Fix comparisons of Ref objects #41

When the original file had the same object twice, once normally and once as a reference, when writing out, we'd write the object a second time in full, because we had Ref(x)!=y, even when x==y. We handled this correctly in the hashing code, and the writing code, but not in the comparison function. The fix is easy — just deference in one more place, but it took me forever to figure out.