main.tex

\documentclass{report}
% \documentclass{article}
\include{defs}

% generate word count text file wc.tex - This is only applied after compiling the document: i.e. $ pdflatex main.tex
\immediate\write18{bash wc.sh}

\begin{document}

% title page
\input{titlepage.tex}

% preface
% \input{sections/0-preface}

% roman numbering for abstract, TOC, glossary etc.
\pagenumbering{roman}

% abstract
\clearpage
\begin{abstract}
\input{chapters/abstract/abstract.tex}
\end{abstract}

% table of contents
\clearpage
\tableofcontents

% workload distribution
\clearpage

\input{chapters/acknowledgements/acknowledgements.tex}

\addcontentsline{toc}{section}{Acknowledgments}

% glossary & acronyms
\clearpage
\addcontentsline{toc}{section}{Acronyms and Terms}
\printglossary[type=acronym, title=Acronyms, style=mcolindex]
\printglossary[type=main, title=Terms]

% main document
\clearpage
\pagenumbering{arabic}
\glsresetall

% \pagebreak
% \input{chapters/example/example.tex}

\pagebreak
\input{chapters/introduction/introduction.tex}

\pagebreak
\input{chapters/system-setup/system-setup.tex}

\pagebreak
\input{chapters/state-of-the-art/state-of-the-art.tex}

\pagebreak
\input{chapters/modeling/modeling.tex}

\pagebreak
\input{chapters/1-problem/1-problem.tex}

\pagebreak
\input{chapters/2-problem/2-problem.tex}

\pagebreak
\input{chapters/3-problem/3-problem.tex}

\pagebreak
\input{chapters/discussion-conclusion/discussion-conclusion.tex}

% \pagebreak
% \input{chapters/conclusion/conclusion.tex}

% bibliography
\pagebreak
% \printbibliography[heading=bibintoc
% \begin{multicols}{2}[\printbibheading]
% \printbibliography[heading=none]
% \end{multicols}
\printbibliography

\newpage

\appendix

\input{chapters/appendix/appendix.tex}

\end{document}