buildConfig.js

({
    baseUrl: './src/',
    dir: 'build',
    include: ['main'],
    logLevel: 0,
    mainConfigFile: './src/main.js',
    name: 'main',
    wrap: false,
    optimize: 'none',
    preserveLicenseComments: false
})

bundle.js

/** @license MIT License (c) copyright B Cavalier & J Hann */

/**
 * A lightweight CommonJS Promises/A and when() implementation
 * when is part of the cujo.js family of libraries (http://cujojs.com/)
 *
 * Licensed under the MIT License at:
 * http://www.opensource.org/licenses/mit-license.php
 *
 * @version 1.7.1
 */

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define("../lib/when", function(){});

when.js

/** @license MIT License (c) copyright B Cavalier & J Hann */

/**
 * A lightweight CommonJS Promises/A and when() implementation
 * when is part of the cujo.js family of libraries (http://cujojs.com/)
 *
 * Licensed under the MIT License at:
 * http://www.opensource.org/licenses/mit-license.php
 *
 * @version 1.7.1
 */

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As you can see, r.js is writing it as define("../lib/when", function(){});, but the minified form of when.js still has it's call to define (using the implicit module name signature).