This is the skeleton dir I have been using to write papers with. The main thing of use is the Rakefile.
Write your paper in doc.tex (or rename it in the Rakefile by setting the "name" variable to something else). I add my autogenerated BibTeX file to basic.bib (usually the output of Papers.app) and add any extra entries to extras.bib.
To build, type "rake". To build and open the resulting pdf on Mac OSX, type "rake view".
By tracking the files listed in the .fls file generated by LaTeX's -recorder option, the Rakefile should be able to tell when any dependencies have changed (figures, etc.).
As I am lazy, I tend to keep a session open running:
while true; do rake; sleep 2; done
This will automatically regenerate the pdf after changes.