ckpackager does not remove plugins completely

Hi,

I am following this guide
http://docs.cksource.com/CKEditor_3.x/Developers_Guide/CKPackager
to compress the final ckeditor.js by remove some plugins I won't need.

However, when I use this new updated ckeditor.js I get javascript errors which are about missing plugin.js files. I see that even if I remove plugin from .pack file the plugins are referenced in ckeditor.js file.

For example,
when I remove a11yhelp from .pack file and use newly created ckeditor.js, I get error about missing http://server/js/ckeditor/plugins/a11yhelp/plugin.js

I could modify the config.js file in source, but I am wondering if there is a better way to handle this.

Thanks.