My question - is it not enough to upload the hibernate tools to get all the hibernate needed libraries? What should I do to make my web project see the hibernate libraries? Should I point to some hibernate tools libraries or should I download them and put to the project/WEB-INF/library?
In JBoss Tools 3.2.1 for Helios it is not enough. Usual approach for hellos release is download required hibernate libraries, create Eclipse User Librariy(ies) and add them to the project trough Java Build Path.
And also what to do with missing annotations?
For Hibernate 3.x download corresponding hibernate-annotations lib and add it to Java Build Path. For hibernate 4.x it library with annotation classes is included in hibernate distribution archive.
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You can also install a JBoss 7 server and use that for your dynamic web or jar project and you should get the JPA classes available to you.