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Para configurar existen la siguiente sección

<configuration>    
  <configSections>
    <section name="simplelabs.framework" type="Simplelabs.Framework.Configuration.FrameworkSettings, Simplelabs.Framework"/>
  </configSections>
  <simplelabs.framework>
    <nhibernate sessionManager="web">
      <sessions>
        <add name="default" virtualPath="~/NHibernate.config"/>
      </sessions>
    </nhibernate>
  </simplelabs.framework>
  <connectionStrings>
    <add name="FrameworkTest" connectionString="Data Source=.;Initial Catalog=FrameworkTest;Integrated Security=True" providerName="System.Data.SqlClient"/>
  </connectionStrings>
  <system.web>
    <httpRuntime targetFramework="4.5"/>
    <compilation debug="true" targetFramework="4.5"/>
  </system.web>
  <system.webServer>
    <validation validateIntegratedModeConfiguration="false"/>
    <modules>
      <add name="simplelabs.NHibernate" type="Simplelabs.Framework.Persistence.NHibernate.NHibernateHttpModule, Simplelabs.Framework"/>
    </modules>
  </system.webServer>
</configuration>

Luego el archivo de configuración para NHibernate.config

<?xml version="1.0" encoding="utf-8" ?>
<hibernate-configuration  xmlns="urn:nhibernate-configuration-2.2" >
  <session-factory>
    <property name="connection.provider">NHibernate.Connection.DriverConnectionProvider</property>
    <property name="dialect">NHibernate.Spatial.Dialect.MsSql2012GeometryDialect, NHibernate.Spatial.MsSql</property>
    <property name="connection.driver_class">NHibernate.Driver.SqlClientDriver</property>
    <property name="connection.connection_string_name">FrameworkTest</property>
    <property name="connection.isolation">ReadCommitted</property>
    <property name="current_session_context_class">web</property>
    <property name="generate_statistics">true</property>
    <property name="cache.provider_class">NHibernate.Caches.SysCache.SysCacheProvider, NHibernate.Caches.SysCache</property>
    <property name="cache.use_query_cache">true</property>
    <property name="cache.use_second_level_cache">true</property>
    <mapping assembly="Domain" />
  </session-factory>
</hibernate-configuration>