improve modifications to domain_decomp

[tommelt]

In PR #26 I made changes to domain_decomp so that we could account for the swapping of indices in nextsim.

This "fix" was implemented by transposing the input data when it is read-in from the netcdf file specified by --grid.

It was the simplest way to get everything working without breaking the tests, the library or the stand-alone binary.

Whilst this works for now I think a proper solution should be found because I think it could be confusing in future e.g., when using decomp tool the dim flags are not in the same order as those in the input --grid file.

Unfortunately I think we need to switch everything else -- instead of the input i.e., dim0 <-> dim1, x <-> y etc.

This is not as trivial as I first thought however as there are many places where this needs to be carefully checked.

This is not a priority at the moment so I am leaving it as an open issue.