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    By using the command \appendix, I succeeded in creating an appendix but the page counter resets once the command \appendix is issued.

    I am not sure exactly where the \appendix command should be used.

    \documentclass[twoside, a4paper, 12pt]{ghasri-thesis}
    \usepack-age{amsthm,amssymb,amsmath}
    \usepackage[top=45mm, bottom=45mm, left=45mm, right=45mm]{geometry}
    \usepackage{hyperref}
    \usepackage{graphicx}
    \usepackage[all]{xy}
    \usepackage[pagebackref=true,colorlinks,linkcolor=blue,citecolor=magenta]{hyperref}
    \graphicspath{{images/}}
    \usepackage[pagebackref=false]{hyperref}
    \usepackage{fancybox}
    \usepackage{fancyhdr}
    \usepackage{tocbibind}
    \usepackage{makeidx}
    \usepackage{multienum} 
    \makeindex
    \appendix
    \usepackage{xepersian}
    \settextfont[Scale=1]{XB Niloofar}
    \setlatintextfont[ExternalLocation,BoldFont={lmroman10-bold},BoldItalicFont={lmroman10-bolditalic},ItalicFont={lmroman10-italic}]{XB Niloofar}
    \setdigitfont[Scale=1]{XB Yas}
    

    This turns all chapters into appendices.

    \baselineskip=.4cm
    \tableofcontents
    \baselineskip=1cm
    \include{1-chapter}
    \include{2-chapter}
    \include{3-chapter}
    \include{4-chapter}
    \include{5-chapter}
    \appendix
    \include{6-chapter}
    

    and this makes the page counter reset once the command \appendix is issued.

    If I need to change chapter 6 to an appendix, then where should I put the command \appendix?

    related to an answer for: How to create an appendix?
    asked by (220 points)
    reshown by

    I think you should separate your chapters by

    \frontmatter
    \mainmatter
    

    and

    \appendix
    

    So, the front matter would be your title, id (if it's a book), etc. The main matter would be your main chapters, and the appendix would mark the start of your appendixes. So, it's very much up to you where you want your\appendix. But the order is like I said and it's not flexible.

    ...