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A while ago I was having issues using configuring fluent NHibernate with an external configuration file. I kept running into the issue of mappings not being registered. I was finally able to get it working appropriately and thought I would share my solution. The key is to configure the normal mappings first and then pass that configuration in when configuring fluent NHibernate.

string configFile = "hibernate.cfg.xml";

//setup the normal map configuration
Configuration normalConfig = new Configuration().Configure(configFile);

//setup the fluent map configuration
Fluently.Configure(normalConfig)
	.Mappings(
		m => m.FluentMappings
		.ConventionDiscovery.Add(DefaultLazy.AlwaysFalse())
		.AddFromAssemblyOf<UserMap>())
	.BuildConfiguration();