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I've somehow managed to completely screw up the model and the generated code from EMF. EMF Compare can't seem to make heads or tails of anything, and the outline view is coming up blank. I'm not sure how to fix it. At this point, the easiest thing to do is to rebuild the model and regenerate all the EMF code; this time, without messing with the ecore (some of the names of the XSD-influenced generated Java methods may seem a little weird, but we'll run with it). We'll tweak the genmodel to change the root package name and to *not* generate a create wizard, and generate only a single-page editor. But leave it at that. The other additions, like the customized create wizard, and "Compare with Foundation Database" functionality will be moved to other bundles.
Managed to tweak it back to sanity. Marking this bug as WORKSFORME.