This is a setup I'm using with a YUI_config to leverage Y.Loader to build static rollup files.

build.js

/*
This is the Node.js file, it will export files directly to 
`tdp-bundle-min.js` which obviously won't work well for you!

This relies on having a YUI_config that can be parsed and
passed into Y.Loader. Everything you need should be in this
gist, though. You may need to change the path to your
YUI_config file (mine is named `bundle.js`).

However, it's an easy change, just scroll down and edit it.

*/
var config = require('./config/config'),
    path   = require('path'),
    YUI    = require('yui').YUI,
    Y      = YUI(global.config.yui.server),

    Queue = require('buildy').Queue;

Y.use('loader', 'oop');

//Y.log( global.config.bundle.groups );

var loader = new Y.Loader({
    base: './node_modules/yui/',
    ignoreRegistered: true,
    require: [ 'tdp' ],
    fetchCSS: false,
    groups : {
      'tdp' : Y.merge(
        Y.clone(global.config.bundle.groups.tdp),
        {
          base : path.join(config.pubDir, config.yui.server.base),
          combine : false
        }
      ),
      'template' : Y.merge(
        Y.clone(global.config.bundle.groups.template),
        {
          base : path.join(config.pubDir, config.yui.server.base, 'template/'),
          combine : false,
          filter  : 'min'
        }
      )

    }
});

var requirements = loader.resolve(true),
    file_list = [],
    queue;

/*
I have to translate the path that Loader expects to where I want them on disk.

This changes tdp-(model|view|whatever)/tdp-(model|view|whatever)-component.js into simply /model/component.js

*/
Y.Array.each( requirements.js, function(file) {
  if ( file.match('tdp-') ) {
    //console.log("Modifying file: " + file);
    file = file.replace(/tdp-(\w+).*?\//, '$1/');
    file = file.replace(/tdp-(\w+)-/, '');
    file = file.replace(/tdp-/, '');
    //console.log(" -> " + file);
  }
  file_list.push( file );
});

new Queue('build TDP')
  .task('files', file_list)
  //.task('jslint')
  .task('concat')
  //.task('replace', { regex: "^.*?(?:logger|Y.log).*?(?:;|\\).*;|(?:\r?\n.*?)*?\\).*;).*;?.*?\r?\n", replace: '', flags: 'mg' })
  .task('jsminify')
  //.task('inspect')
  .task('write', { name: './tdp-bundle-min.js' })
  .run();

bundle.js

(function(module) {
    var comboBase = '/combo?',
        filter    = ( typeof window !== 'undefined' && window.location.search.match(/[?&]filter=([^&]+)/) || [])[1] || 'min';

    // YUI Config.
    YUI_config = {
        filter     : filter,
        combine    : filter === 'min',
        allowRollup: false,
        fetchCSS   : false,
        gallery    : /* whatever gallery version you want in the live app, the builder looks at config.json */
        modules : {
            /* Snip */
        },
        groups     : {
            /* Snip */
        }
    };

    // Export if under node.js
    if ( module ) {
        module.exports = YUI_config;
    }
}(typeof module !== 'undefined' ? module : null));

config.js

/*
Much of this file is taken from Eric Ferraiuolo's wonderful photosnear.me app.

http://github.com/ericf/photosnear.me

*/
var fs   = require('fs'),
    path = require('path'),
    Y    = require('yui/oop'),

// The path to the file you define your YUI_config
    bundle = require('../root/static/scripts/bundle'),

    CONFIG_FILE = 'config.json',
    NODE_ENV    = process.env.NODE_ENV,

    ENV = {
        development : NODE_ENV !== 'production',
        production  : NODE_ENV === 'production'
    };

    appRoot     = process.cwd(),
    configFile  = path.join(__dirname, CONFIG_FILE),

    config      = path.existsSync(configFile) && JSON.parse( fs.readFileSync(configFile, 'utf8') );

//Y.log(bundle);

config.bundle = bundle;

config.yui.server = {
    useSync : true,
    filter  : ENV.production ? 'min' : 'raw',
    base    : '/scripts/',
    gallery : config.yui.gallery,

    groups : {
/*
        server : Y.merge(
            Y.clone(config.yui.server),
            {
                base    : path.join(config.pubDir, config.yui.server.base),
                combine : false
            }
        ),

        tab : Y.merge(
            Y.clone(config.yui.tab),
            {
                base    : path.join(config.pubDir, config.yui.tab.base),
                combine : false
            }
        )
*/
    }
};

global.config = module.exports = config;