Hibernate trying to load Jandex on EntityManagerFactory creation

Question

Currently refreshing my JPA and Hibernate Know-How, I am writing some example code in the form of a todo list swing application.

This is the minimal example that reproduces my problem:

public static void main(String[] args) {
    EntityManagerFactory emf = Persistence.createEntityManagerFactory("SwingTodoPU");
}

This is the stacktrace I get when running the application (I am using Netbeans' default build configuration and no additional build tools like Maven):

Okt 09, 2015 12:10:21 PM org.hibernate.ejb.HibernatePersistence logDeprecation
WARN: HHH015016: Encountered a deprecated javax.persistence.spi.PersistenceProvider [org.hibernate.ejb.HibernatePersistence]; use [org.hibernate.jpa.HibernatePersistenceProvider] instead.
Okt 09, 2015 12:10:21 PM org.hibernate.ejb.HibernatePersistence logDeprecation
WARN: HHH015016: Encountered a deprecated javax.persistence.spi.PersistenceProvider [org.hibernate.ejb.HibernatePersistence]; use [org.hibernate.jpa.HibernatePersistenceProvider] instead.
Okt 09, 2015 12:10:21 PM org.hibernate.ejb.HibernatePersistence logDeprecation
WARN: HHH015016: Encountered a deprecated javax.persistence.spi.PersistenceProvider [org.hibernate.ejb.HibernatePersistence]; use [org.hibernate.jpa.HibernatePersistenceProvider] instead.
Exception in thread "main" java.lang.NoClassDefFoundError: org/jboss/jandex/IndexView
    at org.hibernate.jpa.boot.spi.Bootstrap.getEntityManagerFactoryBuilder(Bootstrap.java:51)
    at org.hibernate.jpa.HibernatePersistenceProvider.getEntityManagerFactoryBuilderOrNull(HibernatePersistenceProvider.java:129)
    at org.hibernate.ejb.HibernatePersistence.getEntityManagerFactoryBuilderOrNull(HibernatePersistence.java:93)
    at org.hibernate.jpa.HibernatePersistenceProvider.getEntityManagerFactoryBuilderOrNull(HibernatePersistenceProvider.java:86)
    at org.hibernate.ejb.HibernatePersistence.getEntityManagerFactoryBuilderOrNull(HibernatePersistence.java:101)
    at org.hibernate.jpa.HibernatePersistenceProvider.createEntityManagerFactory(HibernatePersistenceProvider.java:67)
    at org.hibernate.ejb.HibernatePersistence.createEntityManagerFactory(HibernatePersistence.java:54)
    at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:55)
    at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:39)
    at at.swingtodo.SwingTodo.main(SwingTodo.java:39)
Caused by: java.lang.ClassNotFoundException: org.jboss.jandex.IndexView
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    ... 10 more
Java Result: 1

The persistence unit is configured in src/META-INF/persistence.xml as follows:

<?xml version="1.0" encoding="UTF-8"?>
<persistence version="2.0" xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/persistence http://xmlns.jcp.org/xml/ns/persistence/persistence_2_1.xsd">
  <persistence-unit name="SwingTodoPU" transaction-type="RESOURCE_LOCAL">
    <provider>org.hibernate.jpa.HibernatePersistenceProvider</provider>
    <class>at.swingtodo.entities.Item</class>
    <shared-cache-mode>NONE</shared-cache-mode>
    <validation-mode>NONE</validation-mode>
    <properties>
      <property name="hibernate.cache.provider_class" value="org.hibernate.cache.NoCacheProvider"/>
      <property name="javax.persistence.jdbc.url" value="jdbc:mysql://localhost:3306/tododb?zeroDateTimeBehavior=convertToNull"/>
      <property name="javax.persistence.jdbc.password" value="tododb"/>
      <property name="javax.persistence.jdbc.driver" value="com.mysql.jdbc.Driver"/>
      <property name="javax.persistence.jdbc.user" value="tododb"/>
      <property name="javax.persistence.schema-generation.database.action" value="drop-and-create"/>
    </properties>
  </persistence-unit>
</persistence>

hibernate.cfg.xml:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE hibernate-configuration PUBLIC "-//Hibernate/Hibernate Configuration DTD 3.0//EN" "http://hibernate.sourceforge.net/hibernate-configuration-3.0.dtd">
<hibernate-configuration>
  <session-factory>
    <property name="hibernate.dialect">org.hibernate.dialect.MySQLDialect</property>
    <property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
    <property name="hibernate.connection.url">jdbc:mysql://localhost:3306/tododb?zeroDateTimeBehavior=convertToNull</property>
    <property name="hibernate.connection.username">tododb</property>
    <property name="hibernate.connection.password">tododb</property>
  </session-factory>
</hibernate-configuration>

I understand that Hibernate is trying to use Jandex but I do not understand why it is, even in my minimal example. As you can see, I am not using metadata generation as the OP in this related question "Why is hibernate 4.2 using jandex and classmate [...]". I have also been unable to resolve the warnings that are output before the Exception is thrown (my code is not referencing org.hibernate.ejb.HibernatePersistence)

If possible, I would like to avoid the obvious workaround of satisfying Jandex and its dependencies.

I am using Hibernate 4.3, JPA 2.1, JDK 1.7, and NetBeans 8.0.2.