- Transform writers to standalone objects instead of functions
- Have one writer for all the diagnostics
- Add support to general NetCDF writer

Now with support for all the configurations (including planes ✈️)

Following the CF conventions

[skip ci]

[skip ci][ci skip]

[skip ci][ci skip]

Bump the ref counter because some jobs are now run for longer

This commit introduces breaking changes in the interface.

* get_integrator is now replaced with get_simulation

The immediate reason for this change is that when we have diagnostics,
we also have a bunch of writers that open files and keep them open for
all the writing operations. We must ensure that the files are properly
closed at the end of the simulation. Hence, the integrator is no longer
enough. We could find a way to add this piece of information to the
cache, but now that the cache is more rigid, this becomes a pain.

In any case, we want to work on the atmos interface, especially for
coupler compatibility. At the moment, AtmosSimulation is a thin wrapper
that contains only the integrator at the writers. But this object will
extended to contain more useful and general information.

* simulation was removed from the cache

Now that simulation is its own object, it doesn't need to be in the
cache anymore

We currently print out when the allocations are lower than the hardcoded
limit, but we don't enforce changing this. This commit adds a second
test that fails when the measured allocations are fewer than 50 % of the
ones saved in the file