How do you set a Prefab through javascript?

var waypointPrefab : Prefab;

//i just want to set it here…

function Start () {

waypointPrefab = …(users/***/Prefabs/e.c.t);

}

You usually set the prefabs at the Inspector. You can also read objects from the Resources folder and assign them to prefabs - or even instantiate directly from the resource read. Take a look at Resources.Load - the docs have some useful examples.