manuscript.tex

\documentclass[11pt]{article}

% Include a series of generic definitions and usepackage commands
\input{mediabuilder.tex}
\RequirePackage[top=0.75in,left=0.75in,right=0.75in,bottom=0.75in]{geometry}


\usepackage{pdfpages}
\usepackage[skip=2pt, font=small, format=plain, labelfont=it, textfont=it, tableposition=below]{caption}

\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}

% colors
\definecolor{bluehaze}{RGB}{54,95,145}
\definecolor{maroonhaze}{RGB}{148,54,52}
\definecolor{orangehaze}{RGB}{227,108,10}
\definecolor{black}{RGB}{0,0,0}

%  This is used to allow Shaded environment
$if(highlighting-macros)$
$highlighting-macros$
$endif$


\usepackage{needspace}

\ifxetex
  \usepackage{fontspec,xltxtra,xunicode}
  \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
\else
  \ifluatex
    \usepackage{fontspec}
    \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
  \else
    \usepackage[utf8]{inputenc}
  \fi
\fi
$if(natbib)$
\usepackage{natbib}
\bibliographystyle{plainnat}
$endif$
$if(biblatex)$
\usepackage{biblatex}
$if(biblio-files)$
\bibliography{$biblio-files$}
$endif$
$endif$
$if(lhs)$
\usepackage{listings}
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
$endif$
$if(fancy-enums)$
% Redefine labelwidth for lists; otherwise, the enumerate package will cause
% markers to extend beyond the left margin.
\makeatletter\AtBeginDocument{%
  \renewcommand{\@listi}
    {\setlength{\labelwidth}{4em}}
}\makeatother
\usepackage{enumerate}

% Attempt to smash lists together
\setlist[enumerate]{itemsep=1mm}

$endif$
$if(tables)$
\usepackage{ctable}
\usepackage{float} % provides the H option for float placement
$endif$
$if(url)$
\usepackage{url}
$endif$
$if(graphics)$
\usepackage{graphicx}
% We will generate all images so they have a width \maxwidth. This means
% that they will get their normal width if they fit onto the page, but
% are scaled down if they would overflow the margins.
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth
\else\Gin@nat@width\fi}
\makeatother
\let\Oldincludegraphics\includegraphics
\renewcommand{\includegraphics}[1]{\Oldincludegraphics[width=\maxwidth]{#1}}
$endif$
\usepackage{caption}
\DeclareCaptionLabelFormat{nolabel}{}
\captionsetup{labelformat=nolabel}
\ifxetex
  \usepackage[setpagesize=false, % page size defined by xetex
              unicode=false, % unicode breaks when used with xetex
              xetex]{hyperref}
\else
  \usepackage[unicode=true]{hyperref}
\fi
\hypersetup{breaklinks=true, pdfborder={0 0 0}, colorlinks=true, urlcolor=bluehaze, linkcolor=bluehaze, citecolor=bluehaze, anchorcolor=bluehaze, allcolors=bluehaze}
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
$if(subscript)$
\newcommand{\textsubscr}[1]{\ensuremath{_{\scriptsize\textrm{#1}}}}
$endif$
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
\setlength{\emergencystretch}{3em}  % prevent overfull lines
$if(listings)$
\usepackage{listings}
$endif$
$if(numbersections)$
$else$
\setcounter{secnumdepth}{0}
$endif$
$if(verbatim-in-note)$
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$for(header-includes)$
$header-includes$
$endfor$

$if(title)$
\title{$title$}
$endif$
$if(author)$
\author{$for(author)$$author.name$$sep$ \and $endfor$}
$endif$
$if(date)$
\date{$date$}
$endif$



\usepackage{fancyhdr}
% my page number
\fancyhead{} % empty
\fancyfoot{} % empty out the default, which is page number in center
\renewcommand{\headrulewidth}{0pt}
\pagenumbering{gobble}

\usepackage{titlesec}

%\usepackage{sectsty}% http://ctan.org/pkg/sectsty
\usepackage{xcolor}% http://ctan.org/pkg/xcolor
% \sectionfont{\color{bluehaze}\normalfont\fontsize{12}{3}\selectfont}
$if(linespread)$\linespread{$linespread$}$else$
\linespread{1.0}
$endif$

% Here I am using the needspace thing to make sure that the title headings don't
% show up on the very last line of a page.

\titleformat{\section}
  {\needspace{2.5cm}\normalfont\fontfamily{phv}\fontsize{12pt}{12pt}
    \selectfont\color{black}\bfseries}{\thesection}{1em}{}

\titleformat{\subsection}
  {\needspace{2.5cm}\normalfont\fontfamily{phv}\fontsize{11pt}{11pt}
    \selectfont\color{black}\bfseries}{\thesubsection}{1em}{}

\titleformat{\subsubsection}
  {\needspace{2.5cm}\normalfont\fontfamily{phv}\fontsize{11pt}{11pt}
    \selectfont\color{black}\bfseries}{\thesubsubsection}{1em}{}


% \titlespacing{command}{left spacing}{before spacing}{after spacing}[right]
\titlespacing\section{0pt}{12pt plus 4pt minus 2pt}{-1pt plus 2pt minus 2pt}
\titlespacing\subsection{0pt}{11pt plus 4pt minus 2pt}{-1pt plus 2pt minus 2pt}
\titlespacing\subsubsection{0pt}{0pt plus 4pt minus 2pt}{-2pt plus 2pt minus 2pt}


\titlespacing{\paragraph}{0pt}{1pt plus 4pt minus 2pt}{6pt plus 2pt minus 1pt}


% this code uses titles.sty to make a pagebreak with every header 1
% so each section will begin on a new page.
%\newcommand{\sectionbreak}{\clearpage}



\usepackage{csquotes}
% I use quotes for response to reviewers. this messes with paragraph spacing.
\AtBeginEnvironment{quote}{\itshape\color{bluehaze}\vspace{0em}}
\AtEndEnvironment{quote}{\vspace{0em}}

\setlength{\topsep}{0em}
\setlength{\parskip}{0.6em}
\setlength{\partopsep}{0em}

\usepackage{enumitem}
\setlist[itemize]{leftmargin=*}


% This section was added with pandoc 2.9.
$if(csl-refs)$
\newlength{\cslhangindent}       % set up new length
\setlength{\cslhangindent}{$if(csl-hanging-indent)$2em$else$0em$endif$}
\newenvironment{cslreferences}%
  {\everypar{\setlength{\hangindent}{\cslhangindent}}}%
  {\par} % by default, this env does not change anything
$endif$


% \usepackage{etoolbox}
% \makeatletter
% \AtBeginEnvironment{quote}{\appto\@listi{\parsep\z@ \topsep\z@ \itemsep\z@}}
% \makeatother


\begin{document}

$if(title)$
\maketitle
$endif$

$for(include-before)$
$include-before$

$endfor$

$if(toc)$
\tableofcontents
$endif$

$if(abstract)$
\section{Abstract}
$abstract$
$endif$

$body$

$if(natbib)$
$if(biblio-files)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\bibliography{$biblio-files$}

$endif$
$endif$
$if(biblatex)$
\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$

$endif$
$for(include-after)$
$include-after$

$endfor$
\end{document}