feat(safety): add module-first harness safety evaluation

[JiaenLiu]

Summary

• add an independent post-run safety-audit substrate with typed outcomes, explicit missingness, immutable snapshot materialization, CLI execution, and separate audit sidecars
• add the Proteus module-first harness-safety taxonomy for Agent Loop, Memory, Skills, and Tools, including non-adversarial fault models, bounded adversarial threat models, permission boundaries, and linked behavior/module verdicts
• add plug-in case-suite and evidence-provider contracts plus a generic runtime that evaluates every snapshot from H0 through Hn, derives harness contribution and module causality, and records adjacent-snapshot transitions
• expose proteus audit for instrument integrity and proteus safety --suite <module>:<object> for executable harness-safety suites
• retain actual harness-native safety cases as plug-ins; no Aki-specific case implementation is built into the generic runtime

Motivation

Proteus previously measured harness evolution and task behavior but lacked an independent, harness-neutral way to distinguish model behavior, harness controls, module mechanisms, committed effects, missing evidence, and longitudinal safety change. This change establishes those boundaries without feeding safety results back into evolution or collapsing unlike cases into a scalar score.

User and developer impact

• completed sweeps can be audited without modifying their source trajectories
• adapters can bind native surfaces to the four canonical harness modules
• external suites can plug in concrete scenarios and native evidence providers
• every materialized snapshot, including H0, can produce independent behavior and module verdicts plus transition evidence
• safety and task-evaluation outputs remain separate

Validation

• uv run --no-sync pytest tests/ -q — 148 passed
• Ruff clean for all new safety modules and tests
• Ruff E9/F correctness checks clean for modified CLI and Minimal adapter files
• git diff --check — clean