When I create an mapped-superclass inheritance between 2 entities and do a yaml doctrine2 export the extends property is not set in the derived table
This is correct behaviour. Mapped superclass is php-class only inheritance which can't be described by YML/XML format.
Please check Doctrine2 documentation for more information: http://docs.doctrine-project.org/projects/doctrine-orm/en/latest/reference/inheritance-mapping.html
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