Tracking reports positions relative to the physical CAVE - the user is restricted to moving inside this small space. Many virtual environments occupy a much larger area. Navigation allows the user to explore this larger space.
The concept behind navigation is that the VR display itself, with the user inside, is moved through the virtual world. This is implemented by a navigation transformation which is applied to everything that is rendered in the environment.
The library maintains a transformation matrix which the application can manipulate like the GL modeling transformation.