junk.js

define(["require", "exports", 'jquery'], function(require, exports, $) {
    requirejs.config({ baseUrl: "Scripts", paths: { jquery: "jquery-1.10.2" } }); // <--- Never gets used

    $('#hello').click(); // <--- Won't work, because jquery won't be resolve to the right path
});

junk.ts

declare var requirejs;
requirejs.config({ baseUrl: "Scripts", paths: { jquery: "jquery-1.10.2" } });
import $ = require('jquery');
$('#hello').click();