updated GraphicsAndWindowsTest Javadocs

            private double directionZ = 10.0; // Direction of movement

            /**

             * Called at every frame while the {@link AnimationTimer} is active. This method contains the logic for

             * updating the scene's elements, such as moving objects, checking for boundary conditions, and updating

             * the FPS counter displayed in the scene.

             * Called at every frame while the {@link AnimationTimer} is active to update the scene's elements,

             * including object movements, boundary condition checks, mesh deformation on collision, and FPS counter updates.

             * <p>

             * Movement and boundary checking are based on the bounds of the 3D mesh and the cube within the scene.

             * The FPS counter is updated once every second, based on the number of frames rendered in that interval.

             * This method extends the scene update logic with collision detection between the mesh and a virtual bounding box,

             * causing mesh deformation upon nearing the box's edges. It calculates new positions for 3D objects based on their

             * current positions and direction vectors, simulates movement within the scene, and reverses the movement direction

             * at the scene's boundaries. Additionally, it modifies the mesh's vertices to "squish" the mesh when it comes close

             * to or collides with the bounding box, creating a more dynamic interaction between the scene's objects.

             * <p>

             * Movement, boundary checking, and mesh deformation logic are applied based on the bounds of the 3D mesh and cube within the scene.

             * The FPS counter is updated once every second, based on the number of frames rendered in that interval, to provide real-time

             * performance feedback.

             *

             * @param now The timestamp of the current frame given in nanoseconds. This value can be used to

             *            calculate the time difference between frames for smooth animation and movement.

             * @param now The timestamp of the current frame given in nanoseconds. This value is used to ensure smooth animations and

             *            consistent updates across frames.

             */

            @Override

            public void handle(long now) {