Fix several wrong linkages

A number of changes were done to fix issues arising in the build of the user guide.

Several links were broken or not updated.

A conda environment with the required set of packages was create to help out users.

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
@@ -206,7 +206,7 @@ This configuration uses the three components
 
 - |OCE|, the ocean dynamical core
 - |ICE|, the thermodynamic-dynamic sea ice model.
-- |MBG|, passive tracer transport module and PISCES BGC model :cite:`aumont.ethé.ea_GMD15`
+- |TOP|, passive tracer transport module and PISCES BGC model :cite:`aumont.ethé.ea_GMD15`
 
 All components share the same grid.
 The model is forced with CORE-II normal year atmospheric forcing 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):