Example main.tex

\pdfoutput=1
\pdfcompresslevel=9
\documentclass[a4paper,onecolumn,oneside,12pt,wide,floatssmall]{mwrep}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsthm}
\usepackage{bookman}

\usepackage{geometry}
\usepackage{t1enc}
\usepackage[pdftex, bookmarks]{hyperref}
\def\url#1{{ \tt #1}}

\usepackage{paralist}
\usepackage{subfig}
\usepackage{listings}
\usepackage{placeins}
\usepackage{url}

\usepackage{MnSymbol}
\usepackage{etoolbox}
\usepackage{tocvsec2}


% margins
\textwidth\paperwidth
\advance\textwidth -55mm
\oddsidemargin-0.9in
\advance\oddsidemargin 33mm
\evensidemargin-0.9in
\advance\evensidemargin 33mm
\topmargin -1in
\advance\topmargin 25mm
\setlength\textheight{44\baselineskip}
\addtolength\textheight{\topskip}
\marginparwidth15mm

\clubpenalty=10000
\widowpenalty=10000
\brokenpenalty=10000
\sloppy

\tolerance4500
\pretolerance250
\hfuzz=1.5pt
\hbadness1450

\renewcommand{\chaptermark}[1]{\markboth{\scshape\small\bfseries \
#1}{\small\bfseries \ #1}}
\renewcommand{\sectionmark}[1]{\markboth{\scshape\small\bfseries\thesection.\
#1}{\small\bfseries\thesection.\ #1}}
%\renewcommand{\headrulewidth}{0.5pt}
%\renewcommand{\footrulewidth}{0.pt}
\pagestyle{uheadings}

\usepackage[pdftex]{color,graphicx}

\usepackage[utf8]{inputenc}

\usepackage[sort, compress]{cite}

\definecolor{ListingBackground}{rgb}{0.95,0.95,0.95}
\BeforeBeginEnvironment{lstlisting}{\exhyphenpenalty=100}
\AfterEndEnvironment{lstlisting}{\exhyphenpenalty=10000}

\begin{document}

\pagenumbering{roman}
\renewcommand{\baselinestretch}{1.0}
\raggedbottom
\input{title}

\tableofcontents

\newpage
\pagenumbering{arabic}
\setcounter{page}{1}
\linespread{1.2}
\selectfont

\input{Chap1}
\input{Chap2}
\input{Chap3}
\input{Chap4}
\input{Chap5}
\input{Chap6}

\nocite{*}
\bibliographystyle{plain}
\bibliography{bib/other}

\settocdepth{part}
\include{MyPublications}
\settocdepth{section}

\end{document}