fix(intelligence): VOR read-path skips prose scan when explicit anchors exist

[ManSio]

What

Fix false REFUTED in VOR (VerifyOnRead, ADR-0003): read-path re-scanned the prose of ADR body via _PATH_RE even when the node already had explicit data.anchors captured at write-time. ADR bodies contain historical X -> Y paths, so a rename-sweep resurrected the old path as a checkable anchor and falsely refuted live nodes.

Real case found: ADR-7232a6e2ba34 — its stored anchors (adapters/zed/zed_config.py, src/main.py, pkg:MCP) all still exist, but it was auto-REFUTED because prose /src/utils/paths.py → adapters/local_fs/windows.py (a git R083 rename) leaked into the anchor set.

Root Cause

extract_anchors() (verify_on_read.py:290) extracted explicit data.anchors first, then ALSO scanned prose text. A rename described as old_path -> new_path in the ADR body adds BOTH paths as anchors. The old path no longer exists → classify → SILENT_ABSENCE → REFUTED.

Fix

• extract_anchors(..., read_path: bool = False) — new param.
• VerifyOnRead.run() passes read_path=True for the read-path call.
• When the node has explicit data.anchors, prose is NOT scanned: historical paths never become checkable anchors. Explicit anchors remain authoritative.
• Legacy nodes WITHOUT explicit anchors (auto-collect stored before write-time capture) keep prose scanning → intentional drift detection still works (verified by test).
• Write-path callers in layer.py are unchanged (default read_path=False).

Tests

• test_extract_anchors_read_path_trusts_explicit_anchors — prose history not extracted on read-path, backward compat without flag.
• test_read_path_prose_history_not_refuting_live_node — live node with explicit anchors stays VERIFIED despite historical path in body.
• test_read_path_prose_history_legacy_node_keeps_refuting — legacy node without anchors still refutes on real drift.

Numbers (from EXPERIMENTS_LOG 2026-09-11)

Metric	Value
Auto-REFUTED nodes audited	24
Junk prose anchors (54%)	13
True deletions	10
FALSE rename refute	1 (ADR-7232a6e2ba34)
Synthetic sweep after ONE git mv	30/30 REFUTED → after fix keeps explicit-anchor nodes verified
Latency	extract_anchors ~5.6ms fingerprinted

Verification

• tests/test_verify_on_read.py: 53 passed
• tests/test_memory_retraction.py: 28 passed
• All pre-commit hooks green (verify_diary, stale_detector, check_tool_names, negative_controls, layer boundaries, architecture_linter, ruff)
• Live repro: node with explicit anchors + historical prose → VERIFIED (was REFUTED pre-fix)

[coderabbitai]

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