Integrated physics moist shallow water diagnostics

[nhartney]

Diagnosing the water vapour and cloud fields from the total moisture field in the checkpoint file gives something slightly different to saving those diagnostics in the checkpoint. Saving the diagnostics in the checkpoint (by changing line 189 of diagnostics.py to pick_up=True) gives better convergence results.

The diagnostics are computed in the same way in both approaches and so should give the same thing.