tudothesis
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Consider using colorlink option of hyperref
As digital thesis submission is the new norm, the hyperref features actually have become useful. Hence, I would consider it nice to have a sensible link formatting style by default, like
\usepackage{hyperref}
\hypersetup{
pdfusetitle,
unicode,
colorlinks,
linkcolor={blue!50!black},
citecolor={blue!50!black},
urlcolor={blue!70!black}
}
(or any other colors of your choice) and thereby disabling the hideous boxes around links.