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I think It sould be specificated the exact version of eclipse/wst need by the last version of HibernateTools (HibernateTools-3.1.0.beta2)

In the documentation we read simpli eclipse 3.1.

But must configuration with eclipse 3.1.0 seams doesn't work with this last HibernateTools-3.1.0.beta2 plugin

i have run it successfully on on 3.1.0 so you will need to report specific issues before i change that in the docs.