Thanks Michael for the answer, there are still tons of things I don't 
understand about the API but you've helped me to start in the correct path, 
I will do a lot of research and start with the devkit example you told me. 
I will come back to post (hopefully) the answer.

I guess by intermediate object you mean somehing like "ShapeOrig" node that 
gets created when a deformer, skincluster, etc is applied and contains the 
mesh before the deformer was applied.

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