First attempt at reorganising chap_DYN in line with comments from Gurvan. This introduces a new chapter, provisionally named chap_D2D.tex, that will be expanded to cover the evolution of the barotropic terms by stp2d.F90. It is less clear, at this stage, how best to ensure the treatment of the barotropic terms in MLF is still made clear. Much still to be done.

Removed Sub-domain functionality section from chap_misc.tex since this option has been removed (practically at v4.2 and completely at v5.0)