Quentin 13/12/2022: bugfix les_mean_subgrid + adapt compare.py script for mesonh KTEST (better for testing LES diag)

+ bugfix in check_commit_mesonh broken during last update

Bug correction in compute_updraft_rhcj: bit-repro of small_3D_alt8 now OK
Tolerance threshold modified in comp_DDH due to reference and/or OS version change
Explanations in check_commit_ial about references to use for special test cases

Update script to run all the cases in case run are stored in a
directory different from the reference directory

add -a and -A options to check_commit_testprogs to choose the architecture
add -mesonhprofile to make_fcm.sh to convert a Méso-NH rules into a fcm configuration file
add architecture files for ifort and a new one for gfortran derived from the Méso-NH rules

bf for guessing IAL version of arome_* commits
check if repository is checked before cloning
use 'git mv'/'git rm' instead of mv/rm
guess PATH in prep_code for filepp, mnh_expand and correct_indent

Add env variables and script options to define the git repository on github

Choice of the IAL version to use is now define by the content of the src/arom/ial_version.json file

Compilation system update with the help from Rolf Heilemann Myhre

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