Big IO update, parallel synchronization

[arango]

This is a big update to ROMS IO. It is part of the parallel IO that will be available in the near future. The synchronization with exit_flag is more rigorous now to avoid having the model to hang-up during MPI computations with IO problems.

I built an umbrella over all the non-tiled NetCDF IO manipulations. This will facilitate parallel IO and the code is much cleaner and elegant. All the NetCDF verbose calls are located in a single place (see all new routines in mod_netcdf) to read and write non-tiled variables.

I also added a generic logic for the IO of nested grids. See new IOBOUNDS structure in mod_param.F.

A new routine (def_dim.F) is provided to define any NetCDF dimension with the necessary parallel logic and error checking.

I also corrected few IO bugs.

I tried to test as much as I can. However, I didn't test all the possible combinations of CPP flags.