doc-src/System/system.tex

no need for underscore.sty -- latex.ltx provides \textunderscore and \_ already;

\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}