Bernhard,
These appear to be patches to the core Hibernate library. You would need to apply these patches to Hibernate source and re-compile Hibernate (or at least inject the modified classes into the existing Hibernate JARs). Once you have a modified JAR, you can go to Window > Preferences > MyEclipse > Project Capabilities > Hibernate and replace the JAR that we ship with MyEclipse with this one.
I’m afraid we cannot ship a specially modified version of Hibernate with MyEclipse, we would need this to arrive in a stable Hibernate build from JBoss itself.
Hope this helps.