I took a look at the Makefile, and I'm not entirely comfortable using it while not knowing exactly what it's doing. I normally don't require to know and have control over everything, but with Latex, the less unknowns I have, the better I feel.

This is what I've been using, inherited from a colleague/committee member/friend:

  PAPER = paper_name
  SECTIONS = $(PAPER) abstract introduction design results conclusions

  default: $(PAPER).pdf

  $(PAPER).bbl: $(PAPER).bib
          pdflatex $(PAPER).tex
          bibtex $(PAPER)

  $(PAPER).pdf: $(PAPER).bbl $(foreach SECTION,$(SECTIONS),$(SECTION).tex)
          pdflatex $(PAPER).tex
          pdflatex $(PAPER).tex
          pdflatex $(PAPER).tex

  clean:
          -rm -f *~
          -rm -f $(PAPER).aux $(PAPER).log $(PAPER).out $(PAPER).bbl $(PAPER).blg
          -rm -f $(PAPER).idx $(PAPER).ilg $(PAPER).ind $(PAPER).dvi $(PAPER).toc
          -rm -f $(PAPER).pdf