proper type-setting of cartouches (requires T1);
\usepackage[T1]{fontenc} is default for mkroot;
\usepackage[utf8]{inputenc} is obsolete in lualatex;
\documentclass[11pt,a4paper]{book}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{isabelle}
\usepackage{isabellesym}
\usepackage{latexsym}
\usepackage{textcomp}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage[only,bigsqcap]{stmaryrd}
\usepackage{pdfsetup}
\usepackage{tocloft}
\setlength{\cftsubsecnumwidth}{3em}
\cftsetpnumwidth{2em}
\cftsetrmarg{3em}
\urlstyle{rm}
\isabellestyle{literalunderscore}
\pagestyle{myheadings}
\begin{document}
\title{Homology}
\maketitle
\tableofcontents
\begin{center}
\includegraphics[height=\textheight]{session_graph}
\end{center}
\newpage
\renewcommand{\setisabellecontext}[1]{\markright{\href{#1.html}{#1.thy}}}
\parindent 0pt\parskip 0.5ex
\input{session}
\pagestyle{headings}
\bibliographystyle{abbrv}
\end{document}