refactor(config): RunConfig hygiene pass

[chethanuk]

📋 Summary

With disable_early_shutdown=True, an after-validator overwrote shutdown_error_rate with 1.0, so the value didn't round-trip. A data-designer create --run-config YAML that only set disable_early_shutdown: true also replaced the baseline rate. This PR replaces the mutation with an effective_shutdown_error_rate property and does the rest of the #807 cleanup. Field names, types and defaults don't change.

🔗 Related Issue

Closes #807

🔄 Changes

• The builder and ValidationColumnGenerator read effective_shutdown_error_rate, so enforcement gets the same value as before. It's a plain @property because a computed_field gets dumped and then rejected by extra="forbid" on model_validate.
• ThrottleConfig and _THROTTLE_DEPRECATION_MESSAGE move to run_config_deprecated.py and are imported back into run_config.py, so both import paths and old pickles still resolve.
• Field(description=...) replaces the Attributes: block. 12 fields get a description, and section comments group the fields without reordering them.
• STYLEGUIDE.md still uses normalize_shutdown_settings as its after-validator example. This PR doesn't touch it.

🧪 Testing

• make test passes

• Unit tests added/updated

• E2E tests added/updated (if applicable)

• RunConfig(disable_early_shutdown=True, shutdown_error_rate=0.2) reads back 0.2 with an effective rate of 1.0 and survives model_dump/model_validate and the JSON round-trip. RunConfig.model_json_schema() with descriptions stripped is identical to main.

• DataDesigner.create with a custom column that fails on about half the rows and shutdown_error_rate=0.2: with early shutdown on it stops and salvages 4 of 40 records, with it off it finishes with the 20 good ones.

• The 6 touched test files pass (256), including a legacy-pickle test for the ThrottleConfig move.

✅ Checklist

• Follows commit message conventions
• Commits are signed off (DCO)
• Architecture docs updated (if applicable)

[github-actions]

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[greptile-apps]

Confidence Score: 5/5

The PR appears safe to merge, with runtime consumers, configuration overlays, and deprecated compatibility paths aligned with the new non-mutating semantics.

Summary

This PR separates the configured shutdown error rate from the rate used during execution, allowing RunConfig to round-trip without mutation while preserving existing early-shutdown behavior.

• Adds effective_shutdown_error_rate and routes both dataset generation and parallel validation through it.
• Moves deprecated throttle compatibility code into a dedicated module while preserving public imports and legacy pickle resolution.
• Adds field-level schema descriptions and expands configuration, CLI-overlay, engine, and compatibility tests.

Diagram

%%{init: {'theme': 'neutral'}}%%
flowchart LR
    A[RunConfig input] --> B[Preserved shutdown_error_rate]
    A --> C{disable_early_shutdown?}
    C -- Yes --> D[effective rate 1.0]
    C -- No --> B
    B --> E[effective configured rate]
    D --> F[Dataset builder and validation executor]
    E --> F

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[github-actions]

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