Main.tex

% UCL Thesis LaTeX Template
%  (c) Ian Kirker, 2014
% 
% This is a template/skeleton for PhD/MPhil/MRes theses.
%
% It uses a rather split-up file structure because this tends to
%  work well for large, complex documents.
% We suggest using one file per chapter, but you may wish to use more
%  or fewer separate files than that.
% We've also separated out various bits of configuration into their
%  own files, to keep everything neat.
% Note that the \input command just streams in whatever file you give
%  it, while the \include command adds a page break, and does some
%  extra organisation to make compilation faster. Note that you can't
%  use \include inside an \include-d file.
% We suggest using \input for settings and configuration files that
%  you always want to use, and \include for each section of content.
% If you do that, it also means you can use the \includeonly statement
%  to only compile up the section you're currently interested in.
% You might also want to put figures into their own files to be \input.

% For more information on \input and \include, see:
%  http://tex.stackexchange.com/questions/246/when-should-i-use-input-vs-include


% Formatting rules for theses are here: 
%  http://www.ucl.ac.uk/current-students/research_degrees/thesis_formatting
% Binding and submitting guidelines are here:
%  http://www.ucl.ac.uk/current-students/research_degrees/thesis_binding_submission

% This package goes first and foremost, because it checks all 
%  your syntax for mistakes and some old-fashioned LaTeX commands.
% Note that normally you should load your documentclass before 
%  packages, because some packages change behaviour based on
%  your document settings.
% Also, for those confused by the RequirePackage here vs usepackage
%  elsewhere, usepackage cannot be used before the documentclass
%  command, while RequirePackage can. That's the only functional
%  difference as far as I'm aware.
\RequirePackage[l2tabu, orthodox]{nag}


% ------ Main document class specification ------
% The draft option here prevents images being inserted,
%  and adds chunky black bars to boxes that are exceeding 
%  the page width (to show that they are).
% The oneside option can optionally be replaced by twoside if
%  you intend to print double-sided. Note that this is
%  *specifically permitted* by the UCL thesis formatting
%  guidelines.
%
% Valid options in terms of type are:
%  phd
%  mres
%  mphil
%\documentclass[12pt,phd,draft,a4paper,oneside]{ucl_thesis}
\documentclass[12pt,phd,a4paper,oneside]{ucl_thesis}


% Package configuration:
%  LaTeX uses "packages" to add extra commands and features.
%  There are quite a few useful ones, so we've put them in a 
%   separate file.
\input{MainPackages}

% Sets up links within your document, for e.g. contents page entries
%  and references, and also PDF metadata.
% You should edit this!
\input{LinksAndMetadata}

% And then some settings in separate files.
\input{FloatSettings} % For things like figures and tables
\input{BibSettings}   % For bibliographies

% These control how many number sections your subsections will take
%    e.g. Section 2.3.1.5.6.3
%  and how many of those will get put into the contents pages.
\setcounter{secnumdepth}{3}
\setcounter{tocdepth}{3}


\begin{document}

\nobibliography*
% ^-- This is a dumb trick that works with the bibentry package to let
%  you put bibliography entries whereever you like.
% I used this to put references to papers a chapter's work was 
%  published in at the end of that chapter.
% For more information, see: http://stefaanlippens.net/bibentry

% If you haven't finished making your full BibTex file yet, you
%  might find this useful -- it'll just replace all your
%  citations with little superscript notes.
% Uncomment to use.
%\renewcommand{\cite}[1]{\emph{\textsuperscript{[#1]}}}

% At last, content! Remember filenames are case-sensitive and 
%  *must not* include spaces.
\include{Preamble}
\include{Introduction}
\include{Chapter2}
\include{Chapter3}
\include{Conclusions}
\include{Appendices} 
% You could separate these out into different files if you have
%  particularly large appendices.

% This line manually adds the Bibliography to the table of contents.
% The fact that \include is the last thing before this ensures that it
% is on a clear page, and adding it like this means that it doesn't
% get a chapter or appendix number.
\addcontentsline{toc}{chapter}{Bibliography}

% Actually generates your bibliography.
\bibliography{example}

% All done. \o/
\end{document}