If I read the Hibernate book right, @SecondaryTable is a JPA-only option.
I think Hibernate Tools is using the .hbm.xml data model, so I guess it's not available.
(This is supported by the fact that the HT Ant task sources do not contain SecondaryTable anywhere, not in Java and not in the template.)
In the book, I have seen this construction:
Code:
<join table="ITEM_SHIPMENT" optional="true">
<key column="SHIPMENT_ID"/>
<many-to-one name="auction" column="ITEM_ID" not-null="true" unique="true"/>
</join>
inside the <class> element.
I'd activate .hbm.xml generation, modify the generated .hbm.xml to use the above idiom, then re-generate and see if the <join> survives.
If yes, you have a chance of finding the appropriate options for reveng.xml; if no, you can stop worrying and start looking for an alternative design.