ROOTS

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;

src/Pure
src/FOL
src/HOL
src/ZF
src/CCL
src/CTT
src/Cube
src/FOLP
src/LCF
src/Sequents
src/Doc
src/Tools