more direct use of latex tools: avoid diversion into "isabelle latex -o pdf" and its confusion of ISABELLE_PDFLATEX vs. ISABELLE_LUALATEX;
clarified ISABELLE_MAKEINDEX options;
\documentclass[11pt,a4paper]{article}
\usepackage[T1]{fontenc}
\usepackage[only,bigsqcap]{stmaryrd}
\usepackage{ifthen,proof,amssymb,isabelle,isabellesym}
\isabellestyle{literal}
\usepackage{pdfsetup}\urlstyle{rm}
\hyphenation{Isabelle}
\begin{document}
\title{Notable Examples in Isabelle/HOL}
\maketitle
\tableofcontents
\parindent 0pt \parskip 0.5ex
\input{session}
\bibliographystyle{abbrv}
\bibliography{root}
\end{document}