Index: doc/theses/aaron_moss/comp_II/.gitignore
===================================================================
--- doc/theses/aaron_moss/comp_II/.gitignore	(revision 728df66bde6df9b1ca4ad068be30ea89605f46a3)
+++ doc/theses/aaron_moss/comp_II/.gitignore	(revision 23c27039d154516f4cb778bd20b2ac74a513ba2e)
@@ -1,14 +1,4 @@
 # generated by latex
-*.aux
-*.bbl
-*.blg
-*.brf
-*.dvi
-*.idx
-*.ilg
-*.ind
-*.log
-*.out
+build/*
 *.pdf
 *.ps
-*.toc
Index: doc/theses/aaron_moss/comp_II/Makefile
===================================================================
--- doc/theses/aaron_moss/comp_II/Makefile	(revision 728df66bde6df9b1ca4ad068be30ea89605f46a3)
+++ doc/theses/aaron_moss/comp_II/Makefile	(revision 23c27039d154516f4cb778bd20b2ac74a513ba2e)
@@ -1,7 +1,13 @@
-## Define the appropriate configuration variables.
+## Define the configuration variables.
 
-TeXLIB = .:../LaTeXmacros:../LaTeXmacros/listings:../LaTeXmacros/enumitem:../bibliography/:
-LaTeX  = TEXINPUTS=${TeXLIB} && export TEXINPUTS && latex -halt-on-error
+Build = build
+Figures = figures
+Macros = ../../../LaTeXmacros
+TeXLIB = .:${Macros}:${Build}:../../../bibliography:
+LaTeX  = TEXINPUTS=${TeXLIB} && export TEXINPUTS && latex -halt-on-error -output-directory=${Build}
 BibTeX = BIBINPUTS=${TeXLIB} && export BIBINPUTS && bibtex
+
+MAKEFLAGS = --no-print-directory --silent #
+VPATH = ${Build} ${Figures}
 
 ## Define the text source files.
@@ -29,9 +35,10 @@
 # Directives #
 
+.PHONY : all clean					# not file names
+
 all : ${DOCUMENT}
 
 clean :
-	rm -f *.bbl *.aux *.dvi *.idx *.ilg *.ind *.brf *.out *.log *.toc *.blg *.pstex_t *.cf \
-		${FIGURES} ${PICTURES} ${PROGRAMS} ${GRAPHS} ${basename ${DOCUMENT}}.ps ${DOCUMENT}
+	@rm -frv ${DOCUMENT} ${basename ${DOCUMENT}}.ps ${Build}
 
 # File Dependencies #
@@ -41,36 +48,31 @@
 
 ${basename ${DOCUMENT}}.ps : ${basename ${DOCUMENT}}.dvi
-	dvips $< -o $@
+	dvips ${Build}/$< -o $@
 
-${basename ${DOCUMENT}}.dvi : Makefile ${GRAPHS} ${PROGRAMS} ${PICTURES} ${FIGURES} ${SOURCES} ${basename ${DOCUMENT}}.tex \
-		../LaTeXmacros/common.tex ../LaTeXmacros/indexstyle ../bibliography/cfa.bib
-	# Conditionally create an empty *.ind (index) file for inclusion until makeindex is run.
-	if [ ! -r ${basename $@}.ind ] ; then touch ${basename $@}.ind ; fi
+${basename ${DOCUMENT}}.dvi : Makefile ${Build} ${GRAPHS} ${PROGRAMS} ${PICTURES} ${FIGURES} ${SOURCES} \
+		${Macros}/common.tex ${Macros}/indexstyle ../../../bibliography/pl.bib
 	# Must have *.aux file containing citations for bibtex
 	if [ ! -r ${basename $@}.aux ] ; then ${LaTeX} ${basename $@}.tex ; fi
-	-${BibTeX} ${basename $@}
-	# Some citations reference others so run steps again to resolve these citations
+	-${BibTeX} ${Build}/${basename $@}
+	# Some citations reference others so run again to resolve these citations
 	${LaTeX} ${basename $@}.tex
-	-${BibTeX} ${basename $@}
-	# Make index from *.aux entries and input index at end of document
-	makeindex -s ../LaTeXmacros/indexstyle ${basename $@}.idx
+	-${BibTeX} ${Build}/${basename $@}
+	# Run again to finish citations
 	${LaTeX} ${basename $@}.tex
-	# Run again to get index title into table of contents
-	${LaTeX} ${basename $@}.tex
-
-predefined :
-	sed -f predefined.sed ${basename ${DOCUMENT}}.tex > ${basename $@}.cf
 
 ## Define the default recipes.
 
+${Build}:
+	mkdir -p ${Build}
+
 %.tex : %.fig
-	fig2dev -L eepic $< > $@
+	fig2dev -L eepic $< > ${Build}/$@
 
 %.ps : %.fig
-	fig2dev -L ps $< > $@
+	fig2dev -L ps $< > ${Build}/$@
 
 %.pstex : %.fig
-	fig2dev -L pstex $< > $@
-	fig2dev -L pstex_t -p $@ $< > $@_t
+	fig2dev -L pstex $< > ${Build}/$@
+	fig2dev -L pstex_t -p ${Build}/$@ $< > ${Build}/$@_t
 
 # Local Variables: #
Index: doc/theses/aaron_moss/comp_II/comp_II.tex
===================================================================
--- doc/theses/aaron_moss/comp_II/comp_II.tex	(revision 728df66bde6df9b1ca4ad068be30ea89605f46a3)
+++ doc/theses/aaron_moss/comp_II/comp_II.tex	(revision 23c27039d154516f4cb778bd20b2ac74a513ba2e)
@@ -1,10 +1,2 @@
-% inline code ©...© (copyright symbol) emacs: C-q M-)
-% red highlighting ®...® (registered trademark symbol) emacs: C-q M-.
-% blue highlighting ß...ß (sharp s symbol) emacs: C-q M-_
-% green highlighting ¢...¢ (cent symbol) emacs: C-q M-"
-% LaTex escape §...§ (section symbol) emacs: C-q M-'
-% keyword escape ¶...¶ (pilcrow symbol) emacs: C-q M-^
-% math escape $...$ (dollar symbol)
-
 \documentclass[twoside,11pt]{article}
 
@@ -27,6 +19,4 @@
 \usepackage{mathptmx}                                   % better math font with "times"
 \usepackage[usenames]{color}
-\usepackage[pagewise]{lineno}
-\renewcommand{\linenumberfont}{\scriptsize\sffamily}
 \input{common}                                          % bespoke macros used in the document
 \usepackage[dvips,plainpages=false,pdfpagelabels,pdfpagemode=UseNone,colorlinks=true,pagebackref=true,linkcolor=blue,citecolor=blue,urlcolor=blue,pagebackref=true,breaklinks=true]{hyperref}
@@ -34,6 +24,24 @@
 \renewcommand{\UrlFont}{\small\sf}
 
+\usepackage[pagewise]{lineno}
+\renewcommand{\linenumberfont}{\scriptsize\sffamily}
+
+% Default underscore is too low and wide. Cannot use lstlisting "literate" as replacing underscore
+% removes it as a variable-name character so keywords in variables are highlighted. MUST APPEAR
+% AFTER HYPERREF.
+\renewcommand{\textunderscore}{\leavevmode\makebox[1.2ex][c]{\rule{1ex}{0.075ex}}}
+
 \setlength{\topmargin}{-0.45in}							% move running title into header
 \setlength{\headsep}{0.25in}
+
+\CFAStyle												% use default CFA format-style
+
+% inline code ©...© (copyright symbol) emacs: C-q M-)
+% red highlighting ®...® (registered trademark symbol) emacs: C-q M-.
+% blue highlighting ß...ß (sharp s symbol) emacs: C-q M-_
+% green highlighting ¢...¢ (cent symbol) emacs: C-q M-"
+% LaTex escape §...§ (section symbol) emacs: C-q M-'
+% keyword escape ¶...¶ (pilcrow symbol) emacs: C-q M-^
+% math escape $...$ (dollar symbol)
 
 \usepackage{caption}
@@ -622,5 +630,5 @@
 \addcontentsline{toc}{section}{\refname}
 \bibliographystyle{plain}
-\bibliography{cfa}
+\bibliography{pl}
 
 %\addcontentsline{toc}{section}{\indexname} % add index name to table of contents