Index: NEMO/trunk/doc/rst/source/NEMO_guide.rst
===================================================================
--- NEMO/trunk/doc/rst/source/NEMO_guide.rst	(revision 10279)
+++ NEMO/trunk/doc/rst/source/NEMO_guide.rst	(revision 10460)
@@ -41,5 +41,4 @@
 
 	zooms
-	coarsening
 	coupling
 	assimilation
@@ -56,6 +55,6 @@
 .. Next headings markup acording to readme.rst
 
-How to cite NEMO
-================
+Reference publications
+======================
 
 ..	bibliography:: references.bib
Index: NEMO/trunk/doc/rst/source/assimilation.rst
===================================================================
--- NEMO/trunk/doc/rst/source/assimilation.rst	(revision 10279)
+++ 	(revision )
@@ -1,60 +1,0 @@
-**************************************
-Data assimilation (OBS/SAO, ASM & TAM)
-**************************************
-
-.. contents::
-   :local:
-
-The assimilation interface to NEMO is split into three modules.
-- OBS for the observation operator
-- ASM for the application of increments and model bias correction (based on the assimilation increments).
-- TAM the tangent linear and adjoint model.
-
-Please see the `NEMO manual`_ for more details including information about the input file formats and
-the namelist settings.
-
-Observation and model comparison (OBS)
-======================================
-
-The observation and model comparison code (OBS) reads in observation files (profile temperature and salinity,
-sea surface temperature, sea level anomaly, sea ice concentration, and velocity) and
-calculates an interpolated model equivalent value at the observation location and nearest model timestep.
-The resulting data are saved in a feedback file (or files).
-The code was originally developed for use with the NEMOVAR data assimilation code, but
-can be used for validation or verification of model or any other data assimilation system.
-This is all controlled by the namelist.
-To build with the OBS code active ``key_diaobs`` must be set. 
-
-More details in the `NEMO manual`_ chapter 12.
-
-Standalone observation operator (SAO)
--------------------------------------
-
-The OBS code can also be run after a model run using saved NEMO model data.
-This is accomplished using the standalone observation operator (SAO)
-(previously known the offline observation operator).
-
-To build the SAO use makenemo.
-This means compiling NEMO once (in the normal way) for the chosen configuration.
-Then include ``SAO`` at the end of the relevant line in ``cfg.txt`` file.
-Then recompile with the replacement main program in ``./src/SAO``.
-This is a special version of ``nemogcm.F90`` (which doesn't run the model, but reads in the model fields, and
-observations and runs the OBS code.
-See section 12.4 of the `NEMO manual`_.
-
-Apply assimilation increments (ASM)
-===================================
-
-The ASM code adds the functionality to apply increments to the model variables:
-temperature, salinity, sea surface height, velocity and sea ice concentration.
-These are read into the model from a NetCDF file which may be produced by separate data assimilation code.
-The code can also output model background fields which are used as an input to data assimilation code.
-This is all controlled by the namelist nam_asminc.
-To build the ASM code ``key asminc`` must be set.
-
-More details in the `NEMO manual`_ chapter 13.
-
-Tangent linear and adjoint (TAM)
-================================
-
-This is the tangent linear and adjoint code of NEMO which is useful to 4D VAR assimilation.
Index: NEMO/trunk/doc/rst/source/conf.py
===================================================================
--- NEMO/trunk/doc/rst/source/conf.py	(revision 10279)
+++ NEMO/trunk/doc/rst/source/conf.py	(revision 10460)
@@ -63,5 +63,5 @@
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = ['global.rst']
+exclude_patterns = ['global.rst', 'coarsening.rst']
 
 # The name of the Pygments (syntax highlighting) style to use.
Index: NEMO/trunk/doc/rst/source/coupling.rst
===================================================================
--- NEMO/trunk/doc/rst/source/coupling.rst	(revision 10279)
+++ NEMO/trunk/doc/rst/source/coupling.rst	(revision 10460)
@@ -1,5 +1,5 @@
-**********************
-Coupling (OASIS & SAS)
-**********************
+********
+Coupling
+********
 
 NEMO currently exploits OASIS-3-MCT to implement a generalised coupled interface
Index: NEMO/trunk/doc/rst/source/data_assimilation.rst
===================================================================
--- NEMO/trunk/doc/rst/source/data_assimilation.rst	(revision 10460)
+++ NEMO/trunk/doc/rst/source/data_assimilation.rst	(revision 10460)
@@ -0,0 +1,60 @@
+*****************
+Data assimilation
+*****************
+
+.. contents::
+   :local:
+
+The assimilation interface to NEMO is split into three modules.
+- OBS for the observation operator
+- ASM for the application of increments and model bias correction (based on the assimilation increments).
+- TAM the tangent linear and adjoint model.
+
+Please see the `NEMO manual`_ for more details including information about the input file formats and
+the namelist settings.
+
+Observation and model comparison (OBS)
+======================================
+
+The observation and model comparison code (OBS) reads in observation files (profile temperature and salinity,
+sea surface temperature, sea level anomaly, sea ice concentration, and velocity) and
+calculates an interpolated model equivalent value at the observation location and nearest model timestep.
+The resulting data are saved in a feedback file (or files).
+The code was originally developed for use with the NEMOVAR data assimilation code, but
+can be used for validation or verification of model or any other data assimilation system.
+This is all controlled by the namelist.
+To build with the OBS code active ``key_diaobs`` must be set. 
+
+More details in the `NEMO manual`_ chapter 12.
+
+Standalone observation operator (SAO)
+-------------------------------------
+
+The OBS code can also be run after a model run using saved NEMO model data.
+This is accomplished using the standalone observation operator (SAO)
+(previously known the offline observation operator).
+
+To build the SAO use makenemo.
+This means compiling NEMO once (in the normal way) for the chosen configuration.
+Then include ``SAO`` at the end of the relevant line in ``cfg.txt`` file.
+Then recompile with the replacement main program in ``./src/SAO``.
+This is a special version of ``nemogcm.F90`` (which doesn't run the model, but reads in the model fields, and
+observations and runs the OBS code.
+See section 12.4 of the `NEMO manual`_.
+
+Apply assimilation increments (ASM)
+===================================
+
+The ASM code adds the functionality to apply increments to the model variables:
+temperature, salinity, sea surface height, velocity and sea ice concentration.
+These are read into the model from a NetCDF file which may be produced by separate data assimilation code.
+The code can also output model background fields which are used as an input to data assimilation code.
+This is all controlled by the namelist nam_asminc.
+To build the ASM code ``key asminc`` must be set.
+
+More details in the `NEMO manual`_ chapter 13.
+
+Tangent linear and adjoint (TAM)
+================================
+
+This is the tangent linear and adjoint code of NEMO which is useful to 4D VAR assimilation.
Index: NEMO/trunk/doc/rst/source/interfacing_options.rst
===================================================================
--- NEMO/trunk/doc/rst/source/interfacing_options.rst	(revision 10279)
+++ 	(revision )
@@ -1,36 +1,0 @@
-===================
-Interfacing options
-===================
-
-..
-	contents::
-	:local:
-	:depth: 1
-
-.. include:: zooms.rst
-
-.. bibliography:: zooms.bib
-	:all:
-	:style: unsrt
-	:labelprefix: A
-	:keyprefix: a-
-
-----
-
-.. include:: coarsening.rst
-
-----
-
-.. include:: coupling.rst
-
-----
-
-.. include:: assimilation.rst
-
-----
-
-.. include:: input-output.rst
-
-----
-
-.. include:: tracers.rst
