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;
#!/usr/bin/env bash
set -e
$ISABELLE_LUALATEX root
$ISABELLE_BIBTEX root
$ISABELLE_LUALATEX root
$ISABELLE_LUALATEX root
./isa-index root
$ISABELLE_LUALATEX root