feat(layer5): v1.3 — reasoning-trace prototype at three choice points

[Joncik91]

Why

Spectre v2.0 requires machine-parseable reasoning traces at agent choice points (Layer 5). This PR ships the v1.3 prototype: traces at exactly the three named commit sites, with a minimal six-field schema that can be extended for v2.0 without breaking existing consumers.

Without this, there is no audit trail for why the walker chose a particular exemplar, concern answer, or substitution — only the final locked spec, not the reasoning.

What changed

• bin/_layer5.py (new) — build_trace_record() helper; project_substitution_trace() for substitution dict projection; SPECTRE_LAYER5=off kill switch.
• bin/walker.py — WalkState.layer5_trace: list[dict] field; record_answer emits walker-concern or exemplar-binding traces (6 known exemplar concern IDs get the latter); persist/load/both JSON-mode CLI payloads updated.
• bin/eval_metadata.py — write_sidecar gains layer5_trace: list[dict] | None kwarg; writes layer5_trace key when provided; CLI write-sidecar subcommand passes it through.
• docs/glossary.md — term:layer5-trace and term:layer5-choice-point entries.
• Three new test files — 20 tests covering all three choice points, the env-var kill switch, six-field completeness, and backwards-compat (None → key absent).

Schema (six fields + timestamp)

{
  "choice_point": "walker-concern" | "substitution" | "exemplar-binding",
  "step_or_concern_id": "<id>",
  "options_considered": ["<a>", "<b>"],
  "selected": "<a>",
  "rationale": "<why>",
  "validation_anchor": "<tier-or-check | null>",
  "source_anchor": "<spec-section | null>",
  "timestamp": "<ISO8601>"
}

Lives in .eval.json sidecar under layer5_trace: [...]. No new file type.

Test plan

• tests/test_layer5_walker_trace.py — 6 tests: multichoice appends trace, six fields present, zero-prefab skips, single-prefab skips, accumulates multiple, SPECTRE_LAYER5=off disables.
• tests/test_layer5_substitution_trace.py — 6 tests: None omits key, empty list written, round-trip, projection with options, projection without options returns None, coexists with substitutions.
• tests/test_layer5_exemplar_trace.py — 8 tests: exemplar-binding emitted, six fields present, validation_anchor=tier2-cross-view-gate, non-exemplar concern gets walker-concern, three individual exemplar IDs each verified, env-var kill switch.
• Full suite: pytest tests/ → 1987 passed, 0 failed.

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