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thesis.tex
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\documentclass[12pt,final]{article}
\usepackage{mystyle}
\input{mymacros}
%%% BEGIN DOCUMENT
\begin{document}
\subfile{./tex/tiitelleht}
% If the thesis is printed on both sides of the page then
% the second page must be must be empty. Comment this out
% if you print only to one side of the page comment this out
%\newpage
%\thispagestyle{empty}
%\phantom{Text to fill the page}
% END OF EXTRA PAGE WITHOUT NUMBER
\subfile{./tex/infoleht}
\newpage
\pdfbookmark[section]{\contentsname}{toc}
% disable microtype protrusion to make page numbers perfectly aligned - http://www.khirevich.com/latex/microtype/
\microtypesetup{protrusion=false}
\tableofcontents
\microtypesetup{protrusion=true}
% Remember to remove this from the final thesis version
\newpage
\listoftodos[Unsolved issues]
% END OF TODO PAGE
\subfile{./tex/sissejuhatus}
\subfile{./tex/domeenid}
\subfile{./tex/omadused}
\subfile{./tex/testimine}
\subfile{./tex/kokkuvote}
\newpage
% Use Biblatex if you have problems with Estonian keywords
\printbibliography[heading=bibintoc] %biblatex
%\nocite{*}
\newpage
% https://tex.stackexchange.com/a/121778
\bookmarksetupnext{level=chapter}
\begin{appendices}
% https://tex.stackexchange.com/a/64404
\makeatletter
\addtocontents{toc}{\let\protect\l@section\protect\l@subsection}
\makeatother
\renewcommand\thesection{\Roman{section}}
%\section{Glossary}
%Stuff
\subfile{./tex/itersolve}
\subfile{./tex/lahtekood}
\subfile{./tex/goblint-domeenid}
\subfile{./tex/litsents}
\end{appendices}
\end{document}