copy_nodes_and_elements isn't passing defaults to add_extra_integers

[roystgnr]

And then it's only copying over integers that existed on an old DofObject, so when copying from meshes that don't have some of our own extra integers, we might find our newly copied nodes and elements with values initialized to -1 rather than to any user-specified different default.

(Our existing nodes and elements ought to be getting the proper new defaults via the calls in merge_extra_integer_names)