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\chapter{Introduction}
Intro things \lipsum
\cite{Munn1999,Chomsky1981}
\section{A section}
\lipsum[1]
\subsection{A subsection}
\lipsum[2]

\bibliographystyle{apalike}
\bibliography{MSU-thesis-testfile}

\begin{appendix}
\chapter{An appendix}
This is some text
\end{appendix}