Index: branches/2017/dev_merge_2017/DOC/NEMO_manual.tex
===================================================================
--- branches/2017/dev_merge_2017/DOC/NEMO_manual.tex	(revision 9373)
+++ branches/2017/dev_merge_2017/DOC/NEMO_manual.tex	(revision 9376)
@@ -1,50 +1,64 @@
-%description: Book template
+%% ==============================================================================
+%% NEMO_book.tex: build the NEMO Reference Manual
+%% ==============================================================================
 
-% template of document for LaTeX
-% (C) Xavier Perseguers 2002 - xavier.perseguers@epfl.ch
 
-% ================================================================
-% PREAMBLE
-% ================================================================
+%% Run build_NEMO_manual.sh to generate the PDF version (with pdflatex)
+
+
+%% Preamble
+%% ==============================================================================
 
 \include{texfiles/preamble}
 
-% ================================================================
-% TOP MATTER
-% ================================================================
+\begin{document}
+
+
+%% 'minted' env. & shortcuts for syntax highlighting
+
+\setminted[fortran]{fontsize=\tiny, breaklines}
+\newminted{fortran}{}			% \begin{fortrancode}
+\newmintinline{fortran}{}		% \fortraninline
+\newmintedfile{fortran}{}		% \fortranfile
+\newminted{xml}{fontsize=\tiny, breaklines}
+\newminted{sh}{}
+\newminted{c}{}
+
+
+%% Frontmatter
+%% ==============================================================================
 
 \include{texfiles/top_matter}
 
-% ================================================================
-% DOCUMENT
-% ================================================================
 
-\begin{document}
+%% Frontpage
 
-\maketitle						% generate the title
-
+\maketitle
 \frontmatter
 
-\tableofcontents					% generate a table of contents
-%\listoffigures					% generate a list  of figures
-%\listoftables					        % generate a list of tables
+
+%% ToC i.e. Table of Contents
+
+\dominitoc
+\tableofcontents
+
+
+%% Mainmatter
+%% ==============================================================================
 
 \mainmatter
 
-% ================================================================
-% Abstract - Foreword
-% ================================================================
+
+%% Abstract - Foreword
 
 \subfile{texfiles/chapters/abstract_foreword}
 
-% ================================================================
-% INTRODUCTION
-% ================================================================
+
+% Introduction
 
 \subfile{texfiles/chapters/introduction}
 
-% ================================================================
-% CHAPTERS
-% ================================================================
+
+% Chapters
 
 \subfile{texfiles/chapters/chap_model_basics}
@@ -78,35 +92,42 @@
 \subfile{texfiles/chapters/chap_CONFIG}			% Predefined configurations
 
-% ================================================================
-% APPENDIX
-% ================================================================
+
+% Appendix
 
 \appendix
 
-%\subfile{texfiles/chapters/chap_conservation}
-\subfile{texfiles/chapters/annex_A}			% generalised vertical coordinate
-\subfile{texfiles/chapters/annex_B}			% diffusive operator
-\subfile{texfiles/chapters/annex_C}			% Discrete invariants of the eqs.
-\subfile{texfiles/chapters/annex_iso}	                  % Isoneutral diffusion using triads
-\subfile{texfiles/chapters/annex_D}			% Coding rules
-%\subfile{texfiles/chapters/annex_E}	                  % Notes on some on going staff (no included in the DOC)
-%\subfile{texfiles/chapters/annex_Fox-Kemper}   % Notes on Fox-Kemper (no included in the DOC)
-%\subfile{texfiles/chapters/annex_EVP}        	% Notes on EVP (no included in the DOC)
+\subfile{texfiles/chapters/annex_A}					% Generalised vertical coordinate
 
-% ================================================================
-% INDEX
-% ================================================================
+\subfile{texfiles/chapters/annex_B}					% Diffusive operator
 
-\addcontentsline{toc}{chapter}{Index}
+\subfile{texfiles/chapters/annex_C}					% Discrete invariants of the eqs.
+
+\subfile{texfiles/chapters/annex_iso}				% Isoneutral diffusion using triads
+
+\subfile{texfiles/chapters/annex_D}					% Coding rules
+
+%% Not included
+%\subfile{texfiles/chapters/chap_conservation}	%
+%\subfile{texfiles/chapters/annex_E}				% Notes on some on going staff
+%\subfile{texfiles/chapters/annex_Fox-Kemper}	% Notes on Fox-Kemper
+%\subfile{texfiles/chapters/annex_EVP}				% Notes on EVP
+
+
+%% Backmatter
+%% ==============================================================================
+
+\backmatter
+
+
+%% Index
+
+%\addcontentsline{toc}{chapter}{Index}
 \printindex
 
-% ================================================================
-% BIBLIOGRAPHY
-% ================================================================
 
-%%\bibliographystyle{plainat}
-\bibliographystyle{texfiles/styles/ametsoc}		% AMS biblio style (JPO)
+%% Bibliography
+
 \bibliography{texfiles/bibliography/NEMO_manual}
 
-% ================================================================
+
 \end{document}
