\documentclass[10pt,twoside]{report} 

% Files to include
\includeonly{
    preamble/title,
    preamble/authorship,
    preamble/abstract,
    preamble/acknowledgements,
    chapters/introduction,
    chapters/chap1,
    chapters/chap2,
    chapters/chap3,
    chapters/conclusion,
}

% Boolean variables
\newif \ifcontents \contentsfalse
\newif \ifbib \bibtrue
\newif \iflong \longtrue

% Packages
\usepackage[utf8]{inputenx} 
\usepackage[english]{babel}
\usepackage{microtype}
\usepackage{fancyhdr}
\usepackage{listings}
\usepackage{appendix}
\usepackage{vmargin}
\usepackage{setspace}
\usepackage{mathenv}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amscd}
\usepackage{amsthm}
\usepackage{hyperref}
\usepackage{cleveref}
\usepackage{graphicx}
\usepackage{epstopdf}
\usepackage{subfigure}
\usepackage{color}

% Packages with options
\usepackage[labelfont=sc]{caption}
\usepackage[square, numbers, comma, sort&compress]{natbib}

% Layout options
\setlength{\parskip}{6pt}

% Compilation options
\synctex=1

% Setting for the table of contents
\setcounter{secnumdepth}{3}
\setcounter{tocdepth}{3}

% Macros
\definecolor{darkred}{rgb}{.7,0,0}
\newcommand{\real}[0]{\mathbf R} 
\newcommand{\nat}[0]{\mathbf N} 
\newcommand{\op}[0]{\mathcal} 
\newcommand{\grad}[0]{\,\nabla\,}
\newcommand{\dive}[0] {\,\nabla\,\cdot\,} 
\newcommand{\ip}[2]{\left \langle #1,#2 \right\rangle} 
\newcommand{\norm}[1]{\,\| #1 \|\,} 
\newcommand{\pard}[2]{\partial_{#2} #1} 
\newcommand{\pardl}[2]{\frac{\partial #1}{\partial #2}} 
\newcommand{\pardd}[2]{\partial_{#2}^2 #1} 
\newcommand{\parddl}[2]{\frac{\partial^2 #1}{\partial #2^2}} 
\newcommand{\dx}[0]{\mathrm d}
\newcommand{\hermite}[0]{\mathcal}
\newcommand{\gaussian}[1]{g_{#1}} 
\newcommand{\stdgaussian}[0]{g} 
\newcommand{\test}[1]{C^\infty_c(#1)} 
\newcommand{\flp}[2]{L^{#1}(#2)}
\newcommand{\wlp}[3]{L^{#1}(#2, #3)}
\newcommand{\sobolev}[2]{H^{#1}(#2)}
\newcommand{\wsobolev}[3]{H^{#1}(#2, #3)}
\newcommand{\red}[1]{\textcolor{darkred}{#1}}
\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}

% Theorems
\theoremstyle{plain}
\newtheorem{assumption}{Assumption}[section]
\newtheorem{example}{Example}[section]
\newtheorem{theorem}{Theorem}[section]
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{axiom}[theorem]{Axiom}
\theoremstyle{definition}
\newtheorem{definition}[theorem]{Definition}
\theoremstyle{remark}
\newtheorem{remark}[theorem]{Remark}

\begin{document}

\pagestyle{empty}

\setstretch{1.3} 
\include{preamble/title} \cleardoublepage
\include{preamble/authorship} \cleardoublepage
\include{preamble/abstract} \cleardoublepage
\include{preamble/acknowledgements} \cleardoublepage
\ifcontents \tableofcontents \fi

\pagestyle{plain}


\include{chapters/introduction} \cleardoublepage
\include{chapters/chap1} \cleardoublepage
\include{chapters/chap2} \cleardoublepage
\include{chapters/chap3} \cleardoublepage
\include{chapters/conclusion} \cleardoublepage

\nocite*
\bibliographystyle{unsrtnat} 
\bibliography{Bibliography} 

\end{document}