use jQuery and jQuery Mobile with RequireJS. NOTES: * do NOT use require-jquery.js * use shim config * load jquerymobile at last * do NOT add jquerymobile to deps array in scripts

alpha.js

define(['jquery'], function($) { // do NOT add jquerymobile in deps array.
    $(document).on("pageinit", "#alpha", function() { // #alpha => the id attr of div[data-role="page"]
      // your scripts...
    });
});

app.build.js

({
  // no minification, is done by the min task
  //optimize: 'none',
  baseUrl: 'scripts',
  appDir: "../",
  name: "main",
  out: 'scripts/main.js'
  paths: {
    "jquery": "vendor/jquery.min",
    "jquerymobile": "vendor/jquerymobile.min",
    "jquery.validate": "vendor/jquery.validate.min",
    "underscore": "vendor/lodash.min",
  },
  shim: {
    'underscore': { exports: "_" },
    'jquery': { exports: "$" },
    'jquery.validate': ['jquery'],
    'jquerymobile': ['jquery', 'mobileinit']
  }
})

main.js

require.config( {
    paths: {
        "jquery": "vendor/jquery.min",
        "jquerymobile": "vendor/jquerymobile.min",
        "jquery.validate": "vendor/jquery.validate.min",
        "underscore": "vendor/lodash.min"
    },
    shim: {
        'underscore': { exports: "_" },
        'jquery': { exports: "$" },
        'jquery.validate': ['jquery'],
        'jquerymobile': ['jquery', 'mobileinit']
    }
});

// Includes File Dependencies
require([
    // libraries
    "jquery",
    "underscore",
    "jquery.validate",

    // other files
    "alpha",
    "beta",

    "jquerymobile" // load last
]);

mobileinit.js

define(['jquery'], function($) {
    $(document).on("mobileinit", function() {
      //jqm configuration
      //$.mobile.ajaxEnabled = false;
    });
});