How can I refresh the contents of a jsTree?

var tree = jQuery.jstree._reference("#files");
tree.refresh();

or

var tree = jQuery.jstree._reference("#files");
var currentNode = tree._get_node(null, false);
var parentNode = tree._get_parent(currentNode);
tree.refresh(parentNode);

for jstree3 . I use destroy() function and again create tree running jstree() function

At version 3 you can reload the tree :

$('#treeId').jstree(true).settings.core.data = newData;
$('#treeId').jstree(true).refresh();

Turns out is is as simple as calling:

   tree.jstree("refresh");