Tengo una plantilla de aplicación muy simple que incluye una base de datos derby de Apache incorporada a través de hibernación.

Tengo la siguiente configuración:

    <property name="hibernate.dialect"> org.hibernate.dialect.DerbyTenSevenDialect</property>
    <property name="hibernate.connection.driver_class"> org.apache.derby.jdbc.EmbeddedDriver </property>
    <property name="hibernate.connection.username"></property>
    <property name="hibernate.connection.password"></property>
    <property name="current_session_context_class">thread</property>
    <property name="connection.pool_size">10</property>
    <property name="connection.provider_class">org.hibernate.service.jdbc.connections.internal.C3P0ConnectionProvider</property>
    <property name="hibernate.c3p0.acquire_increment">1</property>
    <property name="hibernate.c3p0.min_size">5</property>
    <property name="hibernate.c3p0.max_size">20</property>
    <property name="hibernate.c3p0.timeout">300</property>
    <property name="hibernate.c3p0.idle_test_period">3000</property>
    <property name="hibernate.c3p0.max_statements">50</property>
    <property name="hibernate.c3p0.testConnectionOnCheckout">true</property>
    <property name="hibernate.hbm2ddl.auto">update</property>
    <property name="cache.use_second_level_cache">false</property>
    <property name="cache.use_query_cache">false</property>
    <property name="cache.provider_class">org.hibernate.cache.NoCacheProvider</property>
    <property name="hibernate.show_sql">false</property>
    <property name="hibernate.format_sql">false</property>

y el método init para SessionFactory es:

public static void init(String hibernateConfigurationResource,String connectionUrl) {
    try {
        configuration = new Configuration();
        configuration.configure(hibernateConfigurationResource);
        if (connectionUrl == null || connectionUrl.length() == 0) {
            connectionUrl = "myDb";
        } else {
            connectionUrl += File.separator + "myDb";
        }
        File f = new File(connectionUrl);
        if (logger.isDebugEnabled()) {
            logger.debug("Using db path: " + f.getAbsolutePath());
        }
        if (!f.exists()) {
            if (logger.isDebugEnabled()) {
                logger.debug("Database does not exist: creating");
            }
            connectionUrl += ";create=true";
        }
        configuration
                .setProperty("hibernate.connection.url", "jdbc:derby:"
                    + connectionUrl);

        serviceRegistry =
            new ServiceRegistryBuilder().applySettings(configuration.getProperties()).buildServiceRegistry();
        sessionFactory = configuration.buildSessionFactory(serviceRegistry);
    } catch (Throwable ex) {
        throw new ExceptionInInitializerError(ex);
    }
}

y en la fase de destrucción, este método se llama:

public static void destroy() throws SQLException {
    String connectionUrl = configuration
            .getProperty("hibernate.connection.url").replace(";create=true", "");
    try {
        if (logger.isDebugEnabled()) {
            logger.debug("Shutting down database: " + connectionUrl);
        }
        DriverManager.getConnection(connectionUrl + ";shutdown=true");
    } catch (SQLNonTransientConnectionException e) {
        if (logger.isDebugEnabled()) {
            logger.debug(e.getMessage());
        }
        String message = e.getMessage();
        if (!(message.startsWith("Database") && message
                .endsWith("shutdown."))) {
            throw e;
        }
    }
    try {
        Session s = sessionFactory.getCurrentSession();
        if (s.isDirty()) {
            s.flush();
        }
        s.disconnect();
        s.close();
        sessionFactory.close();
    } catch (Exception e) {
        logger.error(e);
    }

    Enumeration<Driver> drivers = DriverManager.getDrivers();
    while (drivers.hasMoreElements()) {
        Driver driver = drivers.nextElement();
        try {
            logger.info("Deregistering jdbc driver: " + driver);
            DriverManager.deregisterDriver(driver);
        } catch (SQLException e) {
            logger.warn("Error deregistering driver " + driver, e);
        }

    }
}

Noté que la aplicación se está ejecutando bien, pero tan pronto como detengo el tomcat, veo los siguientes mensajes:

INFO: Stopping service Catalina
apr 17, 2013 4:34:36 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/myWebApp-webapp] appears to have started a thread named [Timer-1] but has failed to stop it. This is very likely to create a memory leak.
apr 17, 2013 4:34:36 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/myWebApp-webapp] appears to have started a thread named [com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#0] but has failed to stop it. This is very likely to create a memory leak.
apr 17, 2013 4:34:36 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/myWebApp-webapp] appears to have started a thread named [com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#1] but has failed to stop it. This is very likely to create a memory leak.
apr 17, 2013 4:34:36 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/myWebApp-webapp] appears to have started a thread named [com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread-#2] but has failed to stop it. This is very likely to create a memory leak.
apr 17, 2013 4:34:36 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/myWebApp-webapp] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@106f4e54]) and a value of type [org.apache.derby.iapi.services.context.ContextManager] (value [org.apache.derby.iapi.services.context.ContextManager@587cc9a3]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
apr 17, 2013 4:34:36 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/myWebApp-webapp] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@106f4e54]) and a value of type [org.apache.derby.iapi.services.context.ContextManager] (value [org.apache.derby.iapi.services.context.ContextManager@2e704a6]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
apr 17, 2013 4:34:36 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/myWebApp-webapp] created a ThreadLocal with key of type [java.lang.ThreadLocal] (value [java.lang.ThreadLocal@106f4e54]) and a value of type [org.apache.derby.iapi.services.context.ContextManager] (value [org.apache.derby.iapi.services.context.ContextManager@36bc4735]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak. 
apr 17, 2013 4:34:36 PM org.apache.coyote.AbstractProtocolHandler stop
INFO: Stopping ProtocolHandler ["http-bio-8080"]
apr 17, 2013 4:34:36 PM org.apache.coyote.AbstractProtocolHandler stop
INFO: Stopping ProtocolHandler ["ajp-bio-8009"]

Estoy bastante seguro de que el problema está en el nivel de agrupación de conexiones, ya que Hibernate no puede cerrar correctamente el proveedor de conexiones c3p0. Intenté también con mysql y el problema sigue ahí.

También soy consciente de la protección de tomcat contra las pérdidas de memoria (que en realidad produce esos mensajes) y estoy ejecutando Tomcat 7.0.39.

Además, no quiero mover el grupo de conexiones fuera de la aplicación (delegar el contenedor).

¿Cómo puedo decirle a Hibernate que cierre todo correctamente y evite esos mensajes? ¿Qué me estoy perdiendo?

¡Gracias de antemano!

EDITAR:

El registro en el cierre solo muestra:

2013-04-18 10:27:13,537 DEBUG [Thread-13] HibernateUtil  - Shutting down database: jdbc:derby:myDb
2013-04-18 10:27:13,555 DEBUG [Thread-13] HibernateUtil  - Database 'myDb' shutdown.
2013-04-18 10:27:13,656 DEBUG [Thread-13] SessionImpl  - Disconnecting session
2013-04-18 10:27:13,656 DEBUG [Thread-13] LogicalConnectionImpl  - Releasing JDBC connection
2013-04-18 10:27:13,658 DEBUG [Thread-13] SessionFactoryImpl  - HHH000031: Closing
2013-04-18 10:27:13,659 INFO  [Thread-13] HibernateUtil  - Deregistering jdbc driver: sun.jdbc.odbc.JdbcOdbcDriver@35849932
2013-04-18 10:27:13,659 INFO  [Thread-13] HibernateUtil  - Deregistering jdbc driver: org.apache.derby.jdbc.AutoloadedDriver40@7d7ff794

En el inicio solo tengo la siguiente línea para la clase AbstractPoolBackedDataSource:

2013-04-18 10:25:38,808 INFO  [Thread-2] AbstractPoolBackedDataSource  - Initializing c3p0 pool... com.mchange.v2.c3p0.PoolBackedDataSource@28fe617e [ connectionPoolDataSource -> com.mchange.v2.c3p0.WrapperConnectionPoolDataSource@8c36e25a [ acquireIncrement -> 1, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, debugUnreturnedConnectionStackTraces -> false, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> 2s05jr8u7u65au1gs0zth|25e62c36, idleConnectionTestPeriod -> 3000, initialPoolSize -> 3, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 0, maxIdleTime -> 300, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 20, maxStatements -> 50, maxStatementsPerConnection -> 0, minPoolSize -> 5, nestedDataSource -> com.mchange.v2.c3p0.DriverManagerDataSource@423e8f48 [ description -> null, driverClass -> null, factoryClassLocation -> null, identityToken -> 2s05jr8u7u65au1gs0zth|363bec9c, jdbcUrl -> jdbc:derby:myDb, properties -> {user=******, password=******} ], preferredTestQuery -> null, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> true, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false; userOverrides: {} ], dataSourceName -> null, factoryClassLocation -> null, identityToken -> 2s05jr8u7u65au1gs0zth|43ba9cea, numHelperThreads -> 3 ]