java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;

I am upgrading jpa, hibernate, spring, and jdk to enable the new features from JPA 2.1. But I am getting the following error:

java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;  

I have read other postings about this, but they do not resolve the error on my machine. For instance, SJuan76's answer to this posting suggests upgrading to jpa 2.1, but I have set the eclipse jpa project facet to version 2.1 and I have also included hibernate-jpa-2.1-api in my pom.xml. You can read all the versions of the various libraries in the complete pom.xml by clicking on this link. What do I need to change in the pom.xml or in the eclipse project to resolve this error?

Note: I can get rid of the error by changing the hibernate version in the pom.xml back to <hibernate.version>4.2.1.Final</hibernate.version>, but this defeats the purpose of upgrading. Does the fact that changing the hibernate version turns the error on and off help us to diagnose the problem?

If the problem is multiple jars conflicting with each other, I could use the eclipse type manager to disable one of the jars, but which jar would I look for?

Here is the complete stack trace:

ERROR ContextLoader - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring/business-config.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1553) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:475) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:973) ~[spring-context-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:750) ~[spring-context-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482) ~[spring-context-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:389) ~[spring-web-3.2.5.RELEASE.jar:3.2.5.RELEASE]
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:294) ~[spring-web-3.2.5.RELEASE.jar:3.2.5.RELEASE]
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112) [spring-web-3.2.5.RELEASE.jar:3.2.5.RELEASE]
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4939) [catalina.jar:7.0.42]
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5434) [catalina.jar:7.0.42]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) [catalina.jar:7.0.42]
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1559) [catalina.jar:7.0.42]
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1549) [catalina.jar:7.0.42]
    at java.util.concurrent.FutureTask.run(FutureTask.java:262) [na:1.7.0_45]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_45]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_45]
    at java.lang.Thread.run(Thread.java:744) [na:1.7.0_45]
Caused by: java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;
    at org.hibernate.cfg.annotations.EntityBinder.processComplementaryTableDefinitions(EntityBinder.java:936) ~[hibernate-core-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.cfg.AnnotationBinder.bindClass(AnnotationBinder.java:824) ~[hibernate-core-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.cfg.Configuration$MetadataSourceQueue.processAnnotatedClassesQueue(Configuration.java:3788) ~[hibernate-core-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.cfg.Configuration$MetadataSourceQueue.processMetadata(Configuration.java:3742) ~[hibernate-core-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.cfg.Configuration.secondPassCompile(Configuration.java:1410) ~[hibernate-core-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1844) ~[hibernate-core-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:850) ~[hibernate-entitymanager-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:843) ~[hibernate-entitymanager-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.boot.registry.classloading.internal.ClassLoaderServiceImpl.withTccl(ClassLoaderServiceImpl.java:397) ~[hibernate-core-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:842) ~[hibernate-entitymanager-4.3.5.Final.jar:4.3.5.Final]
    at org.hibernate.jpa.HibernatePersistenceProvider.createContainerEntityManagerFactory(HibernatePersistenceProvider.java:152) ~[hibernate-entitymanager-4.3.5.Final.jar:4.3.5.Final]
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:336) ~[spring-orm-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:318) ~[spring-orm-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1612) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1549) ~[spring-beans-4.0.6.RELEASE.jar:4.0.6.RELEASE]
    ... 21 common frames omitted
Oct 28, 2014 11:01:16 AM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [spring/business-config.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1553)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:539)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:475)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:973)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:750)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:482)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:389)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:294)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4939)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5434)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1559)
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1549)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.NoSuchMethodError: javax.persistence.Table.indexes()[Ljavax/persistence/Index;
    at org.hibernate.cfg.annotations.EntityBinder.processComplementaryTableDefinitions(EntityBinder.java:936)
    at org.hibernate.cfg.AnnotationBinder.bindClass(AnnotationBinder.java:824)
    at org.hibernate.cfg.Configuration$MetadataSourceQueue.processAnnotatedClassesQueue(Configuration.java:3788)
    at org.hibernate.cfg.Configuration$MetadataSourceQueue.processMetadata(Configuration.java:3742)
    at org.hibernate.cfg.Configuration.secondPassCompile(Configuration.java:1410)
    at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1844)
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:850)
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl$4.perform(EntityManagerFactoryBuilderImpl.java:843)
    at org.hibernate.boot.registry.classloading.internal.ClassLoaderServiceImpl.withTccl(ClassLoaderServiceImpl.java:397)
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:842)
    at org.hibernate.jpa.HibernatePersistenceProvider.createContainerEntityManagerFactory(HibernatePersistenceProvider.java:152)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:336)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:318)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1612)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1549)
... 21 more