cschanhniem · Jul 9, 2026 · Jul 9, 2026
diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate bench-strategy-compare regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check annual-review-check selection-rationale-check batch-priority-check pilot-package-check calibration-intake-check uncertainty-report-check preprint-bundle-check reproducibility-manifest-check candidate-summary-card-check multi-candidate-comparison-check pipeline-decision-audit-check claim-to-evidence-check score-decomposition-check reviewer-briefing-check dataset-release-check
+.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate bench-strategy-compare regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check annual-review-check selection-rationale-check batch-priority-check pilot-package-check calibration-intake-check uncertainty-report-check preprint-bundle-check reproducibility-manifest-check candidate-summary-card-check multi-candidate-comparison-check pipeline-decision-audit-check claim-to-evidence-check score-decomposition-check reviewer-briefing-check audit-chain-check dataset-release-check
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -945,6 +945,9 @@ score-decomposition-check:
 reviewer-briefing-check:
 	.venv/bin/openamp-foundry reviewer-briefing-check --entry-json '{"briefing_id":"RBP-001","batch_id":"BATCH-001","pipeline_version":"0.9.2","prepared_date":"2026-07-10","reviewer_name":"Dr. Test Reviewer","candidate_count":10,"artifact_ids":["CERT-001","SEL-001","SDR-001"],"open_questions":["Is selection rationale adequate?"],"scope_description":"Review candidate evidence packages for BATCH-001.","conflict_of_interest_declared":true,"dry_lab_only":true}' --format text
 
+audit-chain-check:
+	.venv/bin/openamp-foundry audit-chain-check --entry-json '{"chain_id":"ACH-001","batch_id":"BATCH-001","pipeline_version":"0.9.3","audit_date":"2026-07-10","has_sequence_input":true,"has_benchmark_results":true,"has_filter_log":true,"has_score_decomposition":true,"has_selection_rationale":true,"has_evidence_certificate":true,"has_claim_mappings":true,"has_pipeline_decision_audit":true,"has_reviewer_briefing":true,"missing_links":[],"auditor":"test@example.com","dry_lab_only":true}' --format text
+
 dataset-release-check:
 	.venv/bin/openamp-foundry dataset-release-check \
 		--entry-json '{"release_id":"DSR-001","dataset_name":"OpenAMP Wave 0.5 Candidates","dataset_version":"1.0.0","release_date":"2026-07-09","license_identifier":"CC-BY-4.0","data_sources":["UniProt AMP database","APD3","in-house pipeline"],"contains_sequences":true,"contains_activity_data":false,"dual_use_assessed":true,"usage_policy_url":"https://openamp.example.org/data-policy","contact_email":"data@openamp.example.org","release_approved":true,"dry_lab_only":true}' \

diff --git a/docs/evidence/AUDIT_CHAIN_GUIDE.md b/docs/evidence/AUDIT_CHAIN_GUIDE.md
@@ -0,0 +1,61 @@
+# Audit Chain Completeness Guide
+
+## Purpose
+
+The audit chain completeness checker validates that an evidence package for a
+batch contains all required chain links — from raw sequence input through
+pipeline scoring, filtering, candidate selection, and submission readiness.
+A gap anywhere in the chain blocks external reproducibility.
+
+## Schema Fields
+
+| Field | Type | Description |
+|---|---|---|
+| chain_id | str | Unique identifier (prefix "ACH-") |
+| batch_id | str | Batch under audit |
+| pipeline_version | str | Pipeline version string |
+| audit_date | str | ISO 8601 date of this audit |
+| has_sequence_input | bool | Raw sequences are documented |
+| has_benchmark_results | bool | Benchmark comparison results exist |
+| has_filter_log | bool | Candidate filter decisions are logged |
+| has_score_decomposition | bool | Score decomposition reports exist |
+| has_selection_rationale | bool | Selection rationale documents exist |
+| has_evidence_certificate | bool | Evidence certificates are present |
+| has_claim_mappings | bool | Claim-to-evidence mappings exist |
+| has_pipeline_decision_audit | bool | Pipeline decision audit entries exist |
+| has_reviewer_briefing | bool | Reviewer briefing package exists |
+| missing_links | list[str] | Auto-populated: names of chain links that are False |
+| auditor | str | Person or system performing this audit |
+| dry_lab_only | bool | Always True |
+
+## Chain Links (all required)
+
+1. `has_sequence_input` — without this, the pipeline has no traceable starting point
+2. `has_benchmark_results` — performance claims need benchmark backing
+3. `has_filter_log` — what was excluded must be recorded alongside what was included
+4. `has_score_decomposition` — composite scores must be decomposable
+5. `has_selection_rationale` — why *these* candidates and not others
+6. `has_evidence_certificate` — certificate of computational evidence
+7. `has_claim_mappings` — every claim traces to an artifact
+8. `has_pipeline_decision_audit` — filter/threshold decisions are traceable
+9. `has_reviewer_briefing` — external auditor has a complete briefing
+
+## Validation Rules
+
+1. chain_id must start with "ACH-"
+2. auditor must not be empty
+3. dry_lab_only must be True
+4. All 9 chain links must be True (any False is an error)
+5. missing_links must match the set of chain links that are False
+
+## Warning Conditions
+
+- Single auditor: auditor contains no "@" character → warn that a named human auditor is recommended
+- Future audit date: audit_date appears to be after the current year (year > 2030) → warn about implausible date
+
+## Honest Use Boundary
+
+Audit chain completeness is a meta-check: it verifies that all *other* evidence
+artifacts exist, not that they are scientifically correct. A passing audit chain
+means the evidence package is structurally complete, not that every artifact
+contains accurate science. Human expert review is still required.
diff --git a/docs/evidence/METRICS_CURRENT.md b/docs/evidence/METRICS_CURRENT.md
@@ -5,8 +5,8 @@ Machine-readable snapshot: `outputs/metrics_snapshot.json` regenerated with `mak
 > **Purpose:** One authoritative table of current pipeline metrics. If any doc disagrees
 > with this file, this file wins. Updated whenever benchmark/benchmark config changes.
 >
-> **Last updated:** 2026-07-10 (Phase M M4 — reviewer briefing package — v0.9.2)
-> **New in v0.9.2:** Reviewer briefing package schema (M4 — Loop 131) — docs/evidence/REVIEWER_BRIEFING_GUIDE.md with purpose, schema fields table (11 fields), validation rules (7), warning conditions (4), honest-use boundary. src/openamp_foundry/evidence/reviewer_briefing_package.py with ReviewerBriefingEntry dataclass (11 fields: briefing_id, batch_id, pipeline_version, prepared_date, reviewer_name, candidate_count, artifact_ids, open_questions, scope_description, conflict_of_interest_declared, dry_lab_only=True), ReviewerBriefingResult dataclass (7 fields: briefing_id, batch_id, reviewer_name, passed, errors, warnings, dry_lab_only=True), MINIMUM_ARTIFACT_IDS (3), MAX_SCOPE_LENGTH (500), LONG_SCOPE_THRESHOLD (300), LARGE_BATCH_THRESHOLD (50), MAX_OPEN_QUESTIONS_WARNING (5), MINIMAL_ARTIFACT_WARNING_COUNT (3), validate_reviewer_briefing() (7 error checks: RBP- prefix, non-empty reviewer_name, candidate_count>=1, artifact_ids>=3, non-empty scope_description<=500 chars, conflict_of_interest_declared must be True, dry_lab_only must be True; 4 warning conditions: large batch, many open questions, long scope, minimal artifacts), validate_reviewer_briefing_dict() (10 required fields guard). CLI (openamp-foundry reviewer-briefing-check) with --entry-json, --format text|json. make reviewer-briefing-check target. 52 tests. Phase M M4: reviewer briefing packages now have a machine-validated schema for external auditor handoff.
+> **Last updated:** 2026-07-10 (Phase M M5 — audit chain completeness — v0.9.3)
+> **New in v0.9.3:** Audit chain completeness checker (M5 — Loop 132) — docs/evidence/AUDIT_CHAIN_GUIDE.md with purpose, schema fields table (16 fields: chain_id, batch_id, pipeline_version, audit_date, 9 has_* bools, missing_links, auditor, dry_lab_only), 9 required chain links, validation rules (5), warning conditions (2: single auditor, future date), honest-use boundary. src/openamp_foundry/evidence/audit_chain_completeness.py with AuditChainEntry dataclass (16 fields: chain_id, batch_id, pipeline_version, audit_date, 9 has_* bools, missing_links list[str], auditor, dry_lab_only=True), AuditChainResult dataclass (7 fields: chain_id, batch_id, missing_link_count, passed, errors, warnings, dry_lab_only=True), CHAIN_LINK_FIELDS (9 entries), CHAIN_LINK_COUNT (9), AUDITOR_EMAIL_HINT ("@"), IMPLAUSIBLE_YEAR_THRESHOLD (2030), validate_audit_chain() (5+ error checks: ACH- prefix, non-empty auditor, dry_lab_only must be True, each false chain link errors, missing_links consistency; 2 warnings: no email, future date), validate_audit_chain_dict() (15 required fields guard). CLI (openamp-foundry audit-chain-check) with --entry-json, --format text|json. make audit-chain-check target. 39 tests. Phase M M5: the evidence chain is now machine-checkable end to end. Phase M (Audit Trail Infrastructure) is fully complete with M1-M5.
 > **New in v0.9.1:** Score decomposition report schema (M3 — Loop 130) — docs/evidence/SCORE_DECOMPOSITION_GUIDE.md with purpose, schema fields table (12 fields), valid scoring methods (6), validation rules (9), warning conditions (4), honest-use boundary. src/openamp_foundry/evidence/score_decomposition_report.py with ScoreDecompositionEntry dataclass (12 fields: report_id, batch_id, candidate_id, pipeline_version, composite_score, component_scores, component_weights, scoring_method, score_range_min, score_range_max, reviewer, dry_lab_only=True), ScoreDecompositionResult dataclass (7 fields: report_id, batch_id, candidate_id, scoring_method, passed, errors, warnings, dry_lab_only=True), VALID_SCORING_METHODS (6: additive_weighted, geometric_mean, harmonic_mean, max_component, min_component, rank_aggregation), MINIMUM_COMPONENTS (2), WEIGHT_SUM_TOLERANCE (0.01), DOMINANT_WEIGHT_THRESHOLD (0.6), UNBALANCED_RATIO_THRESHOLD (5.0), MAX_COMPONENTS_WARNING (8), LOW_SCORE_FRACTION (0.2), validate_score_decomposition() (9 error checks: SDR- prefix, score_range_min<score_range_max, composite_score in range, >=2 components, weight keys match score keys, weights sum to ~1.0, valid scoring_method, non-empty reviewer, dry_lab_only must be True; 4 warning conditions: dominant component, unbalanced weights, many components, low composite score), validate_score_decomposition_dict() (11 required fields guard). CLI (openamp-foundry score-decomposition-check) with --entry-json, --format text|json. make score-decomposition-check target. Phase M M3: every composite score is now machine-decomposable into its named components for external audit.
 > **New in v0.9.0:** Claim-to-evidence mapper schema (M2 — Loop 129) — docs/evidence/CLAIM_TO_EVIDENCE_GUIDE.md with purpose, schema fields table (10 fields), valid claim types (7), validation rules (7), warning conditions (4), honest-use boundary, CLI usage. src/openamp_foundry/evidence/claim_to_evidence_mapper.py with ClaimToEvidenceEntry dataclass (10 fields: mapping_id, batch_id, pipeline_version, claim_text, claim_type, supporting_artifact_ids, evidence_level, pre_specified, reviewer, dry_lab_only=True), ClaimToEvidenceResult dataclass (7 fields: mapping_id, batch_id, claim_type, passed, errors, warnings, dry_lab_only=True), VALID_CLAIM_TYPES (7: activity_prediction, calibration_statement, novelty_claim, performance_comparison, reproducibility_claim, safety_assessment, selection_rationale), VALID_EVIDENCE_LEVELS (6: 1-6), MAX_CLAIM_TEXT_LENGTH (500), LONG_CLAIM_TEXT_THRESHOLD (300), WEAK_EVIDENCE_THRESHOLD (2), validate_claim_to_evidence() (7 error checks: CEM- prefix, non-empty claim_text<=500 chars, valid claim_type, non-empty supporting_artifact_ids, valid evidence_level 1-6, non-empty reviewer, dry_lab_only must be True; 4 warning conditions: post-hoc, weak evidence, single artifact, long claim text), validate_claim_to_evidence_dict() (9 required fields guard). CLI (openamp-foundry claim-to-evidence-check) with --entry-json, --format text|json. make claim-to-evidence-check target. Phase M M2: every scientific claim is now machine-mapped to its supporting artifacts for external audit.
 > **New in v0.8.9:** Pipeline decision audit entry schema (M1 — Loop 128) — docs/evidence/PIPELINE_DECISION_AUDIT_GUIDE.md with purpose, required field table (13 fields), valid decision types (7), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/pipeline_decision_audit.py with PipelineDecisionAuditEntry dataclass (13 fields: audit_id, batch_id, pipeline_version, decision_date, decision_type, decision_description, rationale, alternatives_considered, affected_candidate_count, evidence_level, pre_specified, reviewer, dry_lab_only), PipelineDecisionAuditResult dataclass (5 fields: audit_id, batch_id, decision_type, passed, errors, warnings, dry_lab_only=True), VALID_DECISION_TYPES (7: benchmark_updated, calibration_adjusted, candidate_ranked, candidate_rejected, filter_applied, safety_flag_applied, threshold_chosen), VALID_EVIDENCE_LEVELS (6: 1-6), MAX_DESCRIPTION_LENGTH (500), MAX_RATIONALE_LENGTH (1000), validate_pipeline_decision_audit() (12 checks: AUD- prefix, non-empty batch_id/pipeline_version/reviewer, YYYY-MM-DD decision_date, valid decision_type, non-empty description<=500 chars, non-empty rationale<=1000 chars, affected_candidate_count>=0, valid evidence_level, dry_lab_only must be True; post-hoc warns, empty alternatives warns, low evidence warns, zero affected warns), validate_pipeline_decision_audit_dict() (12 required fields guard). CLI (openamp-foundry pipeline-decision-audit-check) with --entry-json, --format text|json. make pipeline-decision-audit-check target. Phase M M1: every pipeline decision is now machine-validated and traceable for external audit.

diff --git a/docs/research/NEXT_100_PR_MAP.md b/docs/research/NEXT_100_PR_MAP.md
@@ -223,7 +223,7 @@ Make every pipeline decision traceable, independently verifiable, and resistant
 | M2 | Add claim-to-evidence mapper schema (complete — Loop 129). | Maps each scientific claim to the artifact that supports it. | B |
 | M3 | Add score decomposition report schema (complete — Loop 130). | Documents how composite scores are computed from components. | B |
 | M4 | Add reviewer briefing package checker (complete — Loop 131). | One-stop summary that external reviewers need before auditing. | B |
-| M5 | Add audit chain completeness checker. | Validates the evidence chain has no gaps from sequences to submission. | B/D |
+| M5 | Add audit chain completeness checker (complete — Loop 132). | Validates the evidence chain has no gaps from sequences to submission. Completes Phase M. | B/D |
 
 ## Prioritization rule
 

diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,13 @@
 # Roadmap
 
+### v0.9.3 — Phase M M5: Audit Chain Completeness Checker (Completes Phase M)
+- Added `AuditChainEntry` schema validating all 9 evidence chain links exist for a batch
+- Detects gaps from sequence input through benchmark, filter, scoring, selection, certificate, claims, decision audit, and reviewer briefing
+- missing_links consistency check catches declaration errors
+- CLI: `openamp-foundry audit-chain-check`
+- 39 tests; all passing
+- Phase M (Audit Trail Infrastructure) complete
+
 ### v0.9.2 — Phase M M4: Reviewer Briefing Package
 - Added `ReviewerBriefingEntry` schema for one-stop external auditor handoff packages
 - Validates CoI declaration, minimum artifact count, scope, candidate count

diff --git a/src/openamp_foundry/cli/commands/reports.py b/src/openamp_foundry/cli/commands/reports.py
@@ -3290,3 +3290,22 @@ def _run_reviewer_briefing_check(args: argparse.Namespace) -> int:
             print("  Reviewer briefing package validated. External auditor handoff is documented.")
 
     return 0 if result.passed else 3
+
+
+def _run_audit_chain_check(args: argparse.Namespace) -> None:
+    import json
+    from openamp_foundry.evidence.audit_chain_completeness import validate_audit_chain_dict
+
+    entry_dict = json.loads(args.entry_json)
+    result = validate_audit_chain_dict(entry_dict)
+
+    if args.format == "json":
+        import dataclasses
+        print(json.dumps(dataclasses.asdict(result), indent=2))
+    else:
+        status = "PASS" if result.passed else "FAIL"
+        print(f"[{status}] Audit Chain Check: {result.chain_id} ({result.missing_link_count} gaps)")
+        for e in result.errors:
+            print(f"  ERROR: {e}")
+        for w in result.warnings:
+            print(f"  WARN:  {w}")