Restore PDF index

doc/Makefile

@@ -166,15 +166,11 @@ 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

doc/src/Manual.rst

@@ -89,7 +89,9 @@ Programmer Documentation
    fix_modify_atc_commands
 
 Indices and tables
-==================
+******************
 
-* :ref:`genindex`
-* :ref:`search`
+.. only:: html
+
+   * :ref:`genindex`
+   * :ref:`search`