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I'm going to resubmit a 'major revisions'-paper to a journal. In the cover letter I describe changes I've made. Obviously, I mention some other papers in the debate:

"I developed and strengthened my criticism of XYZ(2010) in the following way..." etc.

Which reference-style should I use. (Reference section looks stupid at the end of a letter, doesn't it?) Or should I treat references in the manuscript itself as a reference section for the letter?

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    You are overthinking it. It doesn't matter. Whatever is clear for the 3-4 people who are going to read the letter will work. – Federico Poloni Jan 7 '16 at 15:54
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In my opinion, what you really need to worry about here is clarity. Cover letters do not generally have a prescribed style, so you can probably pick whatever style is most clear in place---that will not be a number pointing to a different section or document.

Personally, I'd probably not do any formal citation at all, but instead just reference the work in prose, e.g.,

I developed and strengthened my criticism of XYZ's 2010 paper in the following way..."

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