\documentclass[12pt]{report}

% Custom packages
\input{misc/packages}

% Sets up the bib files
\input{bibliography/bib-setup}

% Make title page
\input{misc/title-page}

% Avoid reset of footnote counter through chapters
\counterwithout{footnote}{chapter}

\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}

\appendix
\appendixpage
\addappheadtotoc
\input{chapters/appendix/appendix}

% end of thesis body
% --------------------------

% Prints out the references
\newpage
\fancyhead[L]{Βιβλιογραφία}
\fancyhead[R]{}
\printbibliography[heading=bibintoc]

\end{document}