I got it to work with Hibernate 4.2.12.Final and Hibernate Spatioal 4.0 after changing org.hibernate.jpa.HibernatePersistenceProvider to org.hibernate.ejb.HibernatePersistence.

I have tried with Hibernate 4.3.5.FINAL and Hibernate Spatial 4.3-SNAPSHOT and I get this exception below. Is this something you know about?

2014-05-04 20:20:21,068 [RMI TCP Connection(2)-127.0.0.1] ERROR org.springframework.web.context.ContextLoader: Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [springContext/spring-common-jdbc.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:304)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:300)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:195)
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:403)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4791)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5285)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.catalina.startup.HostConfig.manageApp(HostConfig.java:1544)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:622)
at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:569)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
at javax.management.remote.rmi.RMIConnectionImpl.doOperation(RMIConnectionImpl.java:1487)
at javax.management.remote.rmi.RMIConnectionImpl.access$300(RMIConnectionImpl.java:97)
at javax.management.remote.rmi.RMIConnectionImpl$PrivilegedOperation.run(RMIConnectionImpl.java:1328)
at javax.management.remote.rmi.RMIConnectionImpl.doPrivilegedOperation(RMIConnectionImpl.java:1420)
at javax.management.remote.rmi.RMIConnectionImpl.invoke(RMIConnectionImpl.java:848)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:322)
at sun.rmi.transport.Transport$1.run(Transport.java:177)
at sun.rmi.transport.Transport$1.run(Transport.java:174)
at java.security.AccessController.doPrivileged(Native Method)
at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:556)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:811)
at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:670)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
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)
... 55 more