In the previsous commit the physics modifications between cy48t1 and cy48t3
have been introduced in PHYEX but still using the cy48t1 pack.
This commit introduces new modifications (in arome/ext) to use the cy48t3 pack.
Results are different due to modifications introduced betwwen cy48t1 and cy48t3
in parts other than the physics.
So, a new reference is needed (modifications in check_commit_ial.sh, INSTALL_pack_ial.md).

Modifications needed after the cleaning done by Ryad

Quentin 19/07/2022: add turb mesonh KTEST to test online LES diag and netCDF groups + change mesonh/aux/mode_budget to MNH/budget.f90

The budget subroutines have been cleaned
Unused subroutines in the arome directory have been removed
Minor update of the check_commit_* scripts

Documentation updated with the inclusion of the tools
Selection of subdirectories to include during copy of repository in check_commit_* scripts
 - to limit volume
 - to reduce the risk of having a broken symlink (that could happen in the build directory)
Missing quotes in prep_code