I've been having a bit of trouble sorting out the appendices on my master's project...currently, the hyperref links in the left panel for the appendices link to chapters 1 and 2 respectively, and sometimes the chapter 1 and 2 links seem to go to the appendices (I am aware that this is to do with the counter being reset). Similarly for the toc entries. Also, the bibliography and index appear under the appendix 2 'chapter' in the table of contents (see the code below) (but for some reason I can't get this minimal code version to show that)...
Code: Select all
\documentclass[openbib]{report}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{makeidx}
\usepackage{parskip}
%\usepackage{fullpage}
\usepackage[toc,page,header]{appendix}
\usepackage{hyperref}
\usepackage{graphicx}
\usepackage{enumerate}
\usepackage{color}
\usepackage{fancyhdr}
\usepackage[super,square]{natbib}
\usepackage{subfig}
\usepackage{framed}
\usepackage{verbatim}
\usepackage[all, cmtip]{xy}
\usepackage[OT2,T1]{fontenc}
\usepackage[Bjarne]{fncychap}
\usepackage{mathrsfs}
\usepackage{makeidx}
\makeindex
\begin{document}
\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{Contents}
\tableofcontents
\chapter{Chapter 1}
...\index{index entry}
\chapter{Chapter 2}
\appendix
\chapter{Appendix 1}
...
\chapter{Appendix 2}
...
\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{Bibliography}
\begin{thebibliography}{99}
\bibitem{asd}Stuff.
\end{thebibliography}
\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{Index}
\vspace{-10pt}
\printindex
\end{document}
