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\documentclass[12pt]{report}
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% Custom packages
\input{misc/packages}
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% Sets up the bib files
\input{bibliography/bib-setup}
% Make title page
\input{misc/title-page}
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% Avoid reset of footnote counter through chapters
\counterwithout{footnote}{chapter}
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\begin{document}
% Makes the cover page
\maketitle
\input{chapters/0.preamble/0.0.preamble}
% start of thesis body
% ---------------------------
\input{chapters/1.introduction/1.0.introduction}
\input{chapters/2.theoretical-background/2.0.theoretical-background}
\input{chapters/3.application-design/3.0.application-design}
\input{chapters/4.application-implementation/4.0.application-implementation}
\input{chapters/5.conclusions-open-areas/5.0.conclusions-open-areas}
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\appendix
\appendixpage
\addappheadtotoc
\input{chapters/appendix/appendix}
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% end of thesis body
% --------------------------
% Prints out the references
\newpage
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\fancyhead[L]{Βιβλιογραφία}
\fancyhead[R]{}
\printbibliography[heading=bibintoc]
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\end{document}