Doxygen writes, in the LATEX_OUTPUT a Makefile that is very useful in order not to run (pdf)latex and makeindex by hand. Here is one of the make rules I am talking about
refman.dvi: refman.tex doxygen.sty echo "Running latex..." latex refman.tex echo "Running makeindex..." makeindex refman.idx echo "Rerunning latex...." latex refman.tex
The problem is that (pdf)latex may have to be run multiple times to get cross-references right. Sometimes running it once after makeindex is indeed enough, but must often you need to run it twice (this is the case for the project I am working on). In rare cases you need to run it three or more times (even though I have never seen more than three runs to be necessary). That is why I propose to replace the above rule by the following and to provide a similar rule for pdflatex when USE_PDFLATEX is set to YES:
refman.dvi: refman.tex doxygen.sty echo "Running latex..." latex refman.tex echo "Running makeindex..." makeindex refman.idx echo "Rerunning latex...." latex refman.tex latex_count=5 while egrep -s 'Rerun (LaTeX|to get cross-references right)' refman.log && [ $latex_count -gt 0 ] ;\ do \ echo "Rerunning latex...." ;\ latex refman.tex ;\ latex_count=`expr $latex_count - 1` ;\ done
Notice that latex is run only if necessary and at most five times after makeindex. This is done because (pdf)latex is not guaranteed to be able to stabilize the cross-references. While this happens only in extremely pathological cases, it is better to take measures against it. That is what latex_count is used for.
All the best,
Roberto