Merge branch '83-makenemo-t-option-not-working-with-agrif-based-configurations' into 'branch_4.2'

Resolve "makenemo "-t" option not working with AGRIF based configurations"

Closes #83 (closed)

See merge request !130 (merged)

(cherry picked from commit 655e45c3)

c5ba3101 set correct directory variables for AGRIF