Of course...
We are aware of this problem and we think about it, but not as high priority.
For the moment, Cook and JDom are using MooTools.
You can rewrite your custom JDom first,
then, for few functions like formalidator, please manualy rewrite.
Cook always write the same component structure, so just reuse always same files to override your projects.
Thanks for sugestion.
Karma +1