SEVERE: org.hibernate.TransientObjectException: object references an unsaved transient instance - save the transient instance before flushing: org.local.model.data.Chapter
   at org.hibernate.engine.ForeignKeys.getEntityIdentifierIfNotUnsaved(ForeignKeys.java:243)
   at org.hibernate.type.EntityType.getIdentifier(EntityType.java:456)
   at org.hibernate.type.ManyToOneType.isDirty(ManyToOneType.java:265)
   at org.hibernate.type.ManyToOneType.isDirty(ManyToOneType.java:275)
   at org.hibernate.type.TypeHelper.findDirty(TypeHelper.java:295)
   at org.hibernate.persister.entity.AbstractEntityPersister.findDirty(AbstractEntityPersister.java:3378)
   at org.hibernate.event.def.DefaultFlushEntityEventListener.dirtyCheck(DefaultFlushEntityEventListener.java:520)
   at org.hibernate.event.def.DefaultFlushEntityEventListener.isUpdateNecessary(DefaultFlushEntityEventListener.java:230)
   at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:154)
   at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:219)
   at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:99)
   at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)
   at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
   at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:383)
   at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:133)

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
   "-//Hibernate/Hibernate Mapping DTD//EN"
   "http://www.hibernate.org/dtd/hibernate-mapping-3.0.dtd" >

<hibernate-mapping package="org.local.model.data">
   <class name="Chapter" table="chapters">
      <meta attribute="sync-DAO">false</meta>

      <id name="Id" type="integer" column="ID">
         <generator class="identity" />
      </id>

      <property name="Name" column="Name" type="string" not-null="true" length="45" />

      <set name="Categories" table="chapters_categories" lazy="false" cascade="all-delete-orphan" order-by="CategoryID">
         <key column="ChapterID" not-null="true" />
         <one-to-many class="org.local.model.data.ChapterCategory" />
      </set>
   </class>
</hibernate-mapping>

CREATE TABLE `chapters` (
  `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `Name` varchar(45) NOT NULL,
  `Rank` smallint(5) unsigned NOT NULL,
  PRIMARY KEY (`ID`)
) ENGINE=InnoDB AUTO_INCREMENT=1;

<?xml version="1.0"?>
<!DOCTYPE hibernate-mapping PUBLIC
   "-//Hibernate/Hibernate Mapping DTD//EN"
   "http://www.hibernate.org/dtd/hibernate-mapping-3.0.dtd" >

<hibernate-mapping package="org.local.model.data">
   <class name="ChapterCategory" table="chapters_categories">
      <meta attribute="sync-DAO">false</meta>
      <id name="Id" type="integer" column="ID">
         <generator class="identity" />
      </id>

      <many-to-one name="Chapter" class="Chapter" column="ChapterID" not-null="true" lazy="false" insert="false"
         update="false" />
      <many-to-one name="Category" class="Category" column="CategoryID" not-null="true" lazy="false" />

      <property name="QuestionCount" column="QuestionCount" type="short" not-null="true" />
   </class>
</hibernate-mapping>

CREATE TABLE `chapters_categories` (
  `ID` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `ChapterID` int(10) unsigned NOT NULL,
  `CategoryID` int(10) unsigned NOT NULL,
  `QuestionCount` smallint(5) unsigned NOT NULL,
  PRIMARY KEY (`ID`),
  UNIQUE KEY `chapter_category` (`ChapterID`,`CategoryID`),
  KEY `chapter` (`ChapterID`),
  KEY `category` (`CategoryID`),
  CONSTRAINT `category` FOREIGN KEY (`CategoryID`) REFERENCES `categories` (`ID`) ON UPDATE CASCADE,
  CONSTRAINT `chapter` FOREIGN KEY (`ChapterID`) REFERENCES `chapters` (`ID`) ON DELETE CASCADE ON UPDATE CASCADE
) ENGINE=InnoDB AUTO_INCREMENT=1;

   public boolean isAlwaysDirtyChecked() {
      // If we have <tt>not-found="ignore"</tt> association mapped to a
      // formula, we always need to dirty check it, so we can update the
      // second-level cache
      return ignoreNotFound;
   }

public boolean isAlwaysDirtyChecked() {
      // always need to dirty-check, even when non-updateable;
      // this ensures that when the association is updated,
      // the entity containing this association will be updated
      // in the cache
      return true;
   }

<many-to-one name="Chapter" class="Chapter" column="ChapterID" not-null="true" lazy="false" insert="false"
         update="false" not-found="ignore" />

      <many-to-one name="Chapter" class="Chapter" column="ChapterID" not-null="true" lazy="false" insert="false"
         update="false" cascade="all" />