Restructure output directory

[Sbozzolo]

And don't use atmos.p.output_dir

The output structure looks like this:

coupler_output_dir_amip/
├── checkpoints
│       └── checkpoints for the various models
├── output_0000/
│   ├── atmos/
│   │   └── output of the atmos model
│   └── ocean/
│       └── output of the ocean model
├── output_0001/
│   └── ... component model outputs in their folders ...
├── output_0002/
│   └── ... component model outputs in their folders ...
└── output_active -> output_0002/

This is needed both to better support checkpoints and to reduce dependency on the atmos cache

[juliasloan25]

Can you update NEWS.md before merging please?