Revert parts of "Restore PDF index"

We need to update the container image(s) for building the
pdf documentation on ci.lammps.org by adding `latexmk`
and `xindy` before we can re-enable this change to the makefile.

This partially reverts commit 3c3b76a781.

doc/Makefile

@@ -166,11 +166,15 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		deactivate ;\
 	)
 	@cd latex && \
+		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+		mv temp Makefile && \
 		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
 		mv tmp.tex LAMMPS.tex && \
 		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
 		mv tmp.tex LAMMPS.tex && \
 		$(MAKE) $(MFLAGS) && \
+		$(MAKE) $(MFLAGS) && \
+		$(MAKE) $(MFLAGS) && \
 		mv LAMMPS.pdf ../Manual.pdf && \
 		cd ../;
 	@rm -rf latex/_sources