Appendix of long paper added, optionally we can disable it

Given the referee reports, after discussing with the editors of CiSE, we
decided that it is important to include the complete appendix we had before
that included a thorough review of existing tools and methods. However, the
appendix will not be published in the paper (due to the strict word-count
limit). It will only be used in the arXiv/Zenodo versions of the paper.

This actually created a technical problem: we want the commit hash of the
project source to remain the same when the paper is built with an appendix
or without it.

To fix this problem the choice of including an appendix has gone into the
'project' script as a run-time option called '--no-appendix'. So by default
(when someone just runs './project make'), the PDF will have an appendix,
but when we want to submit to the journal, or when the appendix isn't
needed for a certain reason, we can use this new option. The appendix also
has its own separate bibliography.

Some other corrections made in this commit:
 1. Some new references were added that had an '_' in their source, they
    were corrected in 'references.tex'.
 2. I noticed that 'preamble-style.tex' is not actually used in this paper,
    so it has been deleted.

2 files changed, 17 insertions, 3 deletions

diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index f363b6f..29a1ea0 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -48,10 +48,18 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 
           # Put a LaTeX input command for all the necessary macro files.
           # 'hardware-parameters.tex' is created in 'configure.sh'.
-	  rm -f $(mtexdir)/project.tex
+	  projecttex=$(mtexdir)/project.tex
+	  rm -f $$projecttex
 	  for t in $(subst paper,,$(makesrc)) hardware-parameters; do
-	    echo "\input{tex/build/macros/$$t.tex}" >> $(mtexdir)/project.tex
+	    echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex
 	  done
+
+          # Add the necessary macro to include appendix or not.
+	  if [ x"$(noappendix)" = x1 ]; then
+	    echo "\newcommand{\noappendix}{}" >> $$projecttex
+	  fi
+
+        # The paper shouldn't be built.
 	else
 	  echo
 	  echo "-----"
@@ -129,7 +137,12 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
           # option for better security. See
           # https://savannah.nongnu.org/task/?15694 for details.
 	  latex -shell-escape -halt-on-error "$$p"/paper.tex
+
+          # Since we have multiple bibliographies (one for the main body,
+          # and one for the appendix), we use 'multibib'. Multibib creates
+          # a separate '.aux' file for each bibliography.
 	  bibtex paper
+	  bibtex appendix
 
           # Hack: tidy up eprint+doi style that didn't work in .bst file.
           # TODO (better): read Part 4 of
diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf
index d88a0bf..fd66da9 100644
--- a/reproduce/software/config/texlive-packages.conf
+++ b/reproduce/software/config/texlive-packages.conf
@@ -18,4 +18,5 @@
 # want their versions.
 texlive-typewriter-pkgs = courier inconsolata xkeyval upquote
 texlive-packages = times IEEEtran cite xcolor pgfplots ps2eps \
-                   listings ulem etoolbox $(texlive-typewriter-pkgs)
+                   listings ulem etoolbox multibib \
+                   $(texlive-typewriter-pkgs)