Investigate alternatives to "flattening" project resources

[ryanjjung]

@malini and I have discussed the complexity and potential to misuse the exclude_from_project feature, but as yet we haven't found a better way to prevent top-level project resource namespace pollution other than this. For example, we could do a check in the finish function to see if a resource has already been registered, but this would not be aware of what resources exist as outputs prior to resolution.