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DirectoryModuleCatalog use of ReflectionOnlyLoad forces an exact match to dependent assemblies.
Assembly.ReflectionOnlyLoad does not inspect the publishers policies, but requires that the exact version be present on the system. Assembly.Load DOES inspect the publishers policies and will allow a binding redirect.
The DirectoryModuleCatalog does a ReflectionOnlyLoad in order to determine which modules are available in the module directory. The use of ReflectionOnlyLoad puts a restriction on module loading that any referenced assemblies must be the same version that it was built against. Even though during a normal Assembly.Load it may successfully bind to a more current version. This is true with .NET core assemblies like System.Core.
DirectoryModuleCatalog could change to use Assembly.Load instead of ReflectionOnlyLoad. The ModuleCatalog uses a temporary AppDomain and disposes it after discovering all modules, so there shouldn't be a concern of assemblies being left loaded. I have done this in a local copy of Microsoft.Practices.Prism.dll and this seems to correct the problem.