require.js cannot find jquery.js

We already have a AMD implementation with require.js which is being used for a long time and now team has decided to use r.js optimizer to optimize the build. I am following the steps but I think I am missing something:

We have require.config which looks like the following:

require.config({
    waitSeconds : 15,
    baseUrl: window.rootPath + 'scripts',
    paths: {
        jquery: 'empty:',
        jqueryui: 'empty:',
        recaptcha: '//www.google.com/recaptcha/api/js/recaptcha_ajax',
        maxmind: '//j.maxmind.com/app/geoip',
        enduser: '/enduser/scripts/system',
        cookies: '/enduser/scripts/system/cookies',
        errorhandler: '/enduser/scripts/system/errorhandler',
        underscore: '/enduser/scripts/underscore',
        blockui: '/enduser/scripts/jquery.blockui',
        messaging: '/enduser/scripts/system/messaging',
        jgrowl: '/enduser/scripts/jquery.jgrowl',
        knockout: 'knockout-latest.debug',
        kobindings: '/enduser/scripts/system/bindings',
        async: 'plugins/require/async',
        depend: 'plugins/require/depend',
        font: 'plugins/require/font',
        goog: 'plugins/require/goog',
        image: 'plugins/require/image',
        json: 'plugins/require/json',
        noext: 'plugins/require/noext',
        mdown: 'plugins/require/mdown',
        propertyParser: 'plugins/require/propertyParser',
        markdownConverter: 'lib/Markdown.Converter'
    },
    priority: ['jquery']
});

require(["main"]);

Please note that it has CDN paths instead of "empty". But I replaced empty there after reading some threads online. I am running following command on that:

node -o name="filepath" output="output file path"

It's saying tracing dependencies and then it throws an error saying it did not find jquery.js. Any suggestions?