Add new AtmosSimulation constructor

[nefrathenrici]

Purpose

Adds a new AtmosSimulation constructor, closes #3894.

The current AtmosConfig/parsed_args system is monolithic and hard to use programmatically. This PR introduces a more composable constructor that makes it easier to create simulations programmatically and reduces coupling between configuration parsing and simulation setup.

Content

• Added a new AtmosSimulation constructor that provides a cleaner API without requiring AtmosConfig/parsed_args
• Introduced domain abstractions (SphereDomain, ColumnDomain, etc.) to replace parsed_args-based spatial configuration. This could use ClimaCore directly, as mentioned by @Sbozzolo.
• Added default_model_callbacks to get callbacks from model info.
• Added common_callbacks for standard simulation callbacks (NaN checks, conservation, etc.)
• Refactored topography and mesh warp parsed_args into type hierarchies

To-do

• Add unit tests
• Unify get_callbacks and common_callbacks
• Obtain tracers from model info
• Validate
  • diagnostic/checkpoint frequencies match
  • reproducible restarts
  • callback frequencies with dt
• Add netcdf_interpolation_num_points and netcdf_output_at_levels
• Add support for scm forcing callbacks and other missing callbacks
• "verbose" option with all the logging from get_simulation
• More flexible timestepping configuration, some parsed_args are not supported
• Improve simulation validation with informative errors

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• I have read and checked the items on the review checklist.

[nefrathenrici]

this should be a parameter