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2. We have concerns about hardcoding the OR-mapping in the Java annotations. Is it possible to use Hibernate xml mappning files for part of the mappings along with the annotations?
You can use a mix of hbm.xml files, orm.xml files (JPA/EJB3 xml schema) and annotations. AFAIK you can mix annotations and xml for a class.
3. Is it possible to map tables in different schemas to the same network of objects, without hardcoding the schema names in the Java source files?
You should be able to do this using xml