IMPORTANT: Additional Condolidation and refactoring due to new 2D Kernel

[arango]

This update contains several changes due to the consolidation with the coupling research svn branch.

• The 2D state variables no longer have three-time levels but four-time ones in the FB AB3-AM4 time-stepping algorithm. For example, their declarations are changed from:

        real(r8), intent(inout) :: ubar(LBi:UBi,LBj:UBj,3)
        real(r8), intent(inout) :: vbar(LBi:UBi,LBj:UBj,3)
        real(r8), intent(inout) :: zeta(LBi:UBi,LBj:UBj,3)
  

  to

        real(r8), intent(inout) :: ubar(LBi:UBi,LBj:UBj,:)
        real(r8), intent(inout) :: vbar(LBi:UBi,LBj:UBj,:)
        real(r8), intent(inout) :: zeta(LBi:UBi,LBj:UBj,:)
  

  When the option ASSUMED_SHAPE is not activated.

• The logic for time-dependent changes in bathymetry due to bed_thick was moved to different routines when SEDIMENT and SED_MORPH are activated.