Using SVN version of Subversion. Custom repository library embeds the SqlMap.config file into the assembly as a resource. The following is the initialization code that is used to setup the various custom repositories (shared base class):

protected static void Initialize()
{
  ConfigurationSetting configurationSetting = new ConfigurationSetting();
  configurationSetting.Properties.Add("nullableInt", "int?");

  string resource = String.Format("assembly://{0}/Configuration/SqlMap.config", Assembly.GetAssembly(typeof(BaseRepository)).GetName().Name);
  try {
    IConfigurationEngine engine = new DefaultConfigurationEngine(configurationSetting);
    engine.RegisterInterpreter(new XmlConfigurationInterpreter(resource));

    IMapperFactory mapperFactory = engine.BuildMapperFactory();
    _sessionFactory = engine.ModelStore.SessionFactory;
    _dataMapper = ((IDataMapperAccessor) mapperFactory).DataMapper;
  }
  catch (Exception ex) {
    Exception e = ex;
    while (e != null) {
      Console.WriteLine(e.Message);
      Console.WriteLine(e.StackTrace);
      e = e.InnerException;
    }
    throw;
  }

However, when attempting to use the specified custom data repository in a T4 template, a System.IO.FileNotFoundException is generated with the name of the assembly containing the repository.

When tracing the problem, I discovered that if I pass in the fully qualified assembly name (Name=mydata,Version=1.0,etc) to the Assembly.Load function, it would work. My first thought was to just update the assembly:// reference with the full assembly name, however the new Uri() fails validation when creating the Uri. Instead, I updated the AssemblyResource() constructor to do a try catch, first attempting to load the resource as before and then to walk the loaded assembly references looking for a name match.

        assembly = Assembly.Load(resourceAssemblyName);

change to

        try {
          assembly = Assembly.Load(resourceAssemblyName);
        }
        catch (FileNotFoundException) {
          // Attempt to find assembly in loaded assembly list
          int index = 0;
          Assembly[] assemblies = AppDomain.CurrentDomain.GetAssemblies();
          while ((assembly == null) && (index < assemblies.Length)) {
            if (String.Compare(assemblies[index].GetName().Name, resourceAssemblyName) == 0) {
              assembly = assemblies[index];
            }
            index++;
          }
        }

Similar changes were made to TypeResolver.cs and DbProvider.cs. There should probably be a LoadAssembly() function created in a common module shared by all projects.

When not running in the T4 context, the exception is not thrown, so I'm assuming this is a dynamic compiler issue. The additional check to find the referenced assembly for the user shouldn't adversely affect performance.