start replacing local file references with those of the remote code

source/sette.rst

@@ -322,7 +322,7 @@ Any such solutions should be fed back to the system team for incorporation into
 .. _Component scripts:
 
 Component scripts
-================
+=================
 
 ``SETTE`` consists of a suite of scripts and settings files. A complete list is given here but basic
 use of ``SETTE`` only requires familiarisation with the first two listed:

source/setup.rst

@@ -60,7 +60,7 @@ run a NEMO regional configuration.
 
 Option 4: Use the nesting tools to create embedded zooms or regional configurations from an existing grid
 ---------------------------------------------------------------------------------------------------------
-(see :download:`NESTING README <../../../tools/NESTING/README>`).
+(see :coderepo:`NESTING README </tools/NESTING/README>`).
 
 
 Creating a completely new configuration

source/tests.rst

@@ -2,9 +2,6 @@
 Explore the test cases
 **********************
 
-.. todo::
-
-
 .. contents::
    :local:
    :depth: 1
@@ -173,7 +170,7 @@ Benchmark configuration. Allow to run any configuration (including ORCA type or
 CPL_OASIS
 ---------
 
-This test case checks the OASIS interface in OCE/SBC, allowing to set up  a coupled configuration through OASIS. See ``CPL_OASIS/README.md` for more information.
+This test case checks the OASIS interface in OCE/SBC, allowing to set up  a coupled configuration through OASIS. See `CPL_OASIS/README.md` for more information.
 
 DIA_GPU
 -------

source/tools.rst

@@ -37,18 +37,18 @@ DMP_TOOLS
 
 Used to create a netcdf file called :file:`resto.nc` containing
 restoration coefficients for use with the :file:`tra_dmp` module in NEMO
-(see :download:`DMP_TOOLS README <../../../tools/DMP_TOOLS/README>`).
+(see :coderepo:`DMP_TOOLS README </tools/DMP_TOOLS/README>`).
 
 DOMAINcfg
 ---------
 A toolbox allowing the creation of regional configurations from curvilinear grid
-(see :download:`DOMAINcfg README <../../../tools/DOMAINcfg/README.rst>`).
+(see :coderepo:`DOMAINcfg README </tools/DOMAINcfg/README>`).
 
 GRIDGEN
 -------
 This tool allows the creation of a domain configuration file (``domain_cfg.nc``) containing
 the ocean domain information required to define an ocean configuration from scratch.
-(see :download:`GRIDGEN documentation <../../../tools/GRIDGEN/doc_cfg_tools.pdf>`).
+(see :coderepo:`GRIDGEN documentation </tools/GRIDGEN/doc_cfg_tools.pdf>`).
 
 MISCELLANEOUS
 -------------
@@ -62,8 +62,8 @@ MPP_PREP
 This tool provides the user with information to choose the best domain decomposition.
 The tool computes the number of water processors for all possible decompositions,
 up to a maximum number of processors
-(see :download:`MPP_PREP documentation <../../../tools/MPP_PREP/mpp_nc.pdf>` and
-:download:`MPP_PREP archive <../../../tools/MPP_PREP/mpp_prep-1.0.tar.gz>`).
+(see :coderepo:`MPP_PREP documentation </tools/MPP_PREP/mpp_nc.pdf>` and 
+:coderepo:`MPP_PREP archive </tools/MPP_PREP/mpp_prep-1.0.tar.gz>`).
 
 NESTING
 -------
@@ -72,7 +72,7 @@ AGRIF nesting tool allows for the seamless two-way coupling of nested sub-models
 the NEMO framework as long as these are defined on subsets of the original root grid.
 It allows to create the grid coordinates, the surface forcing and the initial conditions required by
 each sub-model when running a NEMO/AGRIF embedded mode
-(see :download:`NESTING README <../../../tools/NESTING/README>`).
+(see :coderepo:`NESTING README </tools/NESTING/README>`).
 
 OBSTOOLS
 --------
@@ -86,7 +86,7 @@ REBUILD_NEMO
 
 REBUILD_NEMO is a tool to rebuild NEMO output files from multiple processors
 (mesh_mask, restart or XIOS output files) into one file
-(see :download:`REBUILD_NEMO README <../../../tools/REBUILD_NEMO/README.rst>`).
+(see :coderepo:`REBUILD_NEMO README </tools/REBUILD_NEMO/README.rst>`).
 
 REBUILD
 -------
@@ -115,21 +115,21 @@ SIREN
 -----
 
 SIREN is a configuration management tool to set up regional configurations with NEMO
-(see :download:`SIREN README <../../../tools/SIREN/README>`).
+(see :coderepo:`SIREN README </tools/SIREN/README>`).
 
 WEIGHTS
 -------
 
 This directory contains software for generating and manipulating interpolation weights for use with
 the Interpolation On the Fly (IOF) option in NEMO v3 onwards
-(see :download:`WEIGHTS README <../../../tools/WEIGHTS/README>`).
+(see :coderepo:`WEIGHTS README </tools/WEIGHTS/README>`).
 
 TOYATM
 ------
 
 This directory contains a simplified model that send/receive atmospheric fields to/from NEMO, for use in the CPL_OASIS sed to test case of the NEMO-OASIS coupling interface.
 This toy requires OASIS3-MCT to be installed and properly defined in the arch file.
-(see :download:`CPL_OASIS README <../../../tests/CPL_OASIS/README.md>`).
+(see :coderepo:`CPL_OASIS README </tests/CPL_OASIS/README.md>`).
 
 ABL_TOOLS
 ---------

source/tracers.rst

@@ -2,10 +2,6 @@
 Oceanic tracers
 ***************
 
-.. todo::
-
-
-
 .. contents::
    :local:
 
@@ -24,7 +20,7 @@ marine biogeochemical cycles.
 Structure
 =========
 
-TOP interface has the following location in the source code `./src/TOP <https://forge.nemo-ocean.eu/nemo/nemo/-/tree/4.2.0/src/TOP>`_ and
+TOP interface has the following location in the source code :coderepo:`./src/TOP </src/TOP>` and
 the following modules are available:
 
 :file:`TRP`