main.tex

\documentclass[letterpaper,12pt,oneside,openany]{book}
\usepackage[top=1in, bottom=1in, left=1in, right=1in]{geometry}
\usepackage[utf8]{inputenc}
\usepackage{graphicx}
\usepackage{pdfpages}
\usepackage{afterpage}

% this is where to put figures you're including (I just made PNGs of everything)
\graphicspath{ {figures/} }

\usepackage[utf8]{inputenc}
\usepackage[greek,ngerman,english]{babel}

\usepackage[space]{grffile}
\usepackage{latexsym}
\usepackage{textcomp}
\usepackage{longtable}
\usepackage{multirow,booktabs}
\usepackage{amsfonts,amsmath,amssymb}
\usepackage{setspace}
\usepackage{caption}
\captionsetup[figure]{hypcap=false}

\usepackage[super,comma,sort&compress]{natbib}

% Add Bibliography to the table of contents
\usepackage[nottoc]{tocbibind}

\PassOptionsToPackage{hyphens}{url}
\usepackage[hyperfigures,breaklinks,pagebackref,hidelinks]{hyperref}
\renewcommand{\thefootnote}{\fnsymbol{footnote}}
\usepackage[nameinlink]{cleveref}

% code to remove things from ToC (from https://tex.stackexchange.com/questions/272070/)
\newcommand*{\BeginNoToc}{%
	\addtocontents{toc}{%
		\edef\protect\SavedTocDepth{\protect\the\protect\value{tocdepth}}%
	}%
	\addtocontents{toc}{%
		\protect\setcounter{tocdepth}{-10}%
	}%
}
\newcommand*{\EndNoToc}{%
	\addtocontents{toc}{%
		\protect\setcounter{tocdepth}{\protect\SavedTocDepth}%
	}%
}

\bibliographystyle{unsrtnat}
\doublespacing

\begin{document}

\frontmatter
% download the official title page from http://graduate.ucsf.edu/forms/
% and fill it out, export a copy to remove the forms, and include it here
% (or eventually the signed scanned version)
\includepdf{titlePageExport.pdf}
\afterpage{\thispagestyle{plain}\null\newpage}
\include{./TeX_files/acknowledgments}
\include{./TeX_files/abstract}
\tableofcontents
\BeginNoToc
\listoftables
\listoffigures
\EndNoToc

\mainmatter
\include{./TeX_files/introduction}
\include{./TeX_files/chapter02}
\include{./TeX_files/chapter03}
\include{./TeX_files/chapter04}
\include{./TeX_files/chapter05}
\include{./TeX_files/chapter06}
\include{./TeX_files/chapter07}

\backmatter
% bibliography, glossary and index would go here.

% I named my biblatex file "biblio.bib". You're on your own with this crap.
\bibliography{biblio}

% print this out, add the right page number, sign it/scan it, then include it as pdf
%\BeginNoToc
\includepdf{publishing_agreement.pdf}
%\EndNoToc
\end{document}