requirejs.config({
    paths: {
        knockout: 'path/to/knockout',
        underscore: 'path/to/underscore',
        jquery: 'path/to/jquery',
        koutils: 'path/to/koutils',
        koui: 'path/to/koui'
    }
});

define(["koui/tree"], function(tree) {
    var command = new tree.Tree({
        //...
    });
});