Thanks for the feedback. At this time there isn't a way with the tool to clean up publishig, but it's something we've been thinking about for a future release.
You might find this blog post useful in the meantime which gives instructions on how to manually relink the dependant files http://blogs.adobe.com/edge/2013/11/04/want-to-relink-an-project-files-on-a-cdn-its-easier -than-you-might-think/
I am glad that it is being considered. It is really a major roadblock to integration.
I went through your instructions on relinking above. Thank you for writing it!!
One problem though is that I'm not sure how to link the _edge.js file to the HTML? (I am using the latest EdgeAnimate CC version)
Hoping you can direct me in the right direction. I'd imagine the answer is right in front of me... but I haven't been able to figure it out.
Thanks so much!!!