Index: MO/trunk/doc/latex/NEMO/main/routines.idx
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/main/routines.idx	(revision 11178)
+++ 	(revision )
@@ -1,1 +1,0 @@
-link ../build/routines.idx
Index: /NEMO/trunk/doc/latex/NEMO/main/subroutines.idx
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/main/subroutines.idx	(revision 11179)
+++ /NEMO/trunk/doc/latex/NEMO/main/subroutines.idx	(revision 11179)
@@ -0,0 +1,1 @@
+link ../build/subroutines.idx
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex	(revision 11179)
@@ -34,5 +34,6 @@
 % 1D model configuration
 % ================================================================
-\section{C1D: 1D Water column model (\protect\key{c1d}) }
+\section[C1D: 1D Water column model (\texttt{\textbf{key\_c1d}})]
+{C1D: 1D Water column model (\protect\key{c1d})}
 \label{sec:CFG_c1d}
 
@@ -227,5 +228,5 @@
 %       GYRE family: double gyre basin
 % -------------------------------------------------------------------------------------------------------------
-\section{GYRE family: double gyre basin }
+\section{GYRE family: double gyre basin}
 \label{sec:CFG_gyre}
 
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex	(revision 11179)
@@ -1332,5 +1332,6 @@
 %       NetCDF4 support
 % ================================================================
-\section{NetCDF4 support (\protect\key{netcdf4})}
+\section[NetCDF4 support (\texttt{\textbf{key\_netcdf4}})]
+{NetCDF4 support (\protect\key{netcdf4})}
 \label{sec:DIA_nc4}
 
@@ -1450,5 +1451,6 @@
 %       Tracer/Dynamics Trends
 % -------------------------------------------------------------------------------------------------------------
-\section{Tracer/Dynamics trends  (\protect\ngn{namtrd})}
+\section[Tracer/Dynamics trends (\texttt{namtrd})]
+{Tracer/Dynamics trends (\protect\ngn{namtrd})}
 \label{sec:DIA_trd}
 
@@ -1497,5 +1499,6 @@
 %       On-line Floats trajectories
 % -------------------------------------------------------------------------------------------------------------
-\section{FLO: On-Line Floats trajectories (\protect\key{floats})}
+\section[FLO: On-Line Floats trajectories (\texttt{\textbf{key\_floats}})]
+{FLO: On-Line Floats trajectories (\protect\key{floats})}
 \label{sec:FLO}
 %--------------------------------------------namflo-------------------------------------------------------
@@ -1605,5 +1608,6 @@
 %       Harmonic analysis of tidal constituents
 % -------------------------------------------------------------------------------------------------------------
-\section{Harmonic analysis of tidal constituents (\protect\key{diaharm}) }
+\section[Harmonic analysis of tidal constituents (\texttt{\textbf{key\_diaharm}})]
+{Harmonic analysis of tidal constituents (\protect\key{diaharm})}
 \label{sec:DIA_diag_harm}
 
@@ -1652,5 +1656,6 @@
 %       Sections transports
 % -------------------------------------------------------------------------------------------------------------
-\section{Transports across sections (\protect\key{diadct}) }
+\section[Transports across sections (\texttt{\textbf{key\_diadct}})]
+{Transports across sections (\protect\key{diadct})}
 \label{sec:DIA_diag_dct}
 
@@ -1976,5 +1981,6 @@
 %       Other Diagnostics
 % -------------------------------------------------------------------------------------------------------------
-\section{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})}
+\section[Other diagnostics (\texttt{\textbf{key\_diahth}}, \texttt{\textbf{key\_diaar5}})]
+{Other diagnostics (\protect\key{diahth}, \protect\key{diaar5})}
 \label{sec:DIA_diag_others}
 
@@ -1982,5 +1988,6 @@
 The available ready-to-add diagnostics modules can be found in directory DIA.
 
-\subsection{Depth of various quantities (\protect\mdl{diahth})}
+\subsection[Depth of various quantities (\textit{diahth.F90})]
+{Depth of various quantities (\protect\mdl{diahth})}
 
 Among the available diagnostics the following ones are obtained when defining the \key{diahth} CPP key:
@@ -1998,5 +2005,6 @@
 % -----------------------------------------------------------
 
-\subsection{Poleward heat and salt transports (\protect\mdl{diaptr})}
+\subsection[Poleward heat and salt transports (\textit{diaptr.F90})]
+{Poleward heat and salt transports (\protect\mdl{diaptr})}
 
 %------------------------------------------namptr-----------------------------------------
@@ -2032,5 +2040,6 @@
 %       CMIP specific diagnostics 
 % -----------------------------------------------------------
-\subsection{CMIP specific diagnostics (\protect\mdl{diaar5})}
+\subsection[CMIP specific diagnostics (\textit{diaar5.F90})]
+{CMIP specific diagnostics (\protect\mdl{diaar5})}
 
 A series of diagnostics has been added in the \mdl{diaar5}.
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DOM.tex	(revision 11179)
@@ -345,5 +345,6 @@
 % Domain: Horizontal Grid (mesh) 
 % ================================================================
-\section{Horizontal grid mesh (\protect\mdl{domhgr})}
+\section[Horizontal grid mesh (\textit{domhgr.F90})]
+{Horizontal grid mesh (\protect\mdl{domhgr})}
 \label{sec:DOM_hgr}
 
@@ -451,5 +452,6 @@
 % Domain: Vertical Grid (domzgr)
 % ================================================================
-\section{Vertical grid (\protect\mdl{domzgr})}
+\section[Vertical grid (\textit{domzgr.F90})]
+{Vertical grid (\protect\mdl{domzgr})}
 \label{sec:DOM_zgr}
 %-----------------------------------------nam_zgr & namdom-------------------------------------------
@@ -480,5 +482,5 @@
       (d) hybrid $s-z$ coordinate,
       (e) hybrid $s-z$ coordinate with partial step, and
-      (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}~\forcode{= .false.}).
+      (f) same as (e) but in the non-linear free surface (\protect\np{ln\_linssh}\forcode{ = .false.}).
       Note that the non-linear free surface can be used with any of the 5 coordinates (a) to (e).
     }
@@ -491,12 +493,12 @@
 It is not intended as an option which can be enabled or disabled in the middle of an experiment.
 Three main choices are offered (\autoref{fig:z_zps_s_sps}):
-$z$-coordinate with full step bathymetry (\np{ln\_zco}~\forcode{= .true.}),
-$z$-coordinate with partial step bathymetry (\np{ln\_zps}~\forcode{= .true.}),
-or generalized, $s$-coordinate (\np{ln\_sco}~\forcode{= .true.}).
+$z$-coordinate with full step bathymetry (\np{ln\_zco}\forcode{ = .true.}),
+$z$-coordinate with partial step bathymetry (\np{ln\_zps}\forcode{ = .true.}),
+or generalized, $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}).
 Hybridation of the three main coordinates are available:
 $s-z$ or $s-zps$ coordinate (\autoref{fig:z_zps_s_sps} and \autoref{fig:z_zps_s_sps}).
 By default a non-linear free surface is used: the coordinate follow the time-variation of the free surface so that
 the transformation is time dependent: $z(i,j,k,t)$ (\autoref{fig:z_zps_s_sps}).
-When a linear free surface is assumed (\np{ln\_linssh}~\forcode{= .true.}),
+When a linear free surface is assumed (\np{ln\_linssh}\forcode{ = .true.}),
 the vertical coordinate are fixed in time, but the seawater can move up and down across the $z_0$ surface
 (in other words, the top of the ocean in not a rigid-lid).
@@ -513,5 +515,5 @@
   N.B. in full step $z$-coordinate, a \ifile{bathy\_level} file can replace the \ifile{bathy\_meter} file,
   so that the computation of the number of wet ocean point in each water column is by-passed}.
-If \np{ln\_isfcav}~\forcode{= .true.}, an extra file input file (\ifile{isf\_draft\_meter}) describing
+If \np{ln\_isfcav}\forcode{ = .true.}, an extra file input file (\ifile{isf\_draft\_meter}) describing
 the ice shelf draft (in meters) is needed.
 
@@ -535,5 +537,5 @@
 %%%
 
-Unless a linear free surface is used (\np{ln\_linssh}~\forcode{= .false.}),
+Unless a linear free surface is used (\np{ln\_linssh}\forcode{ = .false.}),
 the arrays describing the grid point depths and vertical scale factors are three set of
 three dimensional arrays $(i,j,k)$ defined at \textit{before}, \textit{now} and \textit{after} time step.
@@ -541,5 +543,5 @@
 They are updated at each model time step using a fixed reference coordinate system which
 computer names have a $\_0$ suffix.
-When the linear free surface option is used (\np{ln\_linssh}~\forcode{= .true.}), \textit{before},
+When the linear free surface option is used (\np{ln\_linssh}\forcode{ = .true.}), \textit{before},
 \textit{now} and \textit{after} arrays are simply set one for all to their reference counterpart.
 
@@ -553,12 +555,12 @@
 (found in \ngn{namdom} namelist): 
 \begin{description}
-\item[\np{nn\_bathy}~\forcode{= 0}]:
+\item[\np{nn\_bathy}\forcode{ = 0}]:
   a flat-bottom domain is defined.
   The total depth $z_w (jpk)$ is given by the coordinate transformation.
   The domain can either be a closed basin or a periodic channel depending on the parameter \np{jperio}.
-\item[\np{nn\_bathy}~\forcode{= -1}]:
+\item[\np{nn\_bathy}\forcode{ = -1}]:
   a domain with a bump of topography one third of the domain width at the central latitude.
   This is meant for the "EEL-R5" configuration, a periodic or open boundary channel with a seamount.
-\item[\np{nn\_bathy}~\forcode{= 1}]:
+\item[\np{nn\_bathy}\forcode{ = 1}]:
   read a bathymetry and ice shelf draft (if needed).
   The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters) at
@@ -571,5 +573,5 @@
   The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters) at
   each grid point of the model grid.
-  This file is only needed if \np{ln\_isfcav}~\forcode{= .true.}.
+  This file is only needed if \np{ln\_isfcav}\forcode{ = .true.}.
   Defining the ice shelf draft will also define the ice shelf edge and the grounding line position.
 \end{description}
@@ -586,6 +588,6 @@
 %        z-coordinate  and reference coordinate transformation
 % -------------------------------------------------------------------------------------------------------------
-\subsection[$Z$-coordinate (\protect\np{ln\_zco}~\forcode{= .true.}) and ref. coordinate]
-				{$Z$-coordinate (\protect\np{ln\_zco}~\forcode{= .true.}) and reference coordinate}
+\subsection[$Z$-coordinate (\forcode{ln_zco = .true.}) and ref. coordinate]
+{$Z$-coordinate (\protect\np{ln\_zco}\forcode{ = .true.}) and reference coordinate}
 \label{subsec:DOM_zco}
 
@@ -616,5 +618,5 @@
 using parameters provided in the \ngn{namcfg} namelist.
 
-It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr}~\forcode{= 0}).
+It is possible to define a simple regular vertical grid by giving zero stretching (\np{ppacr}\forcode{ = 0}).
 In that case, the parameters \jp{jpk} (number of $w$-levels) and
 \np{pphmax} (total ocean depth in meters) fully define the grid.
@@ -631,5 +633,5 @@
 a smooth hyperbolic tangent transition in between (\autoref{fig:zgr}).
 
-If the ice shelf cavities are opened (\np{ln\_isfcav}~\forcode{= .true.}), the definition of $z_0$ is the same.
+If the ice shelf cavities are opened (\np{ln\_isfcav}\forcode{ = .true.}), the definition of $z_0$ is the same.
 However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to:
 \begin{equation}
@@ -765,5 +767,6 @@
 %        z-coordinate with partial step
 % -------------------------------------------------------------------------------------------------------------
-\subsection{$Z$-coordinate with partial step (\protect\np{ln\_zps}~\forcode{= .true.})}
+\subsection[$Z$-coordinate with partial step (\forcode{ln_zps = .true.})]
+{$Z$-coordinate with partial step (\protect\np{ln\_zps}\forcode{ = .true.})}
 \label{subsec:DOM_zps}
 %--------------------------------------------namdom-------------------------------------------------------
@@ -796,5 +799,6 @@
 %        s-coordinate
 % -------------------------------------------------------------------------------------------------------------
-\subsection{$S$-coordinate (\protect\np{ln\_sco}~\forcode{= .true.})}
+\subsection[$S$-coordinate (\forcode{ln_sco = .true.})]
+{$S$-coordinate (\protect\np{ln\_sco}\forcode{ = .true.})}
 \label{subsec:DOM_sco}
 %------------------------------------------nam_zgr_sco---------------------------------------------------
@@ -803,5 +807,5 @@
 %--------------------------------------------------------------------------------------------------------------
 Options are defined in \ngn{namzgr\_sco}.
-In $s$-coordinate (\np{ln\_sco}~\forcode{= .true.}), the depth and thickness of the model levels are defined from
+In $s$-coordinate (\np{ln\_sco}\forcode{ = .true.}), the depth and thickness of the model levels are defined from
 the product of a depth field and either a stretching function or its derivative, respectively:
 
@@ -826,5 +830,5 @@
 
 The original default NEMO s-coordinate stretching is available if neither of the other options are specified as true
-(\np{ln\_s\_SH94}~\forcode{= .false.} and \np{ln\_s\_SF12}~\forcode{= .false.}).
+(\np{ln\_s\_SH94}\forcode{ = .false.} and \np{ln\_s\_SF12}\forcode{ = .false.}).
 This uses a depth independent $\tanh$ function for the stretching \citep{madec.delecluse.ea_JPO96}:
 
@@ -846,5 +850,5 @@
 
 A stretching function,
-modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln\_s\_SH94}~\forcode{= .true.}),
+modified from the commonly used \citet{song.haidvogel_JCP94} stretching (\np{ln\_s\_SH94}\forcode{ = .true.}),
 is also available and is more commonly used for shelf seas modelling:
 
@@ -946,5 +950,6 @@
 %        z*- or s*-coordinate
 % -------------------------------------------------------------------------------------------------------------
-\subsection{\zstar- or \sstar-coordinate (\protect\np{ln\_linssh}~\forcode{= .false.})}
+\subsection[\zstar- or \sstar-coordinate (\forcode{ln_linssh = .false.})]
+{\zstar- or \sstar-coordinate (\protect\np{ln\_linssh}\forcode{ = .false.})}
 \label{subsec:DOM_zgr_star}
 
@@ -1014,5 +1019,6 @@
 % Domain: Initial State (dtatsd & istate)
 % ================================================================
-\section{Initial state (\protect\mdl{istate} and \protect\mdl{dtatsd})}
+\section[Initial state (\textit{istate.F90} and \textit{dtatsd.F90})]
+{Initial state (\protect\mdl{istate} and \protect\mdl{dtatsd})}
 \label{sec:DTA_tsd}
 %-----------------------------------------namtsd-------------------------------------------
@@ -1025,5 +1031,5 @@
 salinity fields is controlled through the \np{ln\_tsd\_ini} namelist parameter.
 \begin{description}
-\item[\np{ln\_tsd\_init}~\forcode{= .true.}]
+\item[\np{ln\_tsd\_init}\forcode{ = .true.}]
   use a T and S input files that can be given on the model grid itself or on their native input data grid.
   In the latter case,
@@ -1032,5 +1038,5 @@
   The information relative to the input files are given in the \np{sn\_tem} and \np{sn\_sal} structures.
   The computation is done in the \mdl{dtatsd} module.
-\item[\np{ln\_tsd\_init}~\forcode{= .false.}]
+\item[\np{ln\_tsd\_init}\forcode{ = .false.}]
   use constant salinity value of $35.5~psu$ and an analytical profile of temperature
   (typical of the tropical ocean), see \rou{istate\_t\_s} subroutine called from \mdl{istate} module.
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_DYN.tex	(revision 11179)
@@ -65,5 +65,6 @@
 %           Horizontal divergence and relative vorticity
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Horizontal divergence and relative vorticity (\protect\mdl{divcur})}
+\subsection[Horizontal divergence and relative vorticity (\textit{divcur.F90})]
+{Horizontal divergence and relative vorticity (\protect\mdl{divcur})}
 \label{subsec:DYN_divcur}
 
@@ -101,5 +102,6 @@
 %           Sea Surface Height evolution
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Horizontal divergence and relative vorticity (\protect\mdl{sshwzv})}
+\subsection[Horizontal divergence and relative vorticity (\textit{sshwzv.F90})]
+{Horizontal divergence and relative vorticity (\protect\mdl{sshwzv})}
 \label{subsec:DYN_sshwzv}
 
@@ -181,5 +183,6 @@
 %        Vorticity term 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Vorticity term (\protect\mdl{dynvor})}
+\subsection[Vorticity term (\textit{dynvor.F90})]
+{Vorticity term (\protect\mdl{dynvor})}
 \label{subsec:DYN_vor}
 %------------------------------------------nam_dynvor----------------------------------------------------
@@ -203,5 +206,6 @@
 %                 enstrophy conserving scheme
 %-------------------------------------------------------------
-\subsubsection{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{ = .true.})}
+\subsubsection[Enstrophy conserving scheme (\forcode{ln_dynvor_ens = .true.})]
+{Enstrophy conserving scheme (\protect\np{ln\_dynvor\_ens}\forcode{ = .true.})}
 \label{subsec:DYN_vor_ens}
 
@@ -226,5 +230,6 @@
 %                 energy conserving scheme
 %-------------------------------------------------------------
-\subsubsection{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{ = .true.})}
+\subsubsection[Energy conserving scheme (\forcode{ln_dynvor_ene = .true.})]
+{Energy conserving scheme (\protect\np{ln\_dynvor\_ene}\forcode{ = .true.})}
 \label{subsec:DYN_vor_ene}
 
@@ -246,5 +251,6 @@
 %                 mix energy/enstrophy conserving scheme
 %-------------------------------------------------------------
-\subsubsection{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{ = .true.}) }
+\subsubsection[Mixed energy/enstrophy conserving scheme (\forcode{ln_dynvor_mix = .true.})]
+{Mixed energy/enstrophy conserving scheme (\protect\np{ln\_dynvor\_mix}\forcode{ = .true.})}
 \label{subsec:DYN_vor_mix}
 
@@ -271,5 +277,6 @@
 %                 energy and enstrophy conserving scheme
 %-------------------------------------------------------------
-\subsubsection{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.}) }
+\subsubsection[Energy and enstrophy conserving scheme (\forcode{ln_dynvor_een = .true.})]
+{Energy and enstrophy conserving scheme (\protect\np{ln\_dynvor\_een}\forcode{ = .true.})}
 \label{subsec:DYN_vor_een}
 
@@ -364,5 +371,6 @@
 %           Kinetic Energy Gradient term
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Kinetic energy gradient term (\protect\mdl{dynkeg})}
+\subsection[Kinetic energy gradient term (\textit{dynkeg.F90})]
+{Kinetic energy gradient term (\protect\mdl{dynkeg})}
 \label{subsec:DYN_keg}
 
@@ -384,5 +392,6 @@
 %           Vertical advection term
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Vertical advection term (\protect\mdl{dynzad}) }
+\subsection[Vertical advection term (\textit{dynzad.F90})]
+{Vertical advection term (\protect\mdl{dynzad})}
 \label{subsec:DYN_zad}
 
@@ -430,5 +439,6 @@
 %           Coriolis plus curvature metric terms
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Coriolis plus curvature metric terms (\protect\mdl{dynvor}) }
+\subsection[Coriolis plus curvature metric terms (\textit{dynvor.F90})]
+{Coriolis plus curvature metric terms (\protect\mdl{dynvor})}
 \label{subsec:DYN_cor_flux}
 
@@ -451,5 +461,6 @@
 %           Flux form Advection term
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Flux form advection term (\protect\mdl{dynadv}) }
+\subsection[Flux form advection term (\textit{dynadv.F90})]
+{Flux form advection term (\protect\mdl{dynadv})}
 \label{subsec:DYN_adv_flux}
 
@@ -484,5 +495,6 @@
 %                 2nd order centred scheme
 %-------------------------------------------------------------
-\subsubsection{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{ = .true.})}
+\subsubsection[CEN2: $2^{nd}$ order centred scheme (\forcode{ln_dynadv_cen2 = .true.})]
+{CEN2: $2^{nd}$ order centred scheme (\protect\np{ln\_dynadv\_cen2}\forcode{ = .true.})}
 \label{subsec:DYN_adv_cen2}
 
@@ -507,5 +519,6 @@
 %                 UBS scheme
 %-------------------------------------------------------------
-\subsubsection{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{ = .true.})}
+\subsubsection[UBS: Upstream Biased Scheme (\forcode{ln_dynadv_ubs = .true.})]
+{UBS: Upstream Biased Scheme (\protect\np{ln\_dynadv\_ubs}\forcode{ = .true.})}
 \label{subsec:DYN_adv_ubs}
 
@@ -560,5 +573,6 @@
 %           Hydrostatic pressure gradient term
 % ================================================================
-\section{Hydrostatic pressure gradient (\protect\mdl{dynhpg})}
+\section[Hydrostatic pressure gradient (\textit{dynhpg.F90})]
+{Hydrostatic pressure gradient (\protect\mdl{dynhpg})}
 \label{sec:DYN_hpg}
 %------------------------------------------nam_dynhpg---------------------------------------------------
@@ -582,5 +596,6 @@
 %           z-coordinate with full step
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{ = .true.})}
+\subsection[Full step $Z$-coordinate (\forcode{ln_dynhpg_zco = .true.})]
+{Full step $Z$-coordinate (\protect\np{ln\_dynhpg\_zco}\forcode{ = .true.})}
 \label{subsec:DYN_hpg_zco}
 
@@ -627,5 +642,6 @@
 %           z-coordinate with partial step
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{ = .true.})}
+\subsection[Partial step $Z$-coordinate (\forcode{ln_dynhpg_zps = .true.})]
+{Partial step $Z$-coordinate (\protect\np{ln\_dynhpg\_zps}\forcode{ = .true.})}
 \label{subsec:DYN_hpg_zps}
 
@@ -712,5 +728,6 @@
 %           Time-scheme
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{ = .true./.false.})}
+\subsection[Time-scheme (\forcode{ln_dynhpg_imp = .{true,false}.})]
+{Time-scheme (\protect\np{ln\_dynhpg\_imp}\forcode{ = .\{true,false\}}.)}
 \label{subsec:DYN_hpg_imp}
 
@@ -773,5 +790,6 @@
 % Surface Pressure Gradient
 % ================================================================
-\section{Surface pressure gradient (\protect\mdl{dynspg})}
+\section[Surface pressure gradient (\textit{dynspg.F90})]
+{Surface pressure gradient (\protect\mdl{dynspg})}
 \label{sec:DYN_spg}
 %-----------------------------------------nam_dynspg----------------------------------------------------
@@ -811,5 +829,6 @@
 % Explicit free surface formulation
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Explicit free surface (\protect\key{dynspg\_exp})}
+\subsection[Explicit free surface (texttt{\textbf{key\_dynspg\_exp}})]
+{Explicit free surface (\protect\key{dynspg\_exp})}
 \label{subsec:DYN_spg_exp}
 
@@ -837,5 +856,6 @@
 % Split-explict free surface formulation
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Split-explicit free surface (\protect\key{dynspg\_ts})}
+\subsection[Split-explicit free surface (texttt{\textbf{key\_dynspg\_ts}})]
+{Split-explicit free surface (\protect\key{dynspg\_ts})}
 \label{subsec:DYN_spg_ts}
 %------------------------------------------namsplit-----------------------------------------------------------
@@ -1081,5 +1101,6 @@
 % Filtered free surface formulation
 %--------------------------------------------------------------------------------------------------------------
-\subsection{Filtered free surface (\protect\key{dynspg\_flt})}
+\subsection[Filtered free surface (\texttt{\textbf{key\_dynspg\_flt}})]
+{Filtered free surface (\protect\key{dynspg\_flt})}
 \label{subsec:DYN_spg_fltp}
 
@@ -1109,5 +1130,6 @@
 % Lateral diffusion term
 % ================================================================
-\section{Lateral diffusion term and operators (\protect\mdl{dynldf})}
+\section[Lateral diffusion term and operators (\textit{dynldf.F90})]
+{Lateral diffusion term and operators (\protect\mdl{dynldf})}
 \label{sec:DYN_ldf}
 %------------------------------------------nam_dynldf----------------------------------------------------
@@ -1143,6 +1165,6 @@
 
 % ================================================================
-\subsection[Iso-level laplacian (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})]
-				{Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})}
+\subsection[Iso-level laplacian (\forcode{ln_dynldf_lap = .true.})]
+{Iso-level laplacian operator (\protect\np{ln\_dynldf\_lap}\forcode{ = .true.})}
 \label{subsec:DYN_ldf_lap}
 
@@ -1169,6 +1191,6 @@
 %           Rotated laplacian operator
 %--------------------------------------------------------------------------------------------------------------
-\subsection[Rotated laplacian (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})]
-				{Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})}
+\subsection[Rotated laplacian (\forcode{ln_dynldf_iso = .true.})]
+{Rotated laplacian operator (\protect\np{ln\_dynldf\_iso}\forcode{ = .true.})}
 \label{subsec:DYN_ldf_iso}
 
@@ -1228,6 +1250,6 @@
 %           Iso-level bilaplacian operator
 %--------------------------------------------------------------------------------------------------------------
-\subsection[Iso-level bilaplacian (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})]
-				{Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})}
+\subsection[Iso-level bilaplacian (\forcode{ln_dynldf_bilap = .true.})]
+{Iso-level bilaplacian operator (\protect\np{ln\_dynldf\_bilap}\forcode{ = .true.})}
 \label{subsec:DYN_ldf_bilap}
 
@@ -1243,5 +1265,6 @@
 %           Vertical diffusion term
 % ================================================================
-\section{Vertical diffusion term (\protect\mdl{dynzdf})}
+\section[Vertical diffusion term (\textit{dynzdf.F90})]
+{Vertical diffusion term (\protect\mdl{dynzdf})}
 \label{sec:DYN_zdf}
 %----------------------------------------------namzdf------------------------------------------------------
@@ -1372,6 +1395,6 @@
 %   Iterative limiters
 %-----------------------------------------------------------------------------------------
-\subsection   [Directional limiter (\textit{wet\_dry})]
-         {Directional limiter (\mdl{wet\_dry})}
+\subsection[Directional limiter (\textit{wet\_dry.F90})]
+{Directional limiter (\mdl{wet\_dry})}
 \label{subsec:DYN_wd_directional_limiter}
 The principal idea of the directional limiter is that
@@ -1412,10 +1435,10 @@
 %-----------------------------------------------------------------------------------------
 
-\subsection   [Iterative limiter (\textit{wet\_dry})]
-         {Iterative limiter (\mdl{wet\_dry})}
+\subsection[Iterative limiter (\textit{wet\_dry.F90})]
+{Iterative limiter (\mdl{wet\_dry})}
 \label{subsec:DYN_wd_iterative_limiter}
 
-\subsubsection [Iterative flux limiter (\textit{wet\_dry})]
-         {Iterative flux limiter (\mdl{wet\_dry})}
+\subsubsection[Iterative flux limiter (\textit{wet\_dry.F90})]
+{Iterative flux limiter (\mdl{wet\_dry})}
 \label{subsubsec:DYN_wd_il_spg_limiter}
 
@@ -1522,6 +1545,6 @@
 %      Surface pressure gradients
 %----------------------------------------------------------------------------------------
-\subsubsection   [Modification of surface pressure gradients (\textit{dynhpg})]
-         {Modification of surface pressure gradients (\mdl{dynhpg})}
+\subsubsection[Modification of surface pressure gradients (\textit{dynhpg.F90})]
+{Modification of surface pressure gradients (\mdl{dynhpg})}
 \label{subsubsec:DYN_wd_il_spg}
 
@@ -1588,6 +1611,6 @@
 conditions.
 
-\subsubsection   [Additional considerations (\textit{usrdef\_zgr})]
-         {Additional considerations (\mdl{usrdef\_zgr})}
+\subsubsection[Additional considerations (\textit{usrdef\_zgr.F90})]
+{Additional considerations (\mdl{usrdef\_zgr})}
 \label{subsubsec:WAD_additional}
 
@@ -1603,6 +1626,6 @@
 %      The WAD test cases
 %----------------------------------------------------------------------------------------
-\subsection   [The WAD test cases (\textit{usrdef\_zgr})]
-         {The WAD test cases (\mdl{usrdef\_zgr})}
+\subsection[The WAD test cases (\textit{usrdef\_zgr.F90})]
+{The WAD test cases (\mdl{usrdef\_zgr})}
 \label{WAD_test_cases}
 
@@ -1614,5 +1637,6 @@
 % Time evolution term 
 % ================================================================
-\section{Time evolution term (\protect\mdl{dynnxt})}
+\section[Time evolution term (\textit{dynnxt.F90})]
+{Time evolution term (\protect\mdl{dynnxt})}
 \label{sec:DYN_nxt}
 
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LBC.tex	(revision 11179)
@@ -17,5 +17,6 @@
 % Boundary Condition at the Coast
 % ================================================================
-\section{Boundary condition at the coast (\protect\np{rn\_shlat})}
+\section[Boundary condition at the coast (\texttt{rn\_shlat})]
+{Boundary condition at the coast (\protect\np{rn\_shlat})}
 \label{sec:LBC_coast}
 %--------------------------------------------nam_lbc-------------------------------------------------------
@@ -147,5 +148,6 @@
 % Boundary Condition around the Model Domain
 % ================================================================
-\section{Model domain boundary condition (\protect\np{jperio})}
+\section[Model domain boundary condition (\texttt{jperio})]
+{Model domain boundary condition (\protect\np{jperio})}
 \label{sec:LBC_jperio}
 
@@ -158,5 +160,6 @@
 %        Closed, cyclic (\np{jperio}\forcode{ = 0..2}) 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Closed, cyclic (\protect\np{jperio}\forcode{= [0127]})}
+\subsection[Closed, cyclic (\forcode{jperio = [0127]})]
+{Closed, cyclic (\protect\np{jperio}\forcode{ = [0127]})}
 \label{subsec:LBC_jperio012}
 
@@ -206,5 +209,6 @@
 %        North fold (\textit{jperio = 3 }to $6)$ 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{North-fold (\protect\np{jperio}\forcode{ = 3..6})}
+\subsection[North-fold (\forcode{jperio = [3-6]})]
+{North-fold (\protect\np{jperio}\forcode{ = [3-6]})}
 \label{subsec:LBC_north_fold}
 
@@ -232,5 +236,6 @@
 % Exchange with neighbouring processors 
 % ====================================================================
-\section{Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})}
+\section[Exchange with neighbouring processors (\textit{lbclnk.F90}, \textit{lib\_mpp.F90})]
+{Exchange with neighbouring processors (\protect\mdl{lbclnk}, \protect\mdl{lib\_mpp})}
 \label{sec:LBC_mpp}
 
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_LDF.tex	(revision 11179)
@@ -38,5 +38,6 @@
 % Direction of lateral Mixing
 % ================================================================
-\section{Direction of lateral mixing (\protect\mdl{ldfslp})}
+\section[Direction of lateral mixing (\textit{ldfslp.F90})]
+{Direction of lateral mixing (\protect\mdl{ldfslp})}
 \label{sec:LDF_slp}
 
@@ -301,5 +302,6 @@
 % Lateral Mixing Operator
 % ================================================================
-\section{Lateral mixing operators (\protect\mdl{traldf}, \protect\mdl{traldf}) }
+\section[Lateral mixing operators (\textit{traldf.F90})]
+{Lateral mixing operators (\protect\mdl{traldf}, \protect\mdl{traldf})}
 \label{sec:LDF_op}
 
@@ -309,5 +311,6 @@
 % Lateral Mixing Coefficients
 % ================================================================
-\section{Lateral mixing coefficient (\protect\mdl{ldftra}, \protect\mdl{ldfdyn}) }
+\section[Lateral mixing coefficient (\textit{ldftra.F90}, \textit{ldfdyn.F90})]
+{Lateral mixing coefficient (\protect\mdl{ldftra}, \protect\mdl{ldfdyn})}
 \label{sec:LDF_coef}
 
@@ -339,5 +342,6 @@
 which is specified through the \np{rn\_ahm0} and \np{rn\_aht0} namelist parameters.
 
-\subsubsection{Vertically varying mixing coefficients (\protect\key{traldf\_c1d} and \key{dynldf\_c1d})} 
+\subsubsection[Vertically varying mixing coefficients (\texttt{\textbf{key\_traldf\_c1d}} and \texttt{\textbf{key\_dynldf\_c1d}})]
+{Vertically varying mixing coefficients (\protect\key{traldf\_c1d} and \key{dynldf\_c1d})}
 The 1D option is only available when using the $z$-coordinate with full step.
 Indeed in all the other types of vertical coordinate,
@@ -350,5 +354,6 @@
 This profile is hard coded in file \textit{traldf\_c1d.h90}, but can be easily modified by users.
 
-\subsubsection{Horizontally varying mixing coefficients (\protect\key{traldf\_c2d} and \protect\key{dynldf\_c2d})}
+\subsubsection[Horizontally varying mixing coefficients (\texttt{\textbf{key\_traldf\_c2d}} and \texttt{\textbf{key\_dynldf\_c2d}})]
+{Horizontally varying mixing coefficients (\protect\key{traldf\_c2d} and \protect\key{dynldf\_c2d})}
 By default the horizontal variation of the eddy coefficient depends on the local mesh size and
 the type of operator used:
@@ -381,5 +386,6 @@
 ORCA2 and ORCA05 (see \&namcfg namelist).
 
-\subsubsection{Space varying mixing coefficients (\protect\key{traldf\_c3d} and \key{dynldf\_c3d})}
+\subsubsection[Space varying mixing coefficients (\texttt{\textbf{key\_traldf\_c3d}} and \texttt{\textbf{key\_dynldf\_c3d}})]
+{Space varying mixing coefficients (\protect\key{traldf\_c3d} and \key{dynldf\_c3d})}
 
 The 3D space variation of the mixing coefficient is simply the combination of the 1D and 2D cases,
@@ -430,5 +436,6 @@
 % Eddy Induced Mixing
 % ================================================================
-\section{Eddy induced velocity (\protect\mdl{traadv\_eiv}, \protect\mdl{ldfeiv})}
+\section[Eddy induced velocity (\textit{traadv\_eiv.F90}, \textit{ldfeiv.F90})]
+{Eddy induced velocity (\protect\mdl{traadv\_eiv}, \protect\mdl{ldfeiv})}
 \label{sec:LDF_eiv}
 
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex	(revision 11179)
@@ -5,5 +5,5 @@
 % Chapter —— Surface Boundary Condition (SBC, ISF, ICB) 
 % ================================================================
-\chapter{Surface Boundary Condition (SBC, ISF, ICB) }
+\chapter{Surface Boundary Condition (SBC, ISF, ICB)}
 \label{chap:SBC}
 \minitoc
@@ -226,5 +226,6 @@
 % Input Data specification (\mdl{fldread})
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Input data specification (\protect\mdl{fldread})}
+\subsection[Input data specification (\textit{fldread.F90})]
+{Input data specification (\protect\mdl{fldread})}
 \label{subsec:SBC_fldread}
 
@@ -559,5 +560,6 @@
 % Analytical formulation (sbcana module) 
 % ================================================================
-\section{Analytical formulation (\protect\mdl{sbcana})}
+\section[Analytical formulation (\textit{sbcana.F90})]
+{Analytical formulation (\protect\mdl{sbcana})}
 \label{sec:SBC_ana}
 
@@ -584,5 +586,6 @@
 % Flux formulation 
 % ================================================================
-\section{Flux formulation (\protect\mdl{sbcflx})}
+\section[Flux formulation (\textit{sbcflx.F90})]
+{Flux formulation (\protect\mdl{sbcflx})}
 \label{sec:SBC_flx}
 %------------------------------------------namsbc_flx----------------------------------------------------
@@ -606,5 +609,5 @@
 % ================================================================
 \section[Bulk formulation {(\textit{sbcblk\{\_core,\_clio\}.F90})}]
-                        {Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}}
+{Bulk formulation {(\protect\mdl{sbcblk\_core}, \protect\mdl{sbcblk\_clio})}}
 \label{sec:SBC_blk}
 
@@ -625,5 +628,6 @@
 %        CORE Bulk formulea
 % -------------------------------------------------------------------------------------------------------------
-\subsection{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})}
+\subsection[CORE formulea (\textit{sbcblk\_core.F90}, \forcode{ln_core = .true.})]
+{CORE formulea (\protect\mdl{sbcblk\_core}, \protect\np{ln\_core}\forcode{ = .true.})}
 \label{subsec:SBC_blk_core}
 %------------------------------------------namsbc_core----------------------------------------------------
@@ -688,5 +692,6 @@
 %        CLIO Bulk formulea
 % -------------------------------------------------------------------------------------------------------------
-\subsection{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})}
+\subsection[CLIO formulea (\textit{sbcblk\_clio.F90}, \forcode{ln_clio = .true.})]
+{CLIO formulea (\protect\mdl{sbcblk\_clio}, \protect\np{ln\_clio}\forcode{ = .true.})}
 \label{subsec:SBC_blk_clio}
 %------------------------------------------namsbc_clio----------------------------------------------------
@@ -729,5 +734,6 @@
 % Coupled formulation
 % ================================================================
-\section{Coupled formulation (\protect\mdl{sbccpl})}
+\section[Coupled formulation (\textit{sbccpl.F90})]
+{Coupled formulation (\protect\mdl{sbccpl})}
 \label{sec:SBC_cpl}
 %------------------------------------------namsbc_cpl----------------------------------------------------
@@ -770,5 +776,6 @@
 %        Atmospheric pressure
 % ================================================================
-\section{Atmospheric pressure (\protect\mdl{sbcapr})}
+\section[Atmospheric pressure (\textit{sbcapr.F90})]
+{Atmospheric pressure (\protect\mdl{sbcapr})}
 \label{sec:SBC_apr}
 %------------------------------------------namsbc_apr----------------------------------------------------
@@ -806,5 +813,6 @@
 %        Surface Tides Forcing
 % ================================================================
-\section{Surface tides (\protect\mdl{sbctide})}
+\section[Surface tides (\textit{sbctide.F90})]
+{Surface tides (\protect\mdl{sbctide})}
 \label{sec:SBC_tide}
 
@@ -857,5 +865,6 @@
 %        River runoffs
 % ================================================================
-\section{River runoffs (\protect\mdl{sbcrnf})}
+\section[River runoffs (\textit{sbcrnf.F90})]
+{River runoffs (\protect\mdl{sbcrnf})}
 \label{sec:SBC_rnf}
 %------------------------------------------namsbc_rnf----------------------------------------------------
@@ -982,5 +991,6 @@
 %        Ice shelf melting
 % ================================================================
-\section{Ice shelf melting (\protect\mdl{sbcisf})}
+\section[Ice shelf melting (\textit{sbcisf.F90})]
+{Ice shelf melting (\protect\mdl{sbcisf})}
 \label{sec:SBC_isf}
 %------------------------------------------namsbc_isf----------------------------------------------------
@@ -1227,5 +1237,6 @@
 %        Interactions with waves (sbcwave.F90, ln_wave)
 % -------------------------------------------------------------------------------------------------------------
-\section{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})}
+\section[Interactions with waves (\textit{sbcwave.F90}, \texttt{ln\_wave})]
+{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln\_wave})}
 \label{sec:SBC_wave}
 %------------------------------------------namsbc_wave--------------------------------------------------------
@@ -1258,5 +1269,6 @@
 
 % ================================================================
-\subsection{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})}
+\subsection[Neutral drag coefficient from wave model (\texttt{ln\_cdgw})]
+{Neutral drag coefficient from wave model (\protect\np{ln\_cdgw})}
 \label{subsec:SBC_wave_cdgw}
 
@@ -1271,5 +1283,6 @@
 % 3D Stokes Drift (ln_sdw, nn_sdrift)
 % ================================================================
-\subsection{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})}
+\subsection[3D Stokes Drift (\texttt{ln\_sdw}, \texttt{nn\_sdrift})]
+{3D Stokes Drift (\protect\np{ln\_sdw, nn\_sdrift})}
 \label{subsec:SBC_wave_sdw}
 
@@ -1367,5 +1380,6 @@
 % Stokes-Coriolis term (ln_stcor)
 % ================================================================
-\subsection{Stokes-Coriolis term (\protect\np{ln\_stcor})}
+\subsection[Stokes-Coriolis term (\texttt{ln\_stcor})]
+{Stokes-Coriolis term (\protect\np{ln\_stcor})}
 \label{subsec:SBC_wave_stcor}
 
@@ -1381,5 +1395,6 @@
 % Waves modified stress (ln_tauwoc, ln_tauw)
 % ================================================================
-\subsection{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})} 
+\subsection[Wave modified sress (\texttt{ln\_tauwoc}, \texttt{ln\_tauw})]
+{Wave modified sress (\protect\np{ln\_tauwoc, ln\_tauw})}
 \label{subsec:SBC_wave_tauw}
 
@@ -1428,5 +1443,6 @@
 %        Diurnal cycle
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Diurnal cycle (\protect\mdl{sbcdcy})}
+\subsection[Diurnal cycle (\textit{sbcdcy.F90})]
+{Diurnal cycle (\protect\mdl{sbcdcy})}
 \label{subsec:SBC_dcy}
 %------------------------------------------namsbc_rnf----------------------------------------------------
@@ -1514,5 +1530,6 @@
 %        Surface restoring to observed SST and/or SSS
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
+\subsection[Surface restoring to observed SST and/or SSS (\textit{sbcssr.F90})]
+{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
 \label{subsec:SBC_ssr}
 %------------------------------------------namsbc_ssr----------------------------------------------------
@@ -1593,5 +1610,6 @@
 % {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?}
 
-\subsection{Interface to CICE (\protect\mdl{sbcice\_cice})}
+\subsection[Interface to CICE (\textit{sbcice\_cice.F90})]
+{Interface to CICE (\protect\mdl{sbcice\_cice})}
 \label{subsec:SBC_cice}
 
@@ -1626,5 +1644,6 @@
 %        Freshwater budget control 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Freshwater budget control (\protect\mdl{sbcfwb})}
+\subsection[Freshwater budget control (\textit{sbcfwb.F90})]
+{Freshwater budget control (\protect\mdl{sbcfwb})}
 \label{subsec:SBC_fwb}
 
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_TRA.tex	(revision 11179)
@@ -55,10 +55,11 @@
 
 The user has the option of extracting each tendency term on the RHS of the tracer equation for output
-(\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}~\forcode{= .true.}), as described in \autoref{chap:DIA}.
+(\np{ln\_tra\_trd} or \np{ln\_tra\_mxl}\forcode{ = .true.}), as described in \autoref{chap:DIA}.
 
 % ================================================================
 % Tracer Advection
 % ================================================================
-\section{Tracer advection (\protect\mdl{traadv})}
+\section[Tracer advection (\textit{traadv.F90})]
+{Tracer advection (\protect\mdl{traadv})}
 \label{sec:TRA_adv}
 %------------------------------------------namtra_adv-----------------------------------------------------
@@ -81,5 +82,5 @@
 Indeed, it is obtained by using the following equality: $\nabla \cdot (\vect U \, T) = \vect U \cdot \nabla T$ which
 results from the use of the continuity equation, $\partial_t e_3 + e_3 \; \nabla \cdot \vect U = 0$
-(which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie \np{ln\_linssh}~\forcode{= .true.}).
+(which reduces to $\nabla \cdot \vect U = 0$ in linear free surface, \ie \np{ln\_linssh}\forcode{ = .true.}).
 Therefore it is of paramount importance to design the discrete analogue of the advection tendency so that
 it is consistent with the continuity equation in order to enforce the conservation properties of
@@ -119,5 +120,5 @@
 \begin{description}
 \item[linear free surface:]
-  (\np{ln\_linssh}~\forcode{= .true.})
+  (\np{ln\_linssh}\forcode{ = .true.})
   the first level thickness is constant in time:
   the vertical boundary condition is applied at the fixed surface $z = 0$ rather than on
@@ -127,5 +128,5 @@
   the first level tracer value.
 \item[non-linear free surface:]
-  (\np{ln\_linssh}~\forcode{= .false.})
+  (\np{ln\_linssh}\forcode{ = .false.})
   convergence/divergence in the first ocean level moves the free surface up/down.
   There is no tracer advection through it so that the advective fluxes through the surface are also zero.
@@ -183,10 +184,11 @@
 %        2nd and 4th order centred schemes
 % -------------------------------------------------------------------------------------------------------------
-\subsection{CEN: Centred scheme (\protect\np{ln\_traadv\_cen}~\forcode{= .true.})}
+\subsection[CEN: Centred scheme (\forcode{ln_traadv_cen = .true.})]
+{CEN: Centred scheme (\protect\np{ln\_traadv\_cen}\forcode{ = .true.})}
 \label{subsec:TRA_adv_cen}
 
 %        2nd order centred scheme  
 
-The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen}~\forcode{= .true.}.
+The centred advection scheme (CEN) is used when \np{ln\_traadv\_cen}\forcode{ = .true.}.
 Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by
 setting \np{nn\_cen\_h} and \np{nn\_cen\_v} to $2$ or $4$.
@@ -220,5 +222,5 @@
   \tau_u^{cen4} = \overline{T - \frac{1}{6} \, \delta_i \Big[ \delta_{i + 1/2}[T] \, \Big]}^{\,i + 1/2}
 \end{equation}
-In the vertical direction (\np{nn\_cen\_v}~\forcode{= 4}),
+In the vertical direction (\np{nn\_cen\_v}\forcode{ = 4}),
 a $4^{th}$ COMPACT interpolation has been prefered \citep{demange_phd14}.
 In the COMPACT scheme, both the field and its derivative are interpolated, which leads, after a matrix inversion,
@@ -250,8 +252,9 @@
 %        FCT scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection{FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}~\forcode{= .true.})}
+\subsection[FCT: Flux Corrected Transport scheme (\forcode{ln_traadv_fct = .true.})]
+{FCT: Flux Corrected Transport scheme (\protect\np{ln\_traadv\_fct}\forcode{ = .true.})}
 \label{subsec:TRA_adv_tvd}
 
-The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct}~\forcode{= .true.}.
+The Flux Corrected Transport schemes (FCT) is used when \np{ln\_traadv\_fct}\forcode{ = .true.}.
 Its order ($2^{nd}$ or $4^{th}$) can be chosen independently on horizontal (iso-level) and vertical direction by
 setting \np{nn\_fct\_h} and \np{nn\_fct\_v} to $2$ or $4$.
@@ -300,8 +303,9 @@
 %        MUSCL scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}~\forcode{= .true.})}
+\subsection[MUSCL: Monotone Upstream Scheme for Conservative Laws (\forcode{ln_traadv_mus = .true.})]
+{MUSCL: Monotone Upstream Scheme for Conservative Laws (\protect\np{ln\_traadv\_mus}\forcode{ = .true.})}
 \label{subsec:TRA_adv_mus}
 
-The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus}~\forcode{= .true.}.
+The Monotone Upstream Scheme for Conservative Laws (MUSCL) is used when \np{ln\_traadv\_mus}\forcode{ = .true.}.
 MUSCL implementation can be found in the \mdl{traadv\_mus} module.
 
@@ -331,13 +335,14 @@
 This choice ensure the \textit{positive} character of the scheme.
 In addition, fluxes round a grid-point where a runoff is applied can optionally be computed using upstream fluxes
-(\np{ln\_mus\_ups}~\forcode{= .true.}).
+(\np{ln\_mus\_ups}\forcode{ = .true.}).
 
 % -------------------------------------------------------------------------------------------------------------
 %        UBS scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}~\forcode{= .true.})}
+\subsection[UBS a.k.a. UP3: Upstream-Biased Scheme (\forcode{ln_traadv_ubs = .true.})]
+{UBS a.k.a. UP3: Upstream-Biased Scheme (\protect\np{ln\_traadv\_ubs}\forcode{ = .true.})}
 \label{subsec:TRA_adv_ubs}
 
-The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs}~\forcode{= .true.}.
+The Upstream-Biased Scheme (UBS) is used when \np{ln\_traadv\_ubs}\forcode{ = .true.}.
 UBS implementation can be found in the \mdl{traadv\_mus} module.
 
@@ -369,5 +374,5 @@
 \citep{shchepetkin.mcwilliams_OM05, demange_phd14}.
 Therefore the vertical flux is evaluated using either a $2^nd$ order FCT scheme or a $4^th$ order COMPACT scheme
-(\np{nn\_cen\_v}~\forcode{= 2 or 4}).
+(\np{nn\_cen\_v}\forcode{ = 2 or 4}).
 
 For stability reasons (see \autoref{chap:STP}), the first term  in \autoref{eq:tra_adv_ubs}
@@ -408,9 +413,10 @@
 %        QCK scheme  
 % -------------------------------------------------------------------------------------------------------------
-\subsection{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}~\forcode{= .true.})}
+\subsection[QCK: QuiCKest scheme (\forcode{ln_traadv_qck = .true.})]
+{QCK: QuiCKest scheme (\protect\np{ln\_traadv\_qck}\forcode{ = .true.})}
 \label{subsec:TRA_adv_qck}
 
 The Quadratic Upstream Interpolation for Convective Kinematics with Estimated Streaming Terms (QUICKEST) scheme
-proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck}~\forcode{= .true.}.
+proposed by \citet{leonard_CMAME79} is used when \np{ln\_traadv\_qck}\forcode{ = .true.}.
 QUICKEST implementation can be found in the \mdl{traadv\_qck} module.
 
@@ -431,5 +437,6 @@
 % Tracer Lateral Diffusion
 % ================================================================
-\section{Tracer lateral diffusion (\protect\mdl{traldf})}
+\section[Tracer lateral diffusion (\textit{traldf.F90})]
+{Tracer lateral diffusion (\protect\mdl{traldf})}
 \label{sec:TRA_ldf}
 %-----------------------------------------nam_traldf------------------------------------------------------
@@ -453,5 +460,5 @@
 except for the pure vertical component that appears when a rotation tensor is used.
 This latter component is solved implicitly together with the vertical diffusion term (see \autoref{chap:STP}).
-When \np{ln\_traldf\_msc}~\forcode{= .true.}, a Method of Stabilizing Correction is used in which
+When \np{ln\_traldf\_msc}\forcode{ = .true.}, a Method of Stabilizing Correction is used in which
 the pure vertical component is split into an explicit and an implicit part \citep{lemarie.debreu.ea_OM12}.
 
@@ -459,5 +466,6 @@
 %        Type of operator
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Type of operator (\protect\np{ln\_traldf}\{\_NONE,\_lap,\_blp\}\})]{Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 
+\subsection[Type of operator (\texttt{ln\_traldf}\{\texttt{\_NONE,\_lap,\_blp}\})]
+{Type of operator (\protect\np{ln\_traldf\_NONE}, \protect\np{ln\_traldf\_lap}, or \protect\np{ln\_traldf\_blp}) } 
 \label{subsec:TRA_ldf_op}
 
@@ -465,13 +473,13 @@
 
 \begin{description}
-\item[\np{ln\_traldf\_NONE}~\forcode{= .true.}:]
+\item[\np{ln\_traldf\_NONE}\forcode{ = .true.}:]
   no operator selected, the lateral diffusive tendency will not be applied to the tracer equation.
   This option can be used when the selected advection scheme is diffusive enough (MUSCL scheme for example).
-\item[\np{ln\_traldf\_lap}~\forcode{= .true.}:]
+\item[\np{ln\_traldf\_lap}\forcode{ = .true.}:]
   a laplacian operator is selected.
   This harmonic operator takes the following expression:  $\mathpzc{L}(T) = \nabla \cdot A_{ht} \; \nabla T $,
   where the gradient operates along the selected direction (see \autoref{subsec:TRA_ldf_dir}),
   and $A_{ht}$ is the eddy diffusivity coefficient expressed in $m^2/s$ (see \autoref{chap:LDF}).
-\item[\np{ln\_traldf\_blp}~\forcode{= .true.}]:
+\item[\np{ln\_traldf\_blp}\forcode{ = .true.}]:
   a bilaplacian operator is selected.
   This biharmonic operator takes the following expression:
@@ -493,10 +501,11 @@
 %        Direction of action
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Action direction (\protect\np{ln\_traldf}\{\_lev,\_hor,\_iso,\_triad\})]{Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad}) } 
+\subsection[Action direction (\texttt{ln\_traldf}\{\texttt{\_lev,\_hor,\_iso,\_triad}\})]
+{Direction of action (\protect\np{ln\_traldf\_lev}, \protect\np{ln\_traldf\_hor}, \protect\np{ln\_traldf\_iso}, or \protect\np{ln\_traldf\_triad}) } 
 \label{subsec:TRA_ldf_dir}
 
 The choice of a direction of action determines the form of operator used.
 The operator is a simple (re-entrant) laplacian acting in the (\textbf{i},\textbf{j}) plane when
-iso-level option is used (\np{ln\_traldf\_lev}~\forcode{= .true.}) or
+iso-level option is used (\np{ln\_traldf\_lev}\forcode{ = .true.}) or
 when a horizontal (\ie geopotential) operator is demanded in \textit{z}-coordinate
 (\np{ln\_traldf\_hor} and \np{ln\_zco} equal \forcode{.true.}).
@@ -519,5 +528,6 @@
 %       iso-level operator
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Iso-level (bi -)laplacian operator ( \protect\np{ln\_traldf\_iso}) }
+\subsection[Iso-level (bi-)laplacian operator (\texttt{ln\_traldf\_iso})]
+{Iso-level (bi-)laplacian operator ( \protect\np{ln\_traldf\_iso})}
 \label{subsec:TRA_ldf_lev}
 
@@ -537,10 +547,10 @@
 It is a \textit{horizontal} operator (\ie acting along geopotential surfaces) in
 the $z$-coordinate with or without partial steps, but is simply an iso-level operator in the $s$-coordinate.
-It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}~\forcode{= .true.},
-we have \np{ln\_traldf\_lev}~\forcode{= .true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}~\forcode{= .true.}.
+It is thus used when, in addition to \np{ln\_traldf\_lap} or \np{ln\_traldf\_blp}\forcode{ = .true.},
+we have \np{ln\_traldf\_lev}\forcode{ = .true.} or \np{ln\_traldf\_hor}~=~\np{ln\_zco}\forcode{ = .true.}.
 In both cases, it significantly contributes to diapycnal mixing.
 It is therefore never recommended, even when using it in the bilaplacian case.
 
-Note that in the partial step $z$-coordinate (\np{ln\_zps}~\forcode{= .true.}),
+Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{ = .true.}),
 tracers in horizontally adjacent cells are located at different depths in the vicinity of the bottom.
 In this case, horizontal derivatives in (\autoref{eq:tra_ldf_lap}) at the bottom level require a specific treatment.
@@ -550,10 +560,11 @@
 %         Rotated laplacian operator
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Standard and triad (bi -)laplacian operator}
+\subsection{Standard and triad (bi-)laplacian operator}
 \label{subsec:TRA_ldf_iso_triad}
 
-%&&    Standard rotated (bi -)laplacian operator
+%&&    Standard rotated (bi-)laplacian operator
 %&& ----------------------------------------------
-\subsubsection{Standard rotated (bi -)laplacian operator (\protect\mdl{traldf\_iso})}
+\subsubsection[Standard rotated (bi-)laplacian operator (\textit{traldf\_iso.F90})]
+{Standard rotated (bi-)laplacian operator (\protect\mdl{traldf\_iso})}
 \label{subsec:TRA_ldf_iso}
 The general form of the second order lateral tracer subgrid scale physics (\autoref{eq:PE_zdf})
@@ -574,7 +585,7 @@
 $r_1$ and $r_2$ are the slopes between the surface of computation ($z$- or $s$-surfaces) and
 the surface along which the diffusion operator acts (\ie horizontal or iso-neutral surfaces).
-It is thus used when, in addition to \np{ln\_traldf\_lap}~\forcode{= .true.},
-we have \np{ln\_traldf\_iso}~\forcode{= .true.},
-or both \np{ln\_traldf\_hor}~\forcode{= .true.} and \np{ln\_zco}~\forcode{= .true.}.
+It is thus used when, in addition to \np{ln\_traldf\_lap}\forcode{ = .true.},
+we have \np{ln\_traldf\_iso}\forcode{ = .true.},
+or both \np{ln\_traldf\_hor}\forcode{ = .true.} and \np{ln\_zco}\forcode{ = .true.}.
 The way these slopes are evaluated is given in \autoref{sec:LDF_slp}.
 At the surface, bottom and lateral boundaries, the turbulent fluxes of heat and salt are set to zero using
@@ -592,17 +603,18 @@
 any additional background horizontal diffusion \citep{guilyardi.madec.ea_CD01}.
 
-Note that in the partial step $z$-coordinate (\np{ln\_zps}~\forcode{= .true.}),
+Note that in the partial step $z$-coordinate (\np{ln\_zps}\forcode{ = .true.}),
 the horizontal derivatives at the bottom level in \autoref{eq:tra_ldf_iso} require a specific treatment.
 They are calculated in module zpshde, described in \autoref{sec:TRA_zpshde}.
 
-%&&     Triad rotated (bi -)laplacian operator
+%&&     Triad rotated (bi-)laplacian operator
 %&&  -------------------------------------------
-\subsubsection{Triad rotated (bi -)laplacian operator (\protect\np{ln\_traldf\_triad})}
+\subsubsection[Triad rotated (bi-)laplacian operator (\textit{ln\_traldf\_triad})]
+{Triad rotated (bi-)laplacian operator (\protect\np{ln\_traldf\_triad})}
 \label{subsec:TRA_ldf_triad}
 
-If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}~\forcode{= .true.}; see \autoref{apdx:triad})
+If the Griffies triad scheme is employed (\np{ln\_traldf\_triad}\forcode{ = .true.}; see \autoref{apdx:triad})
 
 An alternative scheme developed by \cite{griffies.gnanadesikan.ea_JPO98} which ensures tracer variance decreases
-is also available in \NEMO (\np{ln\_traldf\_grif}~\forcode{= .true.}).
+is also available in \NEMO (\np{ln\_traldf\_grif}\forcode{ = .true.}).
 A complete description of the algorithm is given in \autoref{apdx:triad}.
 
@@ -632,5 +644,6 @@
 % Tracer Vertical Diffusion
 % ================================================================
-\section{Tracer vertical diffusion (\protect\mdl{trazdf})}
+\section[Tracer vertical diffusion (\textit{trazdf.F90})]
+{Tracer vertical diffusion (\protect\mdl{trazdf})}
 \label{sec:TRA_zdf}
 %--------------------------------------------namzdf---------------------------------------------------------
@@ -663,9 +676,9 @@
 
 The large eddy coefficient found in the mixed layer together with high vertical resolution implies that
-in the case of explicit time stepping (\np{ln\_zdfexp}~\forcode{= .true.})
+in the case of explicit time stepping (\np{ln\_zdfexp}\forcode{ = .true.})
 there would be too restrictive a constraint on the time step.
 Therefore, the default implicit time stepping is preferred for the vertical diffusion since
 it overcomes the stability constraint.
-A forward time differencing scheme (\np{ln\_zdfexp}~\forcode{= .true.}) using
+A forward time differencing scheme (\np{ln\_zdfexp}\forcode{ = .true.}) using
 a time splitting technique (\np{nn\_zdfexp} $> 1$) is provided as an alternative.
 Namelist variables \np{ln\_zdfexp} and \np{nn\_zdfexp} apply to both tracers and dynamics.
@@ -680,5 +693,6 @@
 %        surface boundary condition
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Surface boundary condition (\protect\mdl{trasbc})}
+\subsection[Surface boundary condition (\textit{trasbc.F90})]
+{Surface boundary condition (\protect\mdl{trasbc})}
 \label{subsec:TRA_sbc}
 
@@ -730,5 +744,5 @@
 Such time averaging prevents the divergence of odd and even time step (see \autoref{chap:STP}).
 
-In the linear free surface case (\np{ln\_linssh}~\forcode{= .true.}), an additional term has to be added on
+In the linear free surface case (\np{ln\_linssh}\forcode{ = .true.}), an additional term has to be added on
 both temperature and salinity.
 On temperature, this term remove the heat content associated with mass exchange that has been added to $Q_{ns}$.
@@ -753,5 +767,6 @@
 %        Solar Radiation Penetration 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Solar radiation penetration (\protect\mdl{traqsr})}
+\subsection[Solar radiation penetration (\textit{traqsr.F90})]
+{Solar radiation penetration (\protect\mdl{traqsr})}
 \label{subsec:TRA_qsr}
 %--------------------------------------------namqsr--------------------------------------------------------
@@ -761,7 +776,7 @@
 
 Options are defined through the \ngn{namtra\_qsr} namelist variables.
-When the penetrative solar radiation option is used (\np{ln\_flxqsr}~\forcode{= .true.}),
+When the penetrative solar radiation option is used (\np{ln\_flxqsr}\forcode{ = .true.}),
 the solar radiation penetrates the top few tens of meters of the ocean.
-If it is not used (\np{ln\_flxqsr}~\forcode{= .false.}) all the heat flux is absorbed in the first ocean level.
+If it is not used (\np{ln\_flxqsr}\forcode{ = .false.}) all the heat flux is absorbed in the first ocean level.
 Thus, in the former case a term is added to the time evolution equation of temperature \autoref{eq:PE_tra_T} and
 the surface boundary condition is modified to take into account only the non-penetrative part of the surface 
@@ -792,5 +807,5 @@
 larger depths where it contributes to local heating.
 The way this second part of the solar energy penetrates into the ocean depends on which formulation is chosen.
-In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd}~\forcode{= .true.})
+In the simple 2-waveband light penetration scheme (\np{ln\_qsr\_2bd}\forcode{ = .true.})
 a chlorophyll-independent monochromatic formulation is chosen for the shorter wavelengths,
 leading to the following expression \citep{paulson.simpson_JPO77}:
@@ -820,5 +835,5 @@
 The 2-bands formulation does not reproduce the full model very well.
 
-The RGB formulation is used when \np{ln\_qsr\_rgb}~\forcode{= .true.}.
+The RGB formulation is used when \np{ln\_qsr\_rgb}\forcode{ = .true.}.
 The RGB attenuation coefficients (\ie the inverses of the extinction length scales) are tabulated over
 61 nonuniform chlorophyll classes ranging from 0.01 to 10 g.Chl/L
@@ -827,13 +842,13 @@
 
 \begin{description}
-\item[\np{nn\_chdta}~\forcode{= 0}]
+\item[\np{nn\_chdta}\forcode{ = 0}]
   a constant 0.05 g.Chl/L value everywhere ; 
-\item[\np{nn\_chdta}~\forcode{= 1}]
+\item[\np{nn\_chdta}\forcode{ = 1}]
   an observed time varying chlorophyll deduced from satellite surface ocean color measurement spread uniformly in
   the vertical direction;
-\item[\np{nn\_chdta}~\forcode{= 2}]
+\item[\np{nn\_chdta}\forcode{ = 2}]
   same as previous case except that a vertical profile of chlorophyl is used.
   Following \cite{morel.berthon_LO89}, the profile is computed from the local surface chlorophyll value;
-\item[\np{ln\_qsr\_bio}~\forcode{= .true.}]
+\item[\np{ln\_qsr\_bio}\forcode{ = .true.}]
   simulated time varying chlorophyll by TOP biogeochemical model.
   In this case, the RGB formulation is used to calculate both the phytoplankton light limitation in
@@ -874,5 +889,6 @@
 %        Bottom Boundary Condition
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Bottom boundary condition (\protect\mdl{trabbc})}
+\subsection[Bottom boundary condition (\textit{trabbc.F90})]
+{Bottom boundary condition (\protect\mdl{trabbc})}
 \label{subsec:TRA_bbc}
 %--------------------------------------------nambbc--------------------------------------------------------
@@ -912,5 +928,6 @@
 % Bottom Boundary Layer
 % ================================================================
-\section{Bottom boundary layer (\protect\mdl{trabbl} - \protect\key{trabbl})}
+\section[Bottom boundary layer (\textit{trabbl.F90} - \texttt{\textbf{key\_trabbl}})]
+{Bottom boundary layer (\protect\mdl{trabbl} - \protect\key{trabbl})}
 \label{sec:TRA_bbl}
 %--------------------------------------------nambbl---------------------------------------------------------
@@ -944,5 +961,6 @@
 %        Diffusive BBL
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}~\forcode{= 1})}
+\subsection[Diffusive bottom boundary layer (\forcode{nn_bbl_ldf = 1})]
+{Diffusive bottom boundary layer (\protect\np{nn\_bbl\_ldf}\forcode{ = 1})}
 \label{subsec:TRA_bbl_diff}
 
@@ -983,5 +1001,6 @@
 %        Advective BBL
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Advective bottom boundary layer  (\protect\np{nn\_bbl\_adv}~\forcode{= 1..2})}
+\subsection[Advective bottom boundary layer (\forcode{nn_bbl_adv = [12]})]
+{Advective bottom boundary layer (\protect\np{nn\_bbl\_adv}\forcode{ = [12]})}
 \label{subsec:TRA_bbl_adv}
 
@@ -1014,9 +1033,9 @@
 %%%gmcomment   :  this section has to be really written
 
-When applying an advective BBL (\np{nn\_bbl\_adv}~\forcode{= 1..2}), an overturning circulation is added which
+When applying an advective BBL (\np{nn\_bbl\_adv}\forcode{ = 1..2}), an overturning circulation is added which
 connects two adjacent bottom grid-points only if dense water overlies less dense water on the slope.
 The density difference causes dense water to move down the slope.
 
-\np{nn\_bbl\_adv}~\forcode{= 1}:
+\np{nn\_bbl\_adv}\forcode{ = 1}:
 the downslope velocity is chosen to be the Eulerian ocean velocity just above the topographic step
 (see black arrow in \autoref{fig:bbl}) \citep{beckmann.doscher_JPO97}.
@@ -1025,5 +1044,5 @@
 if the velocity is directed towards greater depth (\ie $\vect U \cdot \nabla H > 0$).
 
-\np{nn\_bbl\_adv}~\forcode{= 2}:
+\np{nn\_bbl\_adv}\forcode{ = 2}:
 the downslope velocity is chosen to be proportional to $\Delta \rho$,
 the density difference between the higher cell and lower cell densities \citep{campin.goosse_T99}.
@@ -1074,5 +1093,6 @@
 % Tracer damping
 % ================================================================
-\section{Tracer damping (\protect\mdl{tradmp})}
+\section[Tracer damping (\textit{tradmp.F90})]
+{Tracer damping (\protect\mdl{tradmp})}
 \label{sec:TRA_dmp}
 %--------------------------------------------namtra_dmp-------------------------------------------------
@@ -1129,5 +1149,6 @@
 % Tracer time evolution
 % ================================================================
-\section{Tracer time evolution (\protect\mdl{tranxt})}
+\section[Tracer time evolution (\textit{tranxt.F90})]
+{Tracer time evolution (\protect\mdl{tranxt})}
 \label{sec:TRA_nxt}
 %--------------------------------------------namdom-----------------------------------------------------
@@ -1151,7 +1172,7 @@
 (\ie fluxes plus content in mass exchanges).
 $\gamma$ is initialized as \np{rn\_atfp} (\textbf{namelist} parameter).
-Its default value is \np{rn\_atfp}~\forcode{= 10.e-3}.
+Its default value is \np{rn\_atfp}\forcode{ = 10.e-3}.
 Note that the forcing correction term in the filter is not applied in linear free surface
-(\jp{lk\_vvl}~\forcode{= .false.}) (see \autoref{subsec:TRA_sbc}).
+(\jp{lk\_vvl}\forcode{ = .false.}) (see \autoref{subsec:TRA_sbc}).
 Not also that in constant volume case, the time stepping is performed on $T$, not on its content, $e_{3t}T$.
 
@@ -1166,5 +1187,6 @@
 % Equation of State (eosbn2) 
 % ================================================================
-\section{Equation of state (\protect\mdl{eosbn2}) }
+\section[Equation of state (\textit{eosbn2.F90})]
+{Equation of state (\protect\mdl{eosbn2})}
 \label{sec:TRA_eosbn2}
 %--------------------------------------------nameos-----------------------------------------------------
@@ -1176,5 +1198,6 @@
 %        Equation of State
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Equation of seawater (\protect\np{nn\_eos}~\forcode{= -1..1})}
+\subsection[Equation of seawater (\forcode{nn_eos = {-1,1}})]
+{Equation of seawater (\protect\np{nn\_eos}\forcode{ = {-1,1}})}
 \label{subsec:TRA_eos}
 
@@ -1210,5 +1233,5 @@
 
 \begin{description}
-\item[\np{nn\_eos}~\forcode{= -1}]
+\item[\np{nn\_eos}\forcode{ = -1}]
   the polyTEOS10-bsq equation of seawater \citep{roquet.madec.ea_OM15} is used.
   The accuracy of this approximation is comparable to the TEOS-10 rational function approximation,
@@ -1229,5 +1252,5 @@
   either computing the air-sea and ice-sea fluxes (forced mode) or
   sending the SST field to the atmosphere (coupled mode).
-\item[\np{nn\_eos}~\forcode{= 0}]
+\item[\np{nn\_eos}\forcode{ = 0}]
   the polyEOS80-bsq equation of seawater is used.
   It takes the same polynomial form as the polyTEOS10, but the coefficients have been optimized to
@@ -1241,5 +1264,5 @@
   Nevertheless, a severe assumption is made in order to have a heat content ($C_p T_p$) which
   is conserved by the model: $C_p$ is set to a constant value, the TEOS10 value.
-\item[\np{nn\_eos}~\forcode{= 1}]
+\item[\np{nn\_eos}\forcode{ = 1}]
   a simplified EOS (S-EOS) inspired by \citet{vallis_bk06} is chosen,
   the coefficients of which has been optimized to fit the behavior of TEOS10
@@ -1303,5 +1326,6 @@
 %        Brunt-V\"{a}is\"{a}l\"{a} Frequency
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}~\forcode{= 0..2})}
+\subsection[Brunt-V\"{a}is\"{a}l\"{a} frequency (\forcode{nn_eos = [0-2]})]
+{Brunt-V\"{a}is\"{a}l\"{a} frequency (\protect\np{nn\_eos}\forcode{ = [0-2]})}
 \label{subsec:TRA_bn2}
 
@@ -1357,5 +1381,6 @@
 % Horizontal Derivative in zps-coordinate 
 % ================================================================
-\section{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})}
+\section[Horizontal derivative in \textit{zps}-coordinate (\textit{zpshde.F90})]
+{Horizontal derivative in \textit{zps}-coordinate (\protect\mdl{zpshde})}
 \label{sec:TRA_zpshde}
 
@@ -1363,9 +1388,9 @@
 I've changed "derivative" to "difference" and "mean" to "average"}
 
-With partial cells (\np{ln\_zps}~\forcode{= .true.}) at bottom and top (\np{ln\_isfcav}~\forcode{= .true.}),
+With partial cells (\np{ln\_zps}\forcode{ = .true.}) at bottom and top (\np{ln\_isfcav}\forcode{ = .true.}),
 in general, tracers in horizontally adjacent cells live at different depths.
 Horizontal gradients of tracers are needed for horizontal diffusion (\mdl{traldf} module) and
 the hydrostatic pressure gradient calculations (\mdl{dynhpg} module).
-The partial cell properties at the top (\np{ln\_isfcav}~\forcode{= .true.}) are computed in the same way as
+The partial cell properties at the top (\np{ln\_isfcav}\forcode{ = .true.}) are computed in the same way as
 for the bottom.
 So, only the bottom interpolation is explained below.
@@ -1383,5 +1408,5 @@
       \protect\label{fig:Partial_step_scheme}
       Discretisation of the horizontal difference and average of tracers in the $z$-partial step coordinate
-      (\protect\np{ln\_zps}~\forcode{= .true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$.
+      (\protect\np{ln\_zps}\forcode{ = .true.}) in the case $(e3w_k^{i + 1} - e3w_k^i) > 0$.
       A linear interpolation is used to estimate $\widetilde T_k^{i + 1}$,
       the tracer value at the depth of the shallower tracer point of the two adjacent bottom $T$-points.
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_ZDF.tex	(revision 11179)
@@ -46,5 +46,6 @@
 %        Constant 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Constant (\protect\key{zdfcst})}
+\subsection[Constant (\texttt{\textbf{key\_zdfcst}})]
+{Constant (\protect\key{zdfcst})}
 \label{subsec:ZDF_cst}
 %--------------------------------------------namzdf---------------------------------------------------------
@@ -72,5 +73,6 @@
 %        Richardson Number Dependent
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Richardson number dependent (\protect\key{zdfric})}
+\subsection[Richardson number dependent (\texttt{\textbf{key\_zdfric}})]
+{Richardson number dependent (\protect\key{zdfric})}
 \label{subsec:ZDF_ric}
 
@@ -129,5 +131,6 @@
 %        TKE Turbulent Closure Scheme 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{TKE turbulent closure scheme (\protect\key{zdftke})}
+\subsection[TKE turbulent closure scheme (\texttt{\textbf{key\_zdftke}})]
+{TKE turbulent closure scheme (\protect\key{zdftke})}
 \label{subsec:ZDF_tke}
 
@@ -408,5 +411,6 @@
 %        TKE discretization considerations
 % -------------------------------------------------------------------------------------------------------------
-\subsection{TKE discretization considerations (\protect\key{zdftke})}
+\subsection[TKE discretization considerations (\texttt{\textbf{key\_zdftke}})]
+{TKE discretization considerations (\protect\key{zdftke})}
 \label{subsec:ZDF_tke_ene}
 
@@ -514,5 +518,6 @@
 %        GLS Generic Length Scale Scheme 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{GLS: Generic Length Scale (\protect\key{zdfgls})}
+\subsection[GLS: Generic Length Scale (\texttt{\textbf{key\_zdfgls}})]
+{GLS: Generic Length Scale (\protect\key{zdfgls})}
 \label{subsec:ZDF_gls}
 
@@ -633,5 +638,6 @@
 %        OSM OSMOSIS BL Scheme 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{OSM: OSMOSIS boundary layer scheme (\protect\key{zdfosm})}
+\subsection[OSM: OSMosis boundary layer scheme (\texttt{\textbf{key\_zdfosm}})]
+{OSM: OSMosis boundary layer scheme (\protect\key{zdfosm})}
 \label{subsec:ZDF_osm}
 
@@ -664,6 +670,6 @@
 %       Non-Penetrative Convective Adjustment 
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Non-penetrative convective adjmt (\protect\np{ln\_tranpc}\forcode{ = .true.})]
-				{Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{ = .true.})}
+\subsection[Non-penetrative convective adjustment (\forcode{ln_tranpc = .true.})]
+{Non-penetrative convective adjustment (\protect\np{ln\_tranpc}\forcode{ = .true.})}
 \label{subsec:ZDF_npc}
 
@@ -736,5 +742,6 @@
 %       Enhanced Vertical Diffusion 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{ = .true.})}
+\subsection[Enhanced vertical diffusion (\forcode{ln_zdfevd = .true.})]
+{Enhanced vertical diffusion (\protect\np{ln\_zdfevd}\forcode{ = .true.})}
 \label{subsec:ZDF_evd}
 
@@ -769,5 +776,6 @@
 %       Turbulent Closure Scheme 
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Turbulent closure scheme (\protect\key{zdf}\{tke,gls,osm\})]{Turbulent Closure Scheme (\protect\key{zdftke}, \protect\key{zdfgls} or \protect\key{zdfosm})}
+\subsection[Turbulent closure scheme (\texttt{\textbf{key\_zdf}}\texttt{\textbf{\{tke,gls,osm\}}})]
+{Turbulent Closure Scheme (\protect\key{zdftke}, \protect\key{zdfgls} or \protect\key{zdfosm})}
 \label{subsec:ZDF_tcs}
 
@@ -795,5 +803,6 @@
 % Double Diffusion Mixing
 % ================================================================
-\section{Double diffusion mixing (\protect\key{zdfddm})}
+\section[Double diffusion mixing (\texttt{\textbf{key\_zdfddm}})]
+{Double diffusion mixing (\protect\key{zdfddm})}
 \label{sec:ZDF_ddm}
 
@@ -887,5 +896,6 @@
 % Bottom Friction
 % ================================================================
-\section{Bottom and top friction (\protect\mdl{zdfbfr})}
+\section[Bottom and top friction (\textit{zdfbfr.F90})]
+{Bottom and top friction (\protect\mdl{zdfbfr})}
 \label{sec:ZDF_bfr}
 
@@ -951,5 +961,6 @@
 %       Linear Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 0..1})}
+\subsection[Linear bottom friction (\forcode{nn_botfr = [01]})]
+{Linear bottom friction (\protect\np{nn\_botfr}\forcode{ = [01])}}
 \label{subsec:ZDF_bfr_linear}
 
@@ -993,5 +1004,6 @@
 %       Non-Linear Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Non-linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 2})}
+\subsection[Non-linear bottom friction (\forcode{nn_botfr = 2})]
+{Non-linear bottom friction (\protect\np{nn\_botfr}\forcode{ = 2})}
 \label{subsec:ZDF_bfr_nonlinear}
 
@@ -1032,6 +1044,6 @@
 %       Bottom Friction Log-layer
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Log-layer btm frict enhncmnt (\protect\np{nn\_botfr}\forcode{ = 2}, \protect\np{ln\_loglayer}\forcode{ = .true.})]
-				{Log-layer bottom friction enhancement (\protect\np{nn\_botfr}\forcode{ = 2}, \protect\np{ln\_loglayer}\forcode{ = .true.})}
+\subsection[Log-layer bottom friction enhancement (\forcode{nn_botfr = 2}, \forcode{ln_loglayer = .true.})]
+{Log-layer bottom friction enhancement (\protect\np{nn\_botfr}\forcode{ = 2}, \protect\np{ln\_loglayer}\forcode{ = .true.})}
 \label{subsec:ZDF_bfr_loglayer}
 
@@ -1109,5 +1121,6 @@
 %       Implicit Bottom Friction
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Implicit bottom friction (\protect\np{ln\_bfrimp}\forcode{ = .true.})}
+\subsection[Implicit bottom friction (\forcode{ln_bfrimp = .true.})]
+{Implicit bottom friction (\protect\np{ln\_bfrimp}\forcode{ = .true.})}
 \label{subsec:ZDF_bfr_imp}
 
@@ -1162,6 +1175,6 @@
 %       Bottom Friction with split-explicit time splitting
 % -------------------------------------------------------------------------------------------------------------
-\subsection[Bottom friction w/ split-explicit time splitting (\protect\np{ln\_bfrimp})]
-				{Bottom friction with split-explicit time splitting (\protect\np{ln\_bfrimp})}
+\subsection[Bottom friction with split-explicit time splitting (\texttt{ln\_bfrimp})]
+{Bottom friction with split-explicit time splitting (\protect\np{ln\_bfrimp})}
 \label{subsec:ZDF_bfr_ts}
 
@@ -1218,5 +1231,6 @@
 % Tidal Mixing
 % ================================================================
-\section{Tidal mixing (\protect\key{zdftmx})}
+\section[Tidal mixing (\texttt{\textbf{key\_zdftmx}})]
+{Tidal mixing (\protect\key{zdftmx})}
 \label{sec:ZDF_tmx}
 
@@ -1297,5 +1311,6 @@
 %        Indonesian area specific treatment 
 % -------------------------------------------------------------------------------------------------------------
-\subsection{Indonesian area specific treatment (\protect\np{ln\_zdftmx\_itf})}
+\subsection[Indonesian area specific treatment (\texttt{ln\_zdftmx\_itf})]
+{Indonesian area specific treatment (\protect\np{ln\_zdftmx\_itf})}
 \label{subsec:ZDF_tmx_itf}
 
@@ -1342,5 +1357,6 @@
 % Internal wave-driven mixing
 % ================================================================
-\section{Internal wave-driven mixing (\protect\key{zdftmx\_new})}
+\section[Internal wave-driven mixing (\texttt{\textbf{key\_zdftmx\_new}})]
+{Internal wave-driven mixing (\protect\key{zdftmx\_new})}
 \label{sec:ZDF_tmx_new}
 
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_misc.tex	(revision 11179)
@@ -102,5 +102,6 @@
 % Closed seas
 % ================================================================
-\section{Closed seas (\protect\mdl{closea})}
+\section[Closed seas (\textit{closea.F90})]
+{Closed seas (\protect\mdl{closea})}
 \label{sec:MISC_closea}
 
@@ -236,8 +237,10 @@
 % Accuracy and Reproducibility
 % ================================================================
-\section{Accuracy and reproducibility (\protect\mdl{lib\_fortran})}
+\section[Accuracy and reproducibility (\textit{lib\_fortran.F90})]
+{Accuracy and reproducibility (\protect\mdl{lib\_fortran})}
 \label{sec:MISC_fortran}
 
-\subsection{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})}
+\subsection[Issues with intrinsinc SIGN function (\texttt{\textbf{key\_nosignedzero}})]
+{Issues with intrinsinc SIGN function (\protect\key{nosignedzero})}
 \label{subsec:MISC_sign}
 
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_model_basics_zstar.tex	(revision 11179)
@@ -73,5 +73,6 @@
 % Surface Pressure Gradient and Sea Surface Height
 % ================================================================
-\section{Surface pressure gradient and sea surface heigth (\protect\mdl{dynspg})}
+\section[Surface pressure gradient and sea surface heigth (\textit{dynspg.F90})]
+{Surface pressure gradient and sea surface heigth (\protect\mdl{dynspg})}
 \label{sec:DYN_hpg_spg}
 %-----------------------------------------nam_dynspg----------------------------------------------------
@@ -97,5 +98,6 @@
 % Explicit
 %-------------------------------------------------------------
-\subsubsection{Explicit (\protect\key{dynspg\_exp})}
+\subsubsection[Explicit (\texttt{\textbf{key\_dynspg\_exp}})]
+{Explicit (\protect\key{dynspg\_exp})}
 \label{subsec:DYN_spg_exp}
 
@@ -133,5 +135,6 @@
 % Split-explicit time-stepping
 %-------------------------------------------------------------
-\subsubsection{Split-explicit time-stepping (\protect\key{dynspg\_ts})}
+\subsubsection[Split-explicit time-stepping (\texttt{\textbf{key\_dynspg\_ts}})]
+{Split-explicit time-stepping (\protect\key{dynspg\_ts})}
 \label{subsec:DYN_spg_ts}
 %--------------------------------------------namdom----------------------------------------------------
@@ -291,5 +294,6 @@
 % Filtered formulation 
 %-------------------------------------------------------------
-\subsubsection{Filtered formulation (\protect\key{dynspg\_flt})}
+\subsubsection[Filtered formulation (\texttt{\textbf{key\_dynspg\_flt}})]
+{Filtered formulation (\protect\key{dynspg\_flt})}
 \label{subsec:DYN_spg_flt}
 
@@ -305,5 +309,6 @@
 % Non-linear free surface formulation 
 %-------------------------------------------------------------
-\subsection{Non-linear free surface formulation (\protect\key{vvl})}
+\subsection[Non-linear free surface formulation (\texttt{\textbf{key\_vvl}})]
+{Non-linear free surface formulation (\protect\key{vvl})}
 \label{subsec:DYN_spg_vvl}
 
Index: /NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex
===================================================================
--- /NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex	(revision 11178)
+++ /NEMO/trunk/doc/latex/NEMO/subfiles/chap_time_domain.tex	(revision 11179)
@@ -88,5 +88,5 @@
 where the subscript $F$ denotes filtered values and $\gamma$ is the Asselin coefficient.
 $\gamma$ is initialized as \np{rn\_atfp} (namelist parameter).
-Its default value is \np{rn\_atfp}~\forcode{= 10.e-3} (see \autoref{sec:STP_mLF}),
+Its default value is \np{rn\_atfp}\forcode{ = 10.e-3} (see \autoref{sec:STP_mLF}),
 causing only a weak dissipation of high frequency motions (\citep{farge-coulombier_phd87}).
 The addition of a time filter degrades the accuracy of the calculation from second to first order.
@@ -132,6 +132,6 @@
 but usually the numerical stability condition imposes a strong constraint on the time step.
 Two solutions are available in \NEMO to overcome the stability constraint:
-$(a)$ a forward time differencing scheme using a time splitting technique (\np{ln\_zdfexp}~\forcode{= .true.}) or
-$(b)$ a backward (or implicit) time differencing scheme                   (\np{ln\_zdfexp}~\forcode{= .false.}).
+$(a)$ a forward time differencing scheme using a time splitting technique (\np{ln\_zdfexp}\forcode{ = .true.}) or
+$(b)$ a backward (or implicit) time differencing scheme                   (\np{ln\_zdfexp}\forcode{ = .false.}).
 In $(a)$, the master time step $\Delta$t is cut into $N$ fractional time steps so that
 the stability criterion is reduced by a factor of $N$.
