Use the tree ID when dealing with layers (rather than the markup id)

This is a fix for #53 and something I think both @khandelwal and @theresaanna will want to review. When we switched over to adding markup_ids distinct from the tree ids, we broke all of the layers associated with interpretations. This is because the layers all reference the tree ids (since the layers know nothing about the markup).

This change switches all layer-handling over to use the original tree id, and adds a *very* simple test to help prevent this in the future.