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 and reduces coupling between configuration parsing and simulation setup. The core changes are in src/simulation/AtmosSimulations.jl

Content

Core Changes

• New AtmosSimulation{FT} constructor: Added a keyword-based constructor that doesn't require AtmosConfig/parsed_args, allowing programmatic simulation creation with explicit parameters
• Callback system refactoring: Modularized callback creation into reusable functions:
  • default_model_callbacks: Creates callbacks from model components
  • common_callbacks: Standard simulation callbacks (progress logging, NaN checking, checkpointing, etc.)
  • Individual callback builders in get_callbacks.jl
• Diagnostics setup: Added setup_diagnostics_and_writers function to handle diagnostics initialization for both old and new constructors
• Updated struct defaults in types.jl to match YAML config defaults:

Utilities

• Added utility functions: convert_time_args, handle_restart, extract_diagnostic_periods, validate_checkpoint_diagnostics_consistency, parse_checkpoint_frequency
• Separated parsed_args and sim_info from functions to enable reuse: args_integrator, get_jacobian, ode_configuration, get_state_restart, get_diagnostics, get_callbacks, build_cache
• Added test for restart functionality with new constructor test/restart_AtmosSimulation.jl

Miscellaneous

• Removed _DEFAULT_ATMOS_MODEL_KWARGS constant - defaults now handled by struct definitions
• Removed some logging statements for cleaner output
• Updated core_default_diagnostics to require topography parameter explicitly

TODOs

• Add unit tests for new constructor

Future Work

• Unify callback system - get_callbacks and common_callbacks have some redundancy
• Add support for missing callbacks (SCM forcing, etc.)
• Obtain tracers from model info automatically
• Validate callback frequencies with dt
• Add netcdf_interpolation_num_points and netcdf_output_at_levels to new constructor
• Ensure get_simulation retains all desired logging
• Add "verbose" option with all logging from get_simulation
• Add more defaults for AtmosModel subtypes
• Improve simulation validation with informative errors (currently nonsensical simulations fail later with confusing errors)
• Catalog config options possible with get_simulation but not with new AtmosSimulation constructor
• Improve remaining jacobian configuration
• Improve callback configuration, further simplify builders