I have changed the test. Following test works...
/// <reference path="../../../project1/Shared/sub1/Javascript/stuff.js" />
test("foo test", function () {
deepEqual(init(), "works", "couldn't access source JS file");
ok(window, "no window context");
ok('MyNamespace' in window, "namespace is bad");
ok('MySubNamespace' in window.MyNamespace, "subnamespace is bad");
});