Remove the experimental learned-damage route

[allamaprabhuani]

Summary

This removes the experimental learned-damage route. It is not part of the released solver scope, and the teaching material does not use it. After this change the classical phase-field damage solve is the only damage-subproblem route.

What was removed

• phast.learned_damage and its package-level exports (DamageDecision, DamagePrediction, DamagePredictionRejected, DamagePredictor, DamageStepContext, DamageUpdateController, load_damage_predictor)
• The phast.training package
• examples/learned_damage/ and docs/user_guide/learned_damage.md
• tests/test_learned_damage.py, tests/test_mesh_graph_net_adapter.py and tests/test_damage_step_context_fem_helpers.py. The last file is removed in full because every test in it exercised DamageStepContext methods.
• The solver configuration fields damage_update, damage_predictor, damage_checkpoint, damage_predictor_options, damage_residual_rtol, damage_residual_atol, damage_bound_tolerance and damage_fallback. These are removed from SolverConfig and SolverSettings, together with:
  • their __post_init__ checks
  • the enum, range and cross-field validation
  • the schema-v2 adapter check
  • their configs/REFERENCE.yaml entries
• From StaggeredSolver:
  • set_damage_predictor and clear_damage_predictor
  • the per-step context builder
  • the controller branch in step_solve_damage
  • the update and last_route route-report fields and the predictor print block
• The AIBridge class
• FEMOperators.compute_physics_loss, which had no remaining callers
• The learned-damage and deep-learning lines in phast doctor

Documentation

• docs/tutorial/03_modular_fem_and_learned_damage.md is renamed to docs/tutorial/03_modular_fem.md, retitled "Modular fracture problems", and keeps only its finite-element content.
• Links are updated in:
  • docs/index.md
  • docs/tutorial/index.md
  • tutorials 05 and 06
  • README.md
• The two learned-damage rows are removed from the capability matrix, and the related entries from DOCUMENTATION_STYLE.md.
• Docstrings and comments in the staggered solver, damage solver and io_utils no longer describe the generic hooks in terms of learned models. set_damage, get_H_nodal, compute_edge_index and the stored edge_index dataset keep their names and behaviour.

Schema

configs/phast.schema.json was regenerated with python -m phast schema --output configs/phast.schema.json. As well as dropping the removed fields, the regeneration adds the rational_at2 degradation option and the stress_degradation field. Both already exist in the code but were missing from the checked-in schema.

Tests

• Baseline on main (1c379fd): pytest -q tests gave 467 passed.
• This branch: 432 passed. The 35 tests no longer present are:
  • the 34 tests in the three deleted learned-damage test files
  • the learned case of test_unsupported_choices_fail_before_execution
• A set comparison of test IDs confirms that every other test that passed on main still passes.
• sphinx -W -b html docs builds without warnings: 54 pages, down from 55 because the learned-damage guide is gone. It also builds cleanly with PHAST_NB_EXECUTION_MODE=force, matching the docs workflow.
• The core CI steps pass locally:
  • python -m phast doctor
  • the five --validate-only configurations
  • the retained DCB replot
• A configuration that still sets solver.damage_update is now rejected as an unknown field, in both the legacy and the schema-v2 input paths.