more robust run of makeindex (amending 0f0a2148a099, Gerwin Klein 2004), using the old status-quo of e.g. doc-src/Intro/Makefile;
%%
%% hyperref setup -- special version for Isabelle documentation
%%
\usepackage{ifpdf}
\usepackage{color}
\definecolor{linkcolor}{rgb}{0,0,0}
\usepackage[colorlinks=true,linkcolor=linkcolor,citecolor=linkcolor,filecolor=linkcolor,urlcolor=linkcolor,pdfpagelabels]{hyperref}
\newcommand{\hfootref}[2]{\href{#1}{#2}\footnote{\url{#1}}}
\gdef\fnote#1{\hyperpage{#1}n}
\gdef\bold#1{\textbf{\hyperpage{#1}}}
\urlstyle{rm}
\ifpdf\relax\else\renewcommand{\url}[1]{\nolinkurl{#1}}\fi