IMPORTANT: organizational improvements in Maneage TeX sources

This only concerns the TeX sources in the default branch. In case you don't
use them, there should only be a clean conflict in 'paper.tex' (that is
obvious and easy to fix). Conflicts may only happen in some of the
'tex/src/preamble-*.tex' files if you have actually changed them for your
project. But generally any conflict that does arise by this commit with
your project branch should be very clear and easy to fix and test.

In short, from now on things will even be easier: any LaTeX configuration
that you want to do for your project can be done in
'tex/src/preamble-project.tex', so you don't have to worry about any other
LaTeX preamble file. They are either templates (like the ones for PGFPlots
and BibLaTeX) or low-level things directly related to Maneage. Until now,
this distinction wasn't too clear.

Here is a summary of the improvements:

 - Two new options to './project make': with '--highlight-new' and
   '--highlight-notes' it is now possible to activate highlighting on the
   command-line. Until now, there was a LaTeX macro for this at the start
   of 'paper.tex' (\highlightchanges). But changing that line would change
   the Git commit hash, making it hard for the readers to trust that this
   is the same PDF. With these two new run-time options, the printed commit
   hash will not changed.

 - paper.tex: the sentences are formatted as one sentence per line (and one
   line per sentence). This helps in version controlling narrative and
   following the changes per sentence. A description of this format (and
   its advantages) is also included in the default text.

 - The internal Maneage preambles have been modified:

    - 'tex/src/preamble-header.tex' and 'tex/src/preamble-style.tex' have
      been merged into one preamble file called
      'tex/src/preamble-maneage-default-style.tex'. This helps a lot in
      simply removing it when you use a journal style file for example.

    - Things like the options to highlight parts of the text are now put in
      a special 'tex/src/preamble-maneage.tex'. This helps highlight that
      these are Maneage-specific features that are independent of the style
      used in the paper.

    - There is a new 'tex/src/preamble-project.tex' that is the place you
      can add your project-specific customizations.

1 files changed, 215 insertions, 0 deletions

diff --git a/tex/src/preamble-maneage-default-style.tex b/tex/src/preamble-maneage-default-style.tex
new file mode 100644
index 0000000..665c846
--- /dev/null
+++ b/tex/src/preamble-maneage-default-style.tex
@@ -0,0 +1,215 @@
+%% General paper's style settings.
+%
+%% This preamble can be completely ignored when including this TeX file in
+%% another style. This is done because this LaTeX build is meant to be an
+%% initial/internal phase or part of a larger effort, so it has a basic
+%% style defined here as a preamble. To ignore it, uncomment or delete the
+%% respective line in `paper.tex'.
+%
+%% Copyright (C) 2019-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%
+%% This file 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.
+%
+%% This file 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.
+%
+%% You should have received a copy of the GNU General Public License along
+%% with this file.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+
+
+%% Font.
+\usepackage[T1]{fontenc}
+\usepackage{newtxtext}
+\usepackage{newtxmath}
+
+
+
+
+
+%% Print size
+\usepackage[a4paper, includeheadfoot, body={18.7cm, 24.5cm}]{geometry}
+
+
+
+
+
+%% Set the distance between the columns if two columns:
+\setlength{\columnsep}{0.75cm}
+
+
+
+
+
+% To allow figures to take up more space on the top of the page:
+\renewcommand{\topfraction}{.99}
+\renewcommand{\bottomfraction}{.7}
+\renewcommand{\textfraction}{.05}
+\renewcommand{\floatpagefraction}{.99}
+\renewcommand{\dbltopfraction}{.99}
+\renewcommand{\dblfloatpagefraction}{.99}
+\setcounter{topnumber}{1}
+\setcounter{bottomnumber}{0}
+\setcounter{totalnumber}{2}
+\setcounter{dbltopnumber}{1}
+
+
+
+
+
+%% Color related settings:
+\usepackage{xcolor}
+\color{black}                   % Text color
+\definecolor{DarkBlue}{RGB}{0,0,90}
+
+
+
+
+
+
+% figure and figure* ordering correction:
+\usepackage{fixltx2e}
+
+
+
+
+
+%% For editing the caption appearence. The `setspace' package defines
+%% the `stretch' variable. `abovecaptionskip' is the distance between
+%% the figure and the caption.
+\usepackage{setspace, caption}
+\captionsetup{font=footnotesize, labelfont={color=DarkBlue,bf}, skip=1pt}
+\captionsetup[figure]{font={stretch=1, small}}
+\setlength{\abovecaptionskip}{3pt plus 1pt minus 1pt}
+\setlength{\belowcaptionskip}{-1.25em}
+
+
+
+
+
+
+%% To make the footnotes align:
+\usepackage[hang]{footmisc}
+\setlength\footnotemargin{10pt}
+
+
+
+
+
+%For including time in the title:
+\usepackage{datetime}
+
+
+
+
+
+%To make links to webpages and include document information in the
+%properties of the PDF
+\usepackage[
+  colorlinks,
+  urlcolor=blue,
+  citecolor=blue,
+  linkcolor=blue,
+  linktocpage]{hyperref}
+\renewcommand\UrlFont{\rmfamily}
+
+
+
+
+
+%% Define the abstract environment
+\renewenvironment{abstract}
+ {\vspace{-0.5cm}\small%
+  \list{}{%
+    \setlength{\leftmargin}{2cm}%
+    \setlength{\rightmargin}{\leftmargin}%
+  }%
+  \item\relax}
+ {\endlist}
+
+
+
+
+
+%% To keep the main page's code clean.
+\newcommand{\includeabstract}[1]{%
+\twocolumn[%
+  \begin{@twocolumnfalse}%
+    \maketitle%
+    \begin{abstract}%
+    #1%
+    \end{abstract}%
+    \vspace{1cm}%
+  \end{@twocolumnfalse}%
+  ]%
+}
+
+
+
+
+
+%% Basic header style
+%% ------------------
+%
+%% The steps below are to use the necessary LaTeX packages to get the demo
+%% Maneage paper running with a reasonably looking, custom paper style. If
+%% you are using a custom journal style, feel free to delete these.
+
+%% General page header settings.
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+\lhead{\footnotesize{\scshape Draft paper}, {\footnotesize nnn:i (pp), Year Month day}}
+\rhead{\scshape\footnotesize YOUR-NAME et al.}
+\cfoot{\thepage}
+\setlength{\voffset}{0.75cm}
+\setlength{\headsep}{0.2cm}
+\setlength{\footskip}{0.75cm}
+\renewcommand{\headrulewidth}{0pt}
+
+%% Specific style for first page.
+\fancypagestyle{firststyle}
+{
+  \lhead{\footnotesize{\scshape Draft paper}, nnn:i (pp), YYYY Month day\\
+  \scriptsize \textcopyright YYYY, Your name. All rights reserved.}
+  \rhead{\footnotesize \footnotesize \today, \currenttime\\}
+}
+
+%To set the style of the titles:
+\usepackage{titlesec}
+\titleformat{\section}
+  {\centering\normalfont\uppercase}
+  {\thesection.}
+  {0em}
+  { }
+\titleformat{\subsection}
+  {\centering\normalsize\slshape}
+  {\thesubsection.}
+  {0em}
+  { }
+\titleformat{\subsubsection}
+  {\centering\small\slshape}
+  {\thesubsubsection.}
+  {0em}
+  { }
+
+% Basic Document information that goes into the PDF meta-data.
+\hypersetup
+{
+    pdfauthor={YOUR NAME},
+    pdfsubject={\projecttitle},
+    pdftitle={\projecttitle},
+    pdfkeywords={SOME, KEYWORDS, FOR, THE, PDF}
+}
+
+%% Title and author information
+\usepackage{authblk}
+\renewcommand\Authfont{\small\scshape}
+\renewcommand\Affilfont{\footnotesize\normalfont}
+\setlength{\affilsep}{0.2cm}