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Why don't you try using extended analytics for the intital extract...load it up into Oracle or SQL tables that you are probably using, and then loading into MDM from there?
The APP file format can easily be modified to import directing into MDM. It already has both a relationship and members section by default.
Better option though would be to convert the APP file into automator scripts. This would allow you to impact an existing version within MDM along with keeping a detailed audit log.