\documentclass[a4paper,11pt,twoside]{article}
%\pdfminorversion=7 % To use charte graphique (pdf 1.7)
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{lscape}
\usepackage{boldline,multirow,tabularx,colortbl,diagbox,makecell,fancybox}
\usepackage{amsfonts,amssymb,amsmath,mathrsfs,array}
\usepackage{pgf,tikz,xcolor}
\usetikzlibrary{calc,positioning,shapes.geometric,shapes.symbols,shapes.misc, fit, shapes, arrows, arrows.meta,fadings,through}
\usepackage[top=2cm, bottom=2cm, left=4cm, right=4cm]{geometry}
\usepackage{hyperref}
\usepackage{titlesec}
\usepackage{eurosym}
\usepackage[english]{babel}
\usepackage{eso-pic} % for background on cover
\usepackage{listings}

% Define colors for code
\definecolor{codegreen}{rgb}{0,0.4,0}
\definecolor{codegray}{rgb}{0.5,0.5,0.5}
\definecolor{codepurple}{rgb}{0.58,0,0.82}
\definecolor{backcolour}{rgb}{0.95,0.95,0.92}

\lstdefinestyle{mystyle}{
    backgroundcolor=\color{backcolour},
    commentstyle=\color{codegreen},
    keywordstyle=\color{magenta},
    numberstyle=\tiny\color{codegray},
    stringstyle=\color{codepurple},
    basicstyle=\ttfamily\small,
    breakatwhitespace=false,
    breaklines=true,
    captionpos=b,
    keepspaces=true,
    numbers=left,
    numbersep=5pt,
    showspaces=false,
    showstringspaces=false,
    showtabs=false,
    tabsize=2
}

\lstset{style=mystyle}


% table des annexes
\usepackage{minitoc}
\usepackage{pdfpages}

\usepackage[style=iso-alphabetic]{biblatex}
\addbibresource{bibliography.bib}


\input{advanced.params/tikz.conf}
\input{advanced.params/misc.commands}
\input{cover/covermain.tex}

\date{\today}

\begin{document}
\dosecttoc{} % generate TOC


% % Remerciements
% \thispagestyle{empty} % removes page number
% \subsection*{Remerciements}
% \input{remerciements}
% \clearpage


% TABLE DES MATIÈRES
\thispagestyle{empty} % removes page number
\setcounter{secnumdepth}{3}
\tableofcontents
\clearpage


% Contenu
\setcounter{page}{1}
\include{content}


% BIBLIOGRAPHIE
\addcontentsline{toc}{section}{Bibliography}
\printbibliography[title={Bibliography}]



% TABLE DES ANNEXES
\clearpage
\appendix
% \thispagestyle{empty} % removes page number
\sectionnn{Table des Annexes}
% Désactivation de la table des matières
\addtocontents{toc}{\protect\setcounter{tocdepth}{0}}
% Personnalisation de la table des annexes
\renewcommand{\stctitle}{}                          % Titre (issue with previous subsection showing up)
\renewcommand\thesubsection{A\arabic{subsection}}   % Numérotation
\renewcommand{\stcSSfont}{}                         % Police normale, pas en gras
\mtcsetrules{secttoc}{off}                          % Désactivation des lignes en haut et en bas de la table
% Affichage de la table des annexes
\secttoc


% ANNEXES
\clearpage
\pagenumbering{Roman}

\subsection{Performance analysis script}
\label{annex:performance}

\input{annex-performance}

\clearpage


% \includepdf[pages={1}, scale=0.96,
% 	pagecommand=\subsection{Questionnaire 1 : Sensibilisation à l’Hygiène et à la Sécurité}]
% {questionnaires}
% \clearpage
%
%
% \includepdf[pages={2}, scale=0.96,
% 	pagecommand=\subsection{Questionnaire 2 : Sensibilisation à l’innovation en entreprise}]
% {questionnaires}
% \clearpage
%
\includepdf[pages={2}, scale=1]
{cover/charte_graphique}

\mtcsetrules{secttoc}{off}
\end{document}