Actually I think I can answer that myself!!
It seems that the contents page is here (
http://www.hibernate.org/hib_docs/v3/reference/en/html/) but my feedback would be to make this the page linked from the 'getting started' pages - from there you are currently thrown into chapter 1.
There doesn't seem to be an explanation of all the terms upfront either, so it's difficult to know about the hbm2java v3 equivalent until chapter 20! - It's not obvious that chapter 20 (Toolset Guide) is anything to do with the new hbm2java! Also no overview of Core, Annotations, Entity Manager and Tools - you have to jump around the documentation / website. Is there a glossary anywhere?
Another minor point is that when you go to the "documentation overview" page (
http://www.hibernate.org/5.html) you could assume that the 'Hibernate Tools' section is the Tool guide - i.e. you might not notice the Toolset Guide is buried deep inside the Hibernate Core for Java reference documentation.
The documentation appears to be very thorough, for advanced users. Novice users (like me) struggle to know where to look because they do not know what the terminology relates to :-(