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I have a main document (manuscript) and a supplemental document.

I wonder if there is a way that I can "link" the two (make them recognize each other) so that section, equation, and figure references across documents are recognized?

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Look at Does hyperref work between two files? – Danie Els Apr 25 '12 at 14:31
possible duplicate how-to-reference-another-document-in-latex – cmhughes Apr 25 '12 at 14:40
Yes, looks that way. Thanks. – crippledlambda Apr 25 '12 at 19:48
up vote 5 down vote accepted

The xr package is probably what you need.

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And also xr-hyper if hyperref is needed. – egreg Apr 25 '12 at 14:31

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