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Updating ecco-branch-mod1 to checkpoint44. Will be tagged ecco-branch-mod2.
Bringing comments up to data and formatting for document extraction.
add variable etaH for non-linear free-surface + Crank-Nickelson
o Added grdchk package handling o Added passive tracer handling
Merge from branch pre38: o essential mods for cubed sphere o debugged atmosphere, dynamcis + physics (aim) o new packages (mom_vecinv, mom_fluxform, ...)
file ini_dynvars.F was initially added on branch pre38.
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