I've recently tried to upgrade from hibernate 5.2.2 to 5.2.9 which caused the application to no longer work. I have the following mapping:

@Embeddable
public class AbilityEntity {
}

public class EmployeeEntity {
@BatchSize(size = 10)
@ElementCollection(fetch = FetchType.EAGER)
@CollectionTable(name = "ability", joinColumns = @JoinColumn(name = "employee_id") )
public Set<AbilityEntity> getAbilities()

}

Starting from 5.2.3 on I'm getting the following error:

{{13-May-2017 01:31:17.518 SEVERE [ContainerBackgroundProcessor[StandardEngine[Catalina]]] org.apache.catalina.core.StandardContext.filterStart Exception starting filter EntityManagerFilter
javax.persistence.PersistenceException: [PersistenceUnit: capacity] Unable to build Hibernate SessionFactory
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.persistenceException(EntityManagerFactoryBuilderImpl.java:951)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:881)
at org.hibernate.jpa.HibernatePersistenceProvider.createEntityManagerFactory(HibernatePersistenceProvider.java:58)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:55)
at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:39)
at de.egore911.capacity.ui.filter.EntityManagerFilter.init(EntityManagerFilter.java:58)
at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4659)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5281)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.startup.HostConfig.reload(HostConfig.java:1390)
at org.apache.catalina.startup.HostConfig.checkResources(HostConfig.java:1291)
at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1552)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:285)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:95)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1141)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1377)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1381)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1349)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.hibernate.tool.schema.spi.SchemaManagementException: Schema-validation: missing table [ability]
at org.hibernate.tool.schema.internal.AbstractSchemaValidator.validateTable(AbstractSchemaValidator.java:121)
at org.hibernate.tool.schema.internal.GroupedSchemaValidatorImpl.validateTables(GroupedSchemaValidatorImpl.java:42)
at org.hibernate.tool.schema.internal.AbstractSchemaValidator.performValidation(AbstractSchemaValidator.java:89)
at org.hibernate.tool.schema.internal.AbstractSchemaValidator.doValidation(AbstractSchemaValidator.java:68)
at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.performDatabaseAction(SchemaManagementToolCoordinator.java:185)
at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.process(SchemaManagementToolCoordinator.java:66)
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:309)
at org.hibernate.boot.internal.SessionFactoryBuilderImpl.build(SessionFactoryBuilderImpl.java:493)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:878)
... 21 more}}

It works when downgrading to 5.2.2 again. What's also interesting is that it works fine on Apache Tomcat 8.5.12 on JDK 1.8.0_102-b14 (Windows), while it does not Apache Tomcat 8.0.30 on JDK 1.8.0_77-b03 (Linux).

Source code of said affected application is at https://github.com/egore/capacity-web