(function (window, document, undefined) {
  "use strict";

  require.config({
    baseUrl: "..",

    paths: {
      // Libraries
      "jquery": "libraries/jquery/jquery",
      // /Libraries

      // Application
      "app": "app/scripts/app",
      // /Application
    },

    shim: {
    }
  });

  require(["jquery", "app"],
  function($,         App) {
    console.log("App v%s with jQuery v%s says, '%s'", App.version, $.fn.jquery, App.greeting);
  });
})(window, document);

(function(window, document, undefined) {
  "use strict";

  require.config({
    baseUrl: "..",

    paths: {
      // Libraries
      "jquery": "libraries/jquery/jquery",
      // /Libraries

      // Application
      "app": "app/scripts/app",
      // /Application
    },

    shim: {
    }
  });

  require(["jquery", "app"],
  function( $,        App) {
    console.log("App v%s with jQuery v%s says, '%s'", App.version, $.fn.jquery, App.greeting);
  });
})(window, document);

Fix indentation.