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appendix will not be published in the paper (due to the strict word-count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.

4 files changed, 24 insertions, 306 deletions

diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex
deleted file mode 100644
index 0561d1c..0000000
--- a/tex/src/preamble-biblatex.tex
+++ /dev/null
@@ -1,145 +0,0 @@
-%% Biblatex settings.
-%%
-%% Settings necessary to make the bibliography with Biblatex. Keeping all
-%% BibLaTeX settings in a separate preamble was done in the spirit of
-%% modularity to 1) easily managable, 2) If a similar BibLaTeX
-%% configuration is necessary in another LaTeX compilation, this file can
-%% just be copied there and used.
-%%
-%% USAGE:
-%%  - `tex/src/references.tex': the file containing Bibtex source of each
-%%     reference. The file suffix doesn't have to be `.bib'. This naming
-%%     helps in clearly identifying the files and avoiding places that
-%%     complain about `.bib' files.
-%
-%% Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-%
-%% This LaTeX file is part of Maneage. Maneage is free software: you can
-%% redistribute it and/or modify it under the terms of the GNU General
-%% Public License as published by the Free Software Foundation, either
-%% version 3 of the License, or (at your option) any later version.
-%
-%% Maneage is distributed in the hope that it will be useful, but WITHOUT
-%% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-%% FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
-%% for more details. See <http://www.gnu.org/licenses/>.
-
-
-
-
-%% To break up highlighted text (for example texttt when some it is on the
-%% line break) and also to no underline emphasized words (like journal
-%% titles in the references).
-\usepackage[normalem]{ulem}
-
-
-
-
-
-%% For quotation signs (sometimes used by BibLaTeX)
-\usepackage{csquotes}
-
-
-
-
-
-%% To define colors
-\usepackage{xcolor}
-
-
-
-
-
-% Basic BibLaTeX settings
-\usepackage[
-    doi=false,
-    url=false,
-    dashed=false,
-    eprint=false,
-    maxbibnames=10,
-    minbibnames=4,
-    hyperref=true,
-    maxcitenames=2,
-    mincitenames=1,
-    giveninits=true,
-    style=authoryear,
-    uniquelist=false,
-    backend=biber,natbib]{biblatex}
-\DeclareFieldFormat[article]{pages}{#1}
-\DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}}
-\addbibresource{tex/src/references.tex}
-\addbibresource{tex/build/macros/dependencies-bib.tex}
-\renewbibmacro{in:}{}
-\AtEveryBibitem{\clearfield{month}}
-\renewcommand*{\bibfont}{\normalsize}
-\DefineBibliographyStrings{english}{references = {References}}
-
-%% Include the adsurl field key into those that are recognized:
-\DeclareSourcemap{
-  \maps[datatype=bibtex]{
-    \map{
-      \step[fieldsource=adsurl,fieldtarget=iswc]
-      \step[fieldsource=gbkurl,fieldtarget=iswc]
-    }
-  }
-}
-
-%% Set the color of the doi link to mymg (magenta) and the ads links
-%% to mypurp (or purple):
-\definecolor{mypurp}{cmyk}{0.75,1,0,0}
-\definecolor{myblue}{rgb}{0,0.669,0.885}
-\newcommand{\doihref}[2]{\href{#1}{\color{myblue}{#2}}}
-\newcommand{\adshref}[2]{\href{#1}{\color{mypurp}{#2}}}
-\newcommand{\blackhref}[2]{\href{#1}{\color{black}{#2}}}
-
-%% Define a format for the printtext commands in
-%% DeclareBibliographyDriver to make links for the doi, ads link and
-%% arxiv link:
-\DeclareFieldFormat{doilink}{
-  \iffieldundef{doi}{#1}{\doihref{http://dx.doi.org/\thefield{doi}}{#1}}}
-\DeclareFieldFormat{adslink}{
-    \iffieldundef{iswc}{#1}{\adshref{\thefield{iswc}}{#1}}}
-\DeclareFieldFormat{arxivlink}{
-  \iffieldundef{eprint}{#1}{\href{http://arxiv.org/abs/\thefield{eprint}}{#1}}}
-
-\DeclareListFormat{doiforbook}{
-  \iffieldundef{doi}{#1}{\doihref{http://dx.doi.org/\thefield{doi}}{#1}}}
-\DeclareFieldFormat{googlebookslink}{
-    \iffieldundef{iswc}{#1}{\adshref{\thefield{iswc}}{#1}}}
-
-%% Set the formatting to make the last three values into the
-%% appropriate link. Note that the % signs are necessary. Without
-%% them, the items will be indented.
-\DeclareBibliographyDriver{article}{%
-  \usebibmacro{bibindex}%
-  \usebibmacro{begentry}%
-  \usebibmacro{author/translator+others}%
-  \newunit%
-  \printtext{\usebibmacro{title}}%
-  \newunit%
-  \printtext[doilink]{\usebibmacro{journal}}%
-  \addcomma%
-  \printtext[adslink]{\printfield{volume}}%
-  \addcomma%
-  \printtext[arxivlink]{\printfield{pages}}%
-  \addperiod%
-}
-
-\DeclareBibliographyDriver{book}{%
-  \usebibmacro{bibindex}%
-  \usebibmacro{begentry}%
-  \usebibmacro{author/translator+others}%
-  \newunit%
-  \printtext{\usebibmacro{title}}%
-  \addperiod%
-  \addspace%
-  \printlist[doiforbook]{publisher}%
-  \addcomma%
-  \addspace%
-  \printfield[googlebookslink]{edition}%
-  \printtext{ ed.}%
-  \addperiod%
-}
-
-%% In order to have et al. instead of et al.,:
-\renewcommand*{\nameyeardelim}{\addspace}
diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex
index 16a9ddc..b4fd764 100644
--- a/tex/src/preamble-project.tex
+++ b/tex/src/preamble-project.tex
@@ -5,6 +5,12 @@
 %% \cite{} output to follow that of the IEEE.
 \usepackage{cite}
 
+%% To have multiple bibliographies (one for the main paper, one for the
+%% appendix). With 'multibib' we need to specify a name for each
+%% bibliography.
+\usepackage{multibib}
+\newcites{appendix}{Bibliography}
+
 %% For the `\url' command.
 \usepackage{url}
 
@@ -51,6 +57,19 @@
 
 
 
+%% Maneage feature for highlighting updates. When this is set, text marked
+%% as \new will be colored in dark green and text that is marked
+%% wtih \tonote will be marked in dark red.
+\ifdefined\highlightchanges
+\newcommand{\new}[1]{\textcolor{green!60!black}{#1}}
+\newcommand{\tonote}[1]{\textcolor{red!60!black}{[#1]}}
+\else
+\newcommand{\new}[1]{\textcolor{black}{#1}}
+\newcommand{\tonote}[1]{{}}
+\fi
+
+
+
 
 %% Custom macros
 \newcommand{\inlinecode}[1]{\textcolor{blue!35!black}{\texttt{#1}}}
diff --git a/tex/src/preamble-style.tex b/tex/src/preamble-style.tex
deleted file mode 100644
index f8b95d6..0000000
--- a/tex/src/preamble-style.tex
+++ /dev/null
@@ -1,156 +0,0 @@
-%% Set the page margins (use `showframe' to see the sides).
-%% A4 is 210mm x 297mm
-\usepackage[a4paper]{geometry}
-
-%% Horizontal space of text: total is 210mm
-\setlength{\hoffset}{0mm}       % remaining: 190mm
-\setlength{\textwidth}{155mm}   % remaining: 160mm
-\setlength{\marginparsep}{0pt}
-\setlength{\marginparwidth}{0pt}
-\setlength{\oddsidemargin}{0pt}
-
-%% Vertical space of text: total is 297mm.
-\setlength{\voffset}{-15.4mm}   % remaining: 287mm (== 10mm (1 inch + \hoffset).
-\setlength{\topmargin}{0mm}     % remaining: 287mm.
-\setlength{\headheight}{10mm}   % remaining: 277mm.
-\setlength{\headsep}{10mm}      % remaining: 272mm.
-\setlength{\textheight}{245mm}  % remaining: 22mm.
-\setlength{\footskip}{7mm}      % remaining: 10mm.
-
-%% To see the layout, add a `\layout' right after `\begin{document}'.
-\usepackage{layout}
-
-%% To display codes.
-\usepackage{listings}
-\input{listings-bash.prf}
-\lstset{
-  frame=none,
-  commentstyle=\color{gray},
-  basicstyle=\small\ttfamily,
-}
-
-%% To allow a prefix to the enumeration.
-\usepackage{enumitem}
-\setlist{nolistsep}   % No space before `\begin{itemize}'
-
-%% Horizontal line with spacing
-\newcommand{\horizontalline}{\vspace{3mm}\hrule\vspace{3mm}}
-
-%% Custom title format
-\usepackage{setspace}
-\makeatletter
-\renewcommand{\maketitle}{\bgroup\setlength{\parindent}{0pt}
-  \begin{flushleft}
-    {\mpbold RESEARCH PAPER}
-
-    \vspace{3mm}
-    {\LARGE\mpmedium \@title}
-
-    \vspace{2mm}
-    \@author
-  \end{flushleft}\egroup
-  \horizontalline
-}
-\makeatother
-
-%% For authors and affiliations
-\newcommand{\authoraffil}[2]{#1\textsuperscript{\mplight#2}}
-
-%% Spacing before and after section titles.
-%% Format: \titlespacing*{<command>}{<left>}{<before-sep>}{<after-sep>}
-\usepackage{titlesec}
-\titlespacing*{\section}      {0pt}{10pt plus 0pt minus 0pt}{0pt plus 0pt minus 0pt}
-\titlespacing*{\subsection}   {0pt}{7pt plus 0pt minus 0pt} {0pt plus 0pt minus 0pt}
-\titlespacing*{\subsubsection}{0pt}{4pt plus 0pt minus 0pt} {0pt plus 0pt minus 0pt}
-\titleformat{\section}{\Large\scshape\bf}{\thesection.{ }}{0pt}{}
-\titleformat{\subsection}{\large\bfseries\itshape}{\thesubsection.{ }}{0pt}{}
-\titleformat{\subsubsection}{\bfseries\itshape}{\thesubsubsection.{ }}{0pt}{}
-
-%% Set the font.
-%% After downloading, put the font in `/usr/share/fonts/TTF'.
-%% https://www.fontspace.com/m-fonts/m-2p
-%% Also for M+: https://mplus-fonts.osdn.jp/about-en.html
-%% https://www.fontpalace.com/font-download/Memento/
-\usepackage{fontspec}
-\usepackage[T1]{fontenc}
-\usepackage{Alegreya}
-\newfontfamily\mplight{AlegreyaSans-Light}
-\newfontfamily\mpbold{AlegreyaSans-Bold}
-\newfontfamily\mpmedium{AlegreyaSans-Medium}
-\newfontfamily\mpregular{AlegreyaSans-Regular}
-
-%% For highlighting updates. When this is set, text marked as \new
-%% will be colored in dark green and text that is marked wtih \tonote
-%% will be marked in dark red.
-\ifdefined\highlightchanges
-\newcommand{\new}[1]{\textcolor{green!60!black}{#1}}
-\newcommand{\tonote}[1]{\textcolor{red!60!black}{[#1]}}
-\else
-\newcommand{\new}[1]{\textcolor{black}{#1}}
-\newcommand{\tonote}[1]{{}}
-\fi
-
-%% To print the creation date on the PDF.
-\usepackage{datetime}
-
-%% To have links.
-\usepackage[
-  colorlinks,
-  urlcolor=gray,
-  citecolor=gray,
-  linkcolor=gray,
-  linktocpage]{hyperref}
-\renewcommand\UrlFont{\rmfamily}
-
-%% To include figures.
-\usepackage{graphicx}
-
-%% To manage captions.
-\usepackage[font={footnotesize}]{caption}
-
-%% To use colors.
-\usepackage{xcolor}
-
-%% Header and footer style.
-\usepackage{lastpage}
-\usepackage{fancyhdr}
-\pagestyle{fancy}
-\lhead{\mplight\footnotesize Art.XX, page {\thepage} of \pageref{LastPage}}
-\chead{}
-\rhead{\mplight\footnotesize Akhlaghi, et al: Maneage, a Customizable Framework for Managing Data Lineage}
-\lfoot{}
-\cfoot{}
-\rfoot{}
-\renewcommand\headrulewidth{0.0pt}
-\renewcommand\footrulewidth{0.0pt}
-\fancypagestyle{firstpage} {
- \lhead{\includegraphics[width=3.5cm]{tex/img/codata.pdf}}
- \chead{}
- \rhead{\mplight\footnotesize
-   Akhlaghi, M, et al. 2020. Maneage, a Customizable Framework\\
-   for Managing Data Lineage. \emph{Data Science Journal}, VV,\\
-   NN, pp.1-\pageref*{LastPage}. DOI: \href{https://doi.org/10.5334/dsj-XXXX-XXX}{\textcolor{black}{https://doi.org/10.5334/dsj-XXXX-XXX}}\\
-   PDF created on: \currenttime{}, \today}
- \lfoot{}
- \cfoot{}
- \rfoot{}
- \renewcommand\headrulewidth{0.1pt}
- \renewcommand\footrulewidth{0.0pt}
-}
-
-%% For creating color boxes
-\usepackage[many]{tcolorbox}
-
-%% Custom macros
-\newcommand{\inlinecode}[1]{\textcolor{blue!35!black}{\texttt{#1}}}
-
-%% To use International Phonetic Alphabet (IPA)
-\usepackage{tipa}
-
-%% Example Makefile macros
-\newcommand{\mkcomment}[1]{\textcolor{red!70!white}{\# #1}}
-\newcommand{\mkvar}[1]{\textcolor{orange!40!black}{#1}}
-\newcommand{\mktarget}[1]{\textcolor{blue!40!black}{#1}}
-\newcommand{\mkprog}[1]{\textcolor{green!30!black}{#1}}
-\newcommand{\mktab}[1]{\textcolor{black!30!white}{\_\_\_TAB\_\_\_}}
-\newcommand{\recipecomment}[1]{{ }{ }{ }{ }{ }{ }{ }{ }{ }\mkcomment{#1}}
diff --git a/tex/src/references.tex b/tex/src/references.tex
index 3d395ec..992f40f 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -171,7 +171,7 @@ archivePrefix = {arXiv},
      author = {Roberto {Di Cosmo} and Francois Pellegrini},
       title = {Encouraging a wider usage of software derived from research},
        year = {2019},
-    journal = {\doihref{https://www.ouvrirlascience.fr/wp-content/uploads/2020/02/Opportunity-Note_software-derived-from-research_EN.pdf}{Ouvrir la science}},
+    journal = {\doihref{https://www.ouvrirlascience.fr/wp-content/uploads/2020/02/Opportunity-Note\_software-derived-from-research\_EN.pdf}{Ouvrir la science}},
      volume = {},
       pages = {},
         doi = {},
@@ -1031,7 +1031,7 @@ archivePrefix = {arXiv},
 archivePrefix = {arXiv},
        eprint = {1506.02822},
  primaryClass = {cs.DC},
-          doi = {10.1007/978-3-319-27308-2_47},
+          doi = {10.1007/978-3-319-27308-2\_47},
        adsurl = {https://ui.adsabs.harvard.edu/abs/2015arXiv150602822C},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
@@ -1203,7 +1203,7 @@ archivePrefix = {arXiv},
     journal = {Provenance and Annotation of Data and Processes (IPAW)},
        year = {2012},
       pages = {203},
-        doi = {10.1007/978-3-642-34222-6_16},
+        doi = {10.1007/978-3-642-34222-6\_16},
 }
 
 
@@ -1307,7 +1307,7 @@ Reproducible Research in Image Processing},
 
 
 @ARTICLE{nowakowski11,
-     author = {Piotr Nowakowski and Eryk Ciepiela and Daniel Har\k{e}\.{z}lak and Joanna Kocot and Marek Kasztelnik and Tomasz Barty\'nski and Jan Meizner and Grzegorz Dyk and Maciej Malawski},
+     author = {Piotr Nowakowski and Eryk Ciepiela and Daniel Hare\.{z}lak and Joanna Kocot and Marek Kasztelnik and Tomasz Barty\'nski and Jan Meizner and Grzegorz Dyk and Maciej Malawski},
       title = {The Collage Authoring Environment},
     journal = {Procedia Computer Science},
      volume = {4},
@@ -1618,7 +1618,7 @@ Reproducible Research in Image Processing},
     journal = {Large Installation System Administration Conference},
        year = {2004},
      volume = {18},
-      pages = {79. \url{https://www.usenix.org/legacy/events/lisa04/tech/full_papers/dolstra/dolstra.pdf}},
+      pages = {79. \url{https://www.usenix.org/legacy/events/lisa04/tech/full\_papers/dolstra/dolstra.pdf}},
 }