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).

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

small_3D_alt7: suppression of the RHCJ option
small_3D_alt8: RHCJ case
The RHCJ case cannot be compared to the reference version because
an incompatible changed has been entered during commit 907e9066

small_3D_alt6: RAHA updraft with the bigaussian pdf
small_3D_alt7: RHCJ updraft with the STAT cloud scheme
               and the LOSIGMAS=F option
Two bug corrections in the original version are needed to run
the small_3D_alt7 test case (corrections described in INSTALL_pack_ial

prep_code used in check_commit_mesonh.sh
--expand option to expand array-syntax into do loops
preparation for other test cases inclusion

REPRO48 variable
big_3D case added to ALL case on HPC

Hard coded path are removed
env.sh added to hep update environment variables (in particular PATH)
Update the separator used to build pack directori names