1. put the following in your LaTeX source, just before generating the bibliography, to mark the last page:
\label{page:last}
2. Use a makefile that looks like this (assuming you use pdflatex):
FILE = proposal $(FILE).pdf: $(FILE).tex pdflatex $(FILE) bibtex $(FILE) pdflatex $(FILE) pdflatex $(FILE) DESC_END = $(shell grep page:last $(FILE).aux | tr '{}' ' ' | awk '{print $$NF}') REFS_START = $(shell expr $(DESC_END) + 1) description.pdf: $(FILE).pdf pdftk $< cat 1-$(DESC_END) output $@ references.pdf: $(FILE).pdf pdftk $< cat $(REFS_START)-end output $@