Also, I corrected a typo in the documentation of each roms.in input script. We needed to have instead:
! or in nested applications
!
! Hadvection == U3 \ ! temperature, Grid 1
! HSIMT \ ! salinity, Grid 1
! U3 \ ! temperature, Grid 2
! HSIMT \ ! salinity, Grid 2
! U3 \ ! temperature, Grid 3
! HSIMT ! salinity, Grid 3
!
! Vadvection == C4 \ ! temperature, Grid 1
! HSIMT \ ! salinity, Grid 1
! C4 \ ! temperature, Grid 2
! HSIMT \ ! salinity, Grid 2
! C4 \ ! temperature, Grid 3
! HSIMT ! salinity, Grid 3
Many thanks to Pierre St-Laurent for reporting this typo in GLOSSARY section.