Index: NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.sty
===================================================================
--- NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.sty	(revision 11125)
+++ 	(revision )
@@ -1,160 +1,0 @@
-%% ==============================================================================
-%% NEMO_manual.sty: all customizations (packages, styles, cmds)
-%% ==============================================================================
-
-
-%% LaTeX packages
-%% ==============================================================================
-\usepackage{natbib}                      %% bib
-\usepackage{caption}                     %% caption
-\usepackage{xcolor}                      %% color
-\usepackage{times}                       %% font
-\usepackage{hyperref}                    %% hyper
-\usepackage{idxlayout}                   %% index
-\usepackage{enumitem}                    %% list
-\usepackage[outputdir=../build]{minted}   %% listing
-\usepackage{amsmath}                     %% maths
-\usepackage{fancyhdr}                    %% page
-\usepackage{minitoc}                     %% toc
-\usepackage{subfiles}                    %% subdocs
-\usepackage[utf8]{inputenc}              %% input encoding
-\usepackage{draftwatermark}              %% watermark
-\usepackage{textcomp}                    %% Companion fonts
-
-%% Extensions in bundle package
-\usepackage{amssymb, graphicx, makeidx, tabularx}
-
-%% Configuration
-\captionsetup{margin=10pt, font={small}, labelsep=colon, labelfont={bf}}
-\idxlayout{font=footnotesize, columns=3}
-\renewcommand{\bibfont}{\footnotesize}
-\renewcommand{\bibsep}{3pt}
-
-
-%% Styles
-%% ==============================================================================
-\pagestyle{fancy}
-\bibliographystyle{../../NEMO/main/ametsoc}
-
-%% Additionnal fonts
-\DeclareMathAlphabet{\mathpzc}{OT1}{pzc}{m}{it}
-
-
-%% Page layout
-\fancyhf{}
-\fancyhead[LE,RO]{\bfseries\thepage}
-\fancyhead[LO]{\bfseries\hspace{-0em}\rightmark}
-\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
-\fancyhead[RE]{\bfseries\leftmark}
-\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
-\renewcommand{\headrulewidth}{0.5pt}
-\renewcommand{\footrulewidth}{0pt  }
-\addtolength{\headheight}{2.6pt}
-
-
-%% Catcodes
-\makeatletter
-\def\LigneVerticale{\vrule height 5cm depth 2cm\hspace{0.1cm}\relax}
-\def\LignesVerticales{\let\LV\LigneVerticale\LV\LV\LV\LV\LV\LV\LV\LV\LV\LV}
-\def\GrosCarreAvecUnChiffre#1{
-	\rlap{\vrule height 0.8cm width 1cm depth 0.2cm}
-	\rlap{\hbox to 1cm{\hss\mbox{\color{white} #1}\hss}}
- 	\vrule height 0pt width 1cm depth 0pt
-}
-\def\@makechapterhead#1{
-	\hbox{
-		\huge\LignesVerticales\hspace{-0.5cm}
-		\GrosCarreAvecUnChiffre{\thechapter}\hspace{0.2cm}
-		\hbox{#1}
-	}
-	\par\vskip
-1cm
-}
-\def\@makeschapterhead#1{
-	\hbox{
-		\huge\LignesVerticales
-		\hbox{#1}
-	}
-	\par\vskip
-2cm
-}
-\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else
-  \hbox{}
-  \vspace*{\fill}
-  \vspace{\fill}
-  \thispagestyle{empty}
-  \newpage
-  \if@twocolumn\hbox{}\newpage\fi\fi\fi}
-\def\@seccntformat#1{\protect\makebox[0pt][r]{\csname the#1\endcsname\quad}}
-\makeatother
-
-
-%% Global custom commands: \newcommand{<name>}[<args>][<first argument value>]{<code>}
-%% ==============================================================================
-
-%% NEMO and Fortran in small capitals
-\newcommand{\NEMO}{\textsc{nemo}}
-\newcommand{\fortran}{\textsc{Fortran}}
-\newcommand{\fninety}{\textsc{Fortran 90}}
-
-%% Common aliases
-\renewcommand{\deg}[1][]{\ensuremath{^{\circ}#1}}
-\newcommand{\zstar }{\ensuremath{z^\star}}
-\newcommand{\sstar }{\ensuremath{s^\star}}
-\newcommand{\ztilde}{\ensuremath{\tilde z}}
-\newcommand{\stilde}{\ensuremath{\tilde s}}
-\newcommand{\ie}{\ensuremath{i.e.}}
-\newcommand{\eg}{\ensuremath{e.g.}}
-
-%% Inline maths
-\newcommand{\fractext}[2]{\textstyle \frac{#1}{#2}}
-\newcommand{\rdt}{\Delta t}
-
-%% Text env. for Gurvan
-\newcommand{\gmcomment}[1]{}
-
-%% Index entries (italic font for files, preformat for code)
-\newcommand{\hf}[1]{\textit{#1.h90}            \index{h90 files!#1}}
-\newcommand{\ifile}[1]{\textit{#1.nc}          \index{Input NetCDF files!#1.nc}}
-\newcommand{\jp}[1]{\texttt{#1}                \index{Model parameters!#1}}
-\newcommand{\key}[1]{\texttt{\textbf{key\_#1}} \index{CPP keys!key\_#1}}
-\newcommand{\mdl}[1]{\textit{#1.F90}           \index{Modules!#1}}
-\newcommand{\ngn}[1]{\texttt{#1}               \index{Namelist Group Names!#1}}
-\newcommand{\np}[1]{\texttt{#1}                \index{Namelist parameters!#1}}
-\newcommand{\rou}[1]{\texttt{#1}               \index{Routines!#1}}
-
-%% Maths
-\newcommand{\lt}{\left}
-\newcommand{\rt}{\right}
-\newcommand{\vect}[1]{\ensuremath{\mathbf{#1}}}
-\newcommand{\pd}[2][]{\ensuremath{\frac{\partial #1}{\partial #2}}}
-
-%% Namelists inclusion
-\newcommand{\nlst}[1]{\forfile{../../../namelists/#1}}
-
-
-%% Minted package: syntax highlighting configuration
-%% ==============================================================================
-
-%% Global highlighting style
-\setminted{style=emacs, fontsize=\scriptsize, breaklines, frame=leftline}
-\setminted[xml]{style=borland} %% Specific per language
-
-%% Oneliner
-\newmint[forline]{fortran}{}   % \forline|...|
-\newmint[xmlline]{xml}{}       % \xmlline|...|
-\newmint[cmd]{console}{}       % \cmd|...|
-
-%% Multi-lines
-\newminted[forlines]{fortran}{}   % \begin{forlines}
-\newminted[xmllines]{xml}{}       % \begin{xmllines}
-\newminted[cmds]{console}{}       % \begin{cmds}
-\newminted[clines]{c}{}           % \begin{clines}
-
-%% File
-\newmintedfile[forfile]{fortran}{}   % \forfile{../namelists/nam...}
-
-%% Inline
-\newmintinline[forcode]{fortran}{fontsize=auto, frame=lines}   % \forcode{...}
-\newmintinline[xmlcode]{xml}{    fontsize=auto, frame=lines}   % \xmlcode{...}
-\newmintinline[snippet]{console}{fontsize=auto, frame=lines}   % \snippet{...}
Index: NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.tex
===================================================================
--- NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.tex	(revision 11125)
+++ NEMO/trunk/doc/latex/NEMO/main/NEMO_manual.tex	(revision 11128)
@@ -11,8 +11,9 @@
 
 %% Custom style (.sty)
-\usepackage{../main/NEMO_manual}
+\usepackage{../../styles/NEMO}
 \hypersetup{
-	pdftitle={NEMO ocean engine}, pdfauthor={Gurvan Madec, and NEMO System Team},
-	colorlinks
+  pdftitle={NEMO ocean engine},
+  pdfauthor={Gurvan Madec, and NEMO System Team},
+  colorlinks
 }
 
Index: NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex
===================================================================
--- NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex	(revision 11125)
+++ NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex	(revision 11128)
@@ -217,5 +217,5 @@
 This \citet{large.yeager_rpt04} dataset is available through
 the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
-The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the NEMO distribution since release v3.3. 
+The "normal year" of \citet{large.yeager_rpt04} has been chosen of the NEMO distribution since release v3.3. 
 
 ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas current area
