I made some changes to the hibernate source and need to rebuild hibernate3.jar. I tried "mvn deploy" but I get a 401 (trying to upload to the jboss repository, which I don't want to do). I followed the instructions here: http://community.jboss.org/wiki/HibernateRelease35wMaven . I'm basically unpacking hibernate-3.5.2.GA.tar.gz, entering the "project" subdirectory and running "mvn deploy", which doesn't generate hibernate3.jar.
The problem is that you are trying to "deploy" the jar. Just run "mvn clean package". This will give you the jar in the target folder of the project. If you are using Maven, run "mvn clean install". This will put the jar into your local maven repo ($HOME/.m2/repositories) and you will be able to use it in other projects as maven dependency.
I ended up following this: http://community.jboss.org/wiki/BuildingHibernateFromSource35 (which was posted a few hours after I posted my question), although the original link seemed to be able to build things as well. Then I followed the second post in this thread: https://forum.hibernate.org/viewtopic.php?f=1&t=997648 and it ended up building the hibernate-distribution-3.5.2-Final.jar and the sources jar.