Agreed on the breaking change. I've created #268 to track it, marked as breaking and assigned to the new 2.0 milestone.

I think for 1.x, I'd prefer to have failures to load assemblies logged in stdout rather than silent swallowing. The good is thing is that with the new bootstrapper, anyone who has a large number of unmanaged assemblies in their output folder can already override the behaviour today and either suppress all file system scanning or pass in the path of a specific assembly containing extensions.