new App();
             app.run(args);
         } finally {
-            Settings.cleanup();
+            Settings.cleanup(true);
         }
     }