Apparently it's not that complicated. It worked for me by modifying the following files:
<project-folder>/nbproject/project.properties
change the following lines:
j2ee.platform=1.5
javac.source=1.5
javac.target=1.5
to
j2ee.platform=1.6
javac.source=1.6
javac.target=1.6
Repeat the same for:
<project-name>/<project-name>-ejb/nbproject/project.properties
<project-name>/<project-name>-war/nbproject/project.properties
In ejb-jar.xml change the line:
<ejb-jar xmlns = "http://java.sun.com/xml/ns/javaee"
version = "3.0"
xmlns:xsi = "http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation = "http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/ejb-jar_3_0.xsd">
to
<ejb-jar xmlns = "http://java.sun.com/xml/ns/javaee"
version = "3.1"
xmlns:xsi = "http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation = "http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/ejb-jar_3_1.xsd">
Next, find persistence.xml and change this line:
<persistence version="1.0" xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_1_0.xsd">
to
<persistence version="2.0" xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd">