I'm supposed to prove, using only primitive rules (the introduction and elimination rules for AND, OR, NOT, conditional, biconditional, existential, universal, and equality) the following:
$$\exists x~\forall y~(x=y) \to \forall x~\forall y~(x=y)$$
I checked this in a tree proof generator and the argument is indeed valid, but I can't figure out how to approach a natural deduction proof using only primitive rules here. What should my starting point be?
Your starting point should be to think about this informally: what are the statements saying that would make this valid? Well, the first statement says that there is something that is identical to everything. But if everything is identical to this one thing, then that means that there is really only that one thing, and nothing else. And so yes, the second statement would therefore also be true: everything (which is just one thing) is identical to everything (still just that one thing)
Now, as far as formally proving this using a natural deduction system goes, that all depends on the specific rules your specific deduction system has: there are many slightly different natural deduction systems, so a proof in one system may not constitute a proof in another. Why don't you post some of your own efforts in trying to make this into a proof, so you can show us some of your own effort, and at the same time it'll give us an idea exactly what system you are working with.