Index: NEMO/trunk/doc/latex/SI3/main/SI3_manual.tex
===================================================================
--- NEMO/trunk/doc/latex/SI3/tex_main/SI3_manual.tex	(revision 10146)
+++ NEMO/trunk/doc/latex/SI3/main/SI3_manual.tex	(revision 11015)
@@ -1,13 +1,5 @@
 %% ==============================================================================
-%% NEMO_book.tex: build the NEMO Reference Manual
+%% SI3 Reference Manual
 %% ==============================================================================
-
-
-%% Run ../build_NEMO_manual.sh to generate the PDF version (with pdflatex)
-
-%% Document layout
-%% ==============================================================================
-
-\documentclass[a4paper, 11pt]{book}
 
 
@@ -15,16 +7,22 @@
 %% ==============================================================================
 
-\usepackage{../../tex_main/NEMO_manual}
-\usepackage{../../tex_sub/NEMO_minted}
+%% Document layout
+\documentclass{book}
 
-\usepackage{bm}
+%% Custom style (.sty)
+\usepackage{../../NEMO/main/NEMO_manual}
+
+%% Include references and index for single subfile compilation
+\newcommand{\biblio}{\bibliography{../main/SI3_manual}}
+\newcommand{\pindex}{\printindex}
 
 \makeindex
 
+%% End of common preamble between main and sub-files
+\begin{document}
 
-%% 
-%% ==============================================================================
-
-\begin{document}
+%% Override custom cmds for full manual compilation
+\renewcommand{\biblio}{}
+\renewcommand{\pindex}{}
 
 
@@ -32,30 +30,33 @@
 %% ==============================================================================
 
+\graphicspath{{../../figures/logos/}}
+
 %% Frontpage
+\title{
+  \includegraphics[height=0.05\textheight]{CMCC}\hfill
+  \includegraphics[height=0.05\textheight]{CNRS}\hfill
+  \includegraphics[height=0.05\textheight]{MOI} \hfill
+  \includegraphics[height=0.05\textheight]{UKMO}\hfill
+  \includegraphics[height=0.05\textheight]{NERC}       \\
+  {\Huge SI$^3$ \\}
+  {\Large Sea Ice modelling Integrated Initiative -- The NEMO Sea Ice engine}\\ 
+  {\small \textcolor{red}{First draft documentation. Needs completion and rewriting}.}
+}
+\author{The NEMO Sea Ice Working Group
+%  \thanks{
+%
+%  }                                                        \\
+%                                                           \\
+  \textit{Issue 27, Notes du P\^{o}le de mod\'{e}lisation} \\
+  \textit{Institut Pierre-Simon Laplace (IPSL)}            \\
+  \textit{ISSN 1288-1619}
+}
+\date{\today}
 
-\title{
-\vspace{1.5cm}
-\rule{400pt}{1.5pt} \\
-\vspace{0.45cm}
- {\Huge SI$^3$ \\}
- {\Large -- Sea Ice modelling Integrated Initiative --}\\
- {\Large The NEMO Sea Ice engine}\\ 
-\date{\today}
-\author{The NEMO Sea Ice Working Group \\
-\\
-\small \textit{Note du P\^ole de mod\'elisation de l'Institut Pierre-Simon Laplace No 31} \\
-\small \textcolor{red}{First draft documentation. Needs completion and rewriting}. \\
-\\
-ISSN No 1288-1619\\
-}
-\rule{400pt}{1.5pt}
-}
-
-\maketitle						% generate the title
-
+\maketitle
 \frontmatter
 
+
 %% ToC i.e. Table of Contents
-
 \dominitoc
 \tableofcontents
@@ -67,39 +68,41 @@
 \mainmatter
 
-\subfile{../tex_sub/todolist}
+\graphicspath{{../../figures/SI3/}}
+
+\subfile{../subfiles/todolist}
 
 %% Abstract - Foreword
 
-\subfile{../tex_sub/abstract_foreword}
+\subfile{../subfiles/abstract_foreword}
 
 % Introduction
 
-\subfile{../tex_sub/introduction}
+\subfile{../subfiles/introduction}
 
 % Chapters
 
-\subfile{../tex_sub/chap_model_basics}
+\subfile{../subfiles/chap_model_basics}
 
-\subfile{../tex_sub/chap_domain}
+\subfile{../subfiles/chap_domain}
 
-\subfile{../tex_sub/chap_dynamics}
+\subfile{../subfiles/chap_dynamics}
 
-\subfile{../tex_sub/chap_transport}
+\subfile{../subfiles/chap_transport}
 
-\subfile{../tex_sub/chap_ridging_rafting}
+\subfile{../subfiles/chap_ridging_rafting}
 
-\subfile{../tex_sub/chap_radiative_transfer}
+\subfile{../subfiles/chap_radiative_transfer}
 
-\subfile{../tex_sub/chap_thermo}
+\subfile{../subfiles/chap_thermo}
 
-\subfile{../tex_sub/chap_interfaces}
+\subfile{../subfiles/chap_interfaces}
 
-\subfile{../tex_sub/chap_output_diagnostics}
+\subfile{../subfiles/chap_output_diagnostics}
 
-\subfile{../tex_sub/chap_single_category_use}
+\subfile{../subfiles/chap_single_category_use}
 
-\subfile{../tex_sub/chap_bdy_agrif}
+\subfile{../subfiles/chap_bdy_agrif}
 
-\subfile{../tex_sub/chap_miscellaneous}
+\subfile{../subfiles/chap_miscellaneous}
 
 %% Appendix
@@ -117,5 +120,5 @@
 \addcontentsline{toc}{chapter}{Bibliography}
 
-\bibliography{../tex_main/SI3_manual.bbl}
+\bibliography{../main/SI3_manual}
 %\bibliography{/Users/ioulianikolskaia/Boulot/LIBRARY/BIBTEX/Martin_biblio.bib} 
 
