main.tex

% manuscript class options:
%   proposal        - Use the proposal title page and exclude several preliminary pages.
%   review          - Show line numbers and timestamp title page.
%   onehalfspacing  - Use 1.5 line spacing instead of double.
%   pagenumhead     - Place page numbers in the header instead of the footer.
%   ieee            - Use customized IEEE biblatex style
%   apa             - Use customized APA biblatex style
%   amsthm          - Use the `amsthm` package. Added as an option to ensure correct loading order.
\documentclass[apa]{manuscript}

\usepackage[utf8]{inputenc}

% Include other packages here, before hyperref.
\usepackage{csquotes}  % Added by default to make biblatex happy when used with babel
\usepackage{enumerate}
\usepackage{booktabs}
\usepackage{subcaption}
\usepackage{appendix}  % Provides the appendices environment

\usepackage{graphicx}
\graphicspath{{images}}  % No need to prepend images/ to the path.

% Other useful packages
% \usepackage{array}
% \usepackage{pgfplots}
% \usepackage{siunitx}
% \usepackage{glossaries-extra}

% Bibliography
\usepackage[backref]{biblatex}
\addbibresource{references.bib}

% These two must be loaded last:
\usepackage{hyperref}
% Support for easy cross-referencing. Should be loaded after hyperref.
\usepackage{cleveref}

\begin{document}

\frontmatter
\printpreliminarypages

\mainmatter
% The guide outlined in these chapters was created by Dr. Rowel Atienza.
\input{chapters/1-introduction}
\input{chapters/2-related_work}
\input{chapters/3-problem_statement}
\input{chapters/4-methodology}
\input{chapters/5-results}
\input{chapters/6-analysis}
\input{chapters/7-conclusion}

\begin{singlespace}
\printbibliography[heading=bibintoc]
\end{singlespace}

% Seems redundant, but we need \appendix so that cross-references will be shown as "Appendix..." and not as "Chapter..." or Section.
% Usage of the appendices environment is required to change the ToC entries to "Appendix A" instead of just "A".
\appendix
\begin{appendices}
\input{chapters/appendices}
\end{appendices}

% \printunsrtglossary  % if using glossaries-extra

\end{document}