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I figure I should be smart enough to figure this out on my own, but I'm just so convinced that I must be wrong. According to the USAO SDNY summer intern page (--LinkRemoved--), none of the four things you need is a cover letter. So, how would you go about mentioning your pref. for civil or criminal on the resume? Just add a random line at the bottom?

That's part of the data sheet. Hopefully they fixed their system from last year -- applying was a nightmare.