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.

5 files changed, 173 insertions, 159 deletions

diff --git a/tex/src/preamble-header.tex b/tex/src/preamble-header.tex
deleted file mode 100644
index 42bb409..0000000
--- a/tex/src/preamble-header.tex
+++ /dev/null
@@ -1,89 +0,0 @@
-%% The headers: title, authors, top of pages and section title formatting
-%% of the final LaTeX file are configured here.
-%
-%% Copyright (C) 2018-2020 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/>.
-
-
-
-
-
-%% 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}
diff --git a/tex/src/preamble-style.tex b/tex/src/preamble-maneage-default-style.tex
index c07837f..665c846 100644
--- a/tex/src/preamble-style.tex
+++ b/tex/src/preamble-maneage-default-style.tex
@@ -150,3 +150,66 @@
   \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}
diff --git a/tex/src/preamble-maneage.tex b/tex/src/preamble-maneage.tex
new file mode 100644
index 0000000..81d8535
--- /dev/null
+++ b/tex/src/preamble-maneage.tex
@@ -0,0 +1,35 @@
+%% Preamble for Maneage-related features.
+%
+%% Copyright (C) 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/>.
+
+
+
+
+
+%% Highlighting
+%% ------------
+%
+%% Maneage feature for highlighting changes they can be set activated
+%% directly on the command-line with the '--highlight-new' or
+%% '--highlight-notes' options
+\ifdefined\highlightnew
+\newcommand{\new}[1]{\textcolor{green!50!black}{#1}}
+\else
+\newcommand{\new}[1]{\textcolor{black}{#1}}
+\fi
+
+\ifdefined\highlightnotes
+\newcommand{\tonote}[1]{\textcolor{red!60!black}{[#1]}}
+\else
+\newcommand{\tonote}[1]{{}}
+\fi
diff --git a/tex/src/preamble-necessary.tex b/tex/src/preamble-necessary.tex
deleted file mode 100644
index bf74c8b..0000000
--- a/tex/src/preamble-necessary.tex
+++ /dev/null
@@ -1,70 +0,0 @@
-%% Necessary (independent of style) macros for this project.
-%%
-%% These are a set of packages that have been commonly necessary in most
-%% LaTeX usages. However, if any are not needed in your work, please feel
-%% free to remove them.
-%
-%% Copyright (C) 2018-2020 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/>.
-
-
-
-
-
-%% 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
-
-
-
-
-
-% Better than verbatim for displaying typed text.
-\usepackage{alltt}
-
-
-
-
-
-% For arithmetic opertions within LaTeX
-\usepackage[nomessages]{fp}
-
-
-
-
-
-%To add a code font to the text:
-\usepackage{courier}
-
-
-
-
-
-%To add some enumerating styles
-\usepackage{enumerate}
-
-
-
-
-
-%Including images if necessary
-\usepackage{graphicx}
diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex
new file mode 100644
index 0000000..4206801
--- /dev/null
+++ b/tex/src/preamble-project.tex
@@ -0,0 +1,75 @@
+%% Necessary macros for this project.
+%%
+%% These are a set of packages that have been commonly necessary in most
+%% LaTeX usages. However, if any are not needed in your work, please feel
+%% free to remove them.
+%
+%% Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) YYYY Your Name <your@email.address>
+%
+%% 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/>.
+
+
+
+
+
+%% Packages you need in your project
+%% ---------------------------------
+%
+%% Here you can add/remove any custom LaTeX package that you need for this
+%% project that aren't provided by the journal's style.
+
+% Better than verbatim for displaying typed text.
+\usepackage{alltt}
+
+% For arithmetic opertions within LaTeX
+\usepackage[nomessages]{fp}
+
+%To add a code font to the text:
+\usepackage{courier}
+
+%To add some enumerating styles
+\usepackage{enumerate}
+
+%Including images if necessary
+\usepackage{graphicx}
+
+
+
+
+
+%% BibLaTeX or PGFPlots templates
+%% ------------------------------
+%
+%% These are ready-made customizations of these two commonly used packages
+%% that you can use as a template for your own project: BibLaTeX (advanced
+%% bibliography management) or PGFPlots (for drawing plots within LaTeX
+%% directly from tables of data). If you don't use them, you can just
+%% delete these two lines and also delete their files from your branch (to
+%% keep the 'tex/src' directory on your branch clean).
+\input{tex/src/preamble-biblatex.tex}
+\input{tex/src/preamble-pgfplots.tex}
+
+
+
+
+
+%% Style of default paper (DELETE IF USING JOURNAL STYLES)
+%% -------------------------------------------------------
+%
+%% This is primarily defined for the default Maneage paper style. So when
+%% you later import your journal's style, delete this line (and these
+%% comments). Also delete the file (to keep your project source branch
+%% clean from files you don't need/use).
+\input{tex/src/preamble-maneage-default-style.tex}