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I am using the classicthesis package.

I would like to get rid of the red boxes surrounding each item in the table of contents. I would love for the links to remain active---just without the red boxes.

In fact, I would love for all links (citations, references to theorems) to remain active without any special notation (no difference in color, no boxes...just transport the reader to the indicated place when clicked upon).

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You need to tell the package hyperref you want zero-width border around your links; just call this after classicthesis has been loaded:

\hypersetup{
            pdfborder={0 0 0}
           }

Here are a few more options with their default values that might be interesting to you:

            colorlinks=true,
            urlcolor=CTurl, 
            linkcolor=CTlink, 
            citecolor=CTcitation

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