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\documentclass{article}
\usepackage{autonum}
\usepackage{amsmath}
\begin{document}
\section{Introduction}
\label{sec:intro}
This is some text.
\begin{equation}
\label{eq:simple}
x = y + z
\end{equation}
\begin{equation}
\label{eq:complex}
\int_0^\infty e^{-x} dx = 1
\end{equation}
% This equation won't show up in aux with autonum since it's not referenced
\begin{equation}
\label{eq:orphan}
a^2 + b^2 = c^2
\end{equation}
We reference \eqref{eq:simple} here, but not the others.
\end{document}
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