This sample thesis extends that in ../sample-thesis-0/ to incorporate
color and indexing, as well as inclusion of a published paper as the
body of a chapter.  In such cases, the University of Utah Thesis
Office requires separate bibliographies in each chapter that has
literature citations.

The easiest way to compile this sample thesis on any Unix platform is
to simply type

	make

That runs the rough equivalent of these commands:

	pdflatex sample-thesis-2.ltx
	bibtex sample-thesis-2
	fgrep -v fsfname sample-thesis-2.idx | makeindex -c -s sample-thesis-2.ist > sample-thesis-2.ind
	fgrep bioname sample-thesis-2.idx | fgrep -v '|see' | makeindex -c -s sample-thesis-2.ist > sample-thesis-2-bioname.ind
	fgrep fsfname sample-thesis-2.idx | fgrep -v '|see' | makeindex -c -s sample-thesis-2.ist > sample-thesis-2-fsfname.ind

Repeat them FOUR (4) times to achieve consistency.

If there are no indexes, then repeat just the first two commands four
times.

During the writing process, the fastest update is done by

	make pdf-pass

It runs pdflatex, bibtex, and makeindex just once.  If the
bibliography and index are already stable, then only pdflatex needs to
be run:

	pdflatex sample-thesis-2.ltx