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When I invoke the Ediotr Gen, the target (heavily customized) Editor is overwritten and the file becomes empty.
It's the current strategy. It's the simplest way to produce easily a enhanced EMF editor. We generate the standard EMF tree editor and we override it with our current code. This will be replaced by a direct call of the Acceleo generators in the next version.
Are you sure that is the intended strategy? I mean the generated editor file literally has no code in it, i.e. it won't work. :)