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

@@ -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