fix cross references within the user guide

source/cfgs.rst

@@ -159,7 +159,7 @@ Analytical forcing for heat, freshwater and wind-stress fields are applied.
 
 This configuration acts also as demonstrator of the **user defined setup**
 (``ln_read_cfg = .false.``) and grid setting are handled through
-the ``&namusr_def`` controls in :file:`namelist.cfg, lines 35-41 : <https://forge.nemo-ocean.eu/nemo/nemo/-/tree/4.2.0/cfgs/GYRE_PISCES/EXPREF/namelist_cfg>`_
+the ``&namusr_def`` controls in :coderepo:`namelist.cfg, lines 35-41 : </cfgs/GYRE_PISCES/EXPREF/namelist_cfg>`
 
 
 Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and
@@ -246,7 +246,7 @@ ORCA2_OFF_PISCES
 | This enables for an offline coupling of TOP components.
 
 Pre-calculated dynamical fields are provided to NEMO using
-the namelist ``&namdta_dyn``  in :file:`namelist_cfg <https://forge.nemo-ocean.eu/nemo/nemo/-/blob/4.2.0/cfgs/ORCA2_OFF_PISCES/EXPREF/namelist_cfg>`_,
+the namelist ``&namdta_dyn``  in :coderepo:`namelist_cfg </cfgs/ORCA2_OFF_PISCES/EXPREF/namelist_cfg>`,
 in this case with a 5 days frequency (120 hours):
 
 

source/install.rst

@@ -153,14 +153,12 @@ Description of 1\ :sup:`st` level tree structure
 +---------------+-------------------------------------------------+
 | :file:`cfgs`  | :doc:`Reference configurations <cfgs>`          |
 +---------------+-------------------------------------------------+
-| :file:`doc`   | :doc:`Documentation <doc>`                      |
-+---------------+-------------------------------------------------+
 | :file:`ext`   | Dependencies included                           |
 |               | (``AGRIF``, ``FCM``, ``PPR`` & ``IOIPSL``)      |
 +---------------+-------------------------------------------------+
 | :file:`mk`    | Compilation scripts                             |
 +---------------+-------------------------------------------------+
-| :file:`src`   | :doc:`NEMO codebase <src>`                      |
+| :file:`src`   | NEMO codebase                                   |
 +---------------+-------------------------------------------------+
 | :file:`tests` | :doc:`Test cases <tests>`                       |
 |               | (unsupported)                                   |

source/setup.rst

@@ -148,7 +148,7 @@ There are two options for creating a :file:`domain_cfg.nc` file:
 - Users can adapt and apply the supplied tool available in :file:`./tools/DOMAINcfg`.
   This tool is based on code extracted from NEMO version 3.6 and will allow similar choices for
   the horizontal and vertical grids that were available internally to that version.
-  See :ref:`tools <DOMAINcfg>` for details.
+  See :doc:`DOMAINcfg tool <tools>` for details.
 
 Option 2: Adapt the usr_def configuration module of NEMO for you own purposes
 -----------------------------------------------------------------------------

source/todos.rst

-*********************
-List of editing tasks
-*********************
-
-.. todolist::