main.tex

\documentclass[12pt]{report}
\usepackage[letterpaper,margin=1.0in,left=1.5in]{geometry}

% for double table of contents: https://tex.stackexchange.com/questions/260445/separate-table-of-contents-for-appendix
\usepackage{etoc}

% packages used
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}

\usepackage[format=plain,font=small,labelfont=bf,textfont=up]{caption}
\usepackage{graphicx}

\usepackage{natbib}
\usepackage{setspace}
\setstretch{1.05}

\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{amsthm}
\usepackage{bbm}
\usepackage{mathtools}
\mathtoolsset{showonlyrefs,showmanualtags}
\usepackage{xcolor}

\usepackage{blindtext} % used only for generating fake text

\usepackage[hidelinks]{hyperref} % this should go last apparently?

\input{content/commands}

\begin{document}
	
%%%%%%%%%%%%%%%%%
% Preamble to Dissertation
%%%%%%%%%%%%%%%%%
	
\pagenumbering{gobble}

\input{content/abstract}

\input{content/title-page}

\input{content/copyright}

\input{content/dedication}

\pagenumbering{roman}
\setcounter{page}{3}

\input{content/acknowledgment}

% set up main table of contents
\etocdepthtag.toc{mtchapter}
\etocsettagdepth{mtchapter}{subsection}
\etocsettagdepth{mtappendix}{none}
\tableofcontents

\newpage
\pagenumbering{arabic}

%%%%%%%%%%%%%%%%%
% Main Body of Dissertation
%%%%%%%%%%%%%%%%%

\input{content/intro}

\input{content/chapter-1}

\input{content/chapter-2}

%%%%%%%%%%%%%%%%%
% Bibliography
%%%%%%%%%%%%%%%%%

\bibliographystyle{apalike}

\begin{singlespace}
	\bibliography{main.bib}
\end{singlespace}

%%%%%%%%%%%%%%%%%
% Appendices
%%%%%%%%%%%%%%%%%

\newpage
\appendix

% set up appendix table of contents
\etocdepthtag.toc{mtappendix}
\etocsettagdepth{mtchapter}{none}
\etocsettagdepth{mtappendix}{subsection}
\tableofcontents

\include{content/appendix}

\end{document}