reminder: provide a way to allow users to modify their existing XMI using the transformation process, as already agreed this should be turned off by default

A great source of inspiration might be Cocoon 2 which is a kick ass XML Pipelining framework (I've had a lot of fun with it in the past: http://jxcal.atilla.org/). Although, I think it would be way overhead to include as a whole in AndroMDA, the specific concept you might be interested in is the sitemap.xml:
http://cocoon.apache.org/2.1/userdocs/concepts/sitemap.html

An other source of inspiration might be the XML Pipeline Definition Language released by the W3C in 2002:
http://www.w3.org/TR/xml-pipeline/

I think I heard of a java implementation once, but I don't remember where. This spec also has the advantage of being quite light compared to cocoon's sitemap.xml (Which is great, don't get me wrong).

Just my two cents ;)

Here is the article I read about the XML Pipeline Definition Language, sorry, it is in french, and I couldn't find the original version:
http://xmlfr.org/actualites/tech/020301-0001

The interesting things are the two links:

- XPipe
http://xpipe.sourceforge.net/

- DSDL
http://www.dsdl.org/

Hope this helps.

Oups, here is the original article in english:
http://www.xmlhack.com/read.php?item=1564

This has been added, nothing complex like Cocoon or anything, buy you can define XSL documents as transformations and they'll be applied to the model before model processing begins. Take a look at the AndroDMA Maven Plugin or the Ant task documentaion on how to use it.