added "metis_advisory_simp" option to orient as many equations as possible in Metis the right way (cf. "More SPASS with Isabelle")
\documentclass[12pt,a4paper]{report}
\usepackage{supertabular}
\usepackage{graphicx}
\usepackage{../iman,../extra,../isar,../ttbox}
\usepackage[nohyphen,strings]{../underscore}
\usepackage{../../lib/texinputs/isabelle,../../lib/texinputs/isabellesym}
\usepackage{../../lib/texinputs/railsetup}
\usepackage{../IsarRef/style}
\usepackage{../pdfsetup}
\hyphenation{Isabelle}
\hyphenation{Isar}
\isadroptag{theory}
\isabellestyle{it}
\title{\includegraphics[scale=0.5]{isabelle} \\[4ex] The Isabelle System Manual}
\author{\emph{Makarius Wenzel} and \emph{Stefan Berghofer} \\
TU M\"unchen}
\makeindex
\begin{document}
\maketitle
\pagenumbering{roman} \tableofcontents \clearfirst
\input{Thy/document/Basics.tex}
\input{Thy/document/Interfaces.tex}
\input{Thy/document/Presentation.tex}
\input{Thy/document/Misc.tex}
\begingroup
\bibliographystyle{abbrv} \small\raggedright\frenchspacing
\bibliography{../manual}
\endgroup
\printindex
\end{document}