docs(lineage): reconcile completion-plan check-offs + ship protocol-to-publication closeout

11-section evidence audit (each newly-done claim adversarially re-verified, several
by running the cited tests) reconciled the application-completion plan against the
A1-A5/Gate-B work of 2026-06-19..21:
- Checked off Phase 0 bounded test lanes and the full Phase 3 protocol-to-publication
  block (P0-P6 + parent), HADES sidecar verification, sidecar contract tests, package
  closeout, the r_not_implemented decision, and the phenotype-validation backlog.
- New per-phase closeout: docs/lineage/modules/studies/2026-06-21-protocol-to-publication-closeout.md.
- Protocol-to-publication plan banner: implementation complete, open pending the live
  study-114 gated re-run.
- Fixed Gate-B5 regression: DR runbook frontmatter missing related_prs (--check-frontmatter
  now passes), regenerated catalog. content-tree + public-docs guards green.

Co-Authored-By: claude-flow <ruv@ruv.net>

Author: sudoshi

docs/lineage/catalog.md

@@ -18,20 +18,20 @@ Generated by `python3 scripts/docs/catalog_lineage_docs.py --write-catalog`.
 
 ## Summary
 
-- Authored Markdown/MDX files: 931
-- Total lines: 419,466
+- Authored Markdown/MDX files: 933
+- Total lines: 419,771
 - Files missing lineage frontmatter: 0
 
 ## Category Counts
 
 | Count | Category |
 |---:|---|
-| 191 | `module-lineage` |
+| 192 | `module-lineage` |
 | 95 | `public-docs-source` |
 | 93 | `closed-plan` |
 | 79 | `legacy-plan` |
 | 74 | `public-dev-blog` |
-| 72 | `operations-lineage` |
+| 73 | `operations-lineage` |
 | 50 | `active-spec` |
 | 42 | `legacy-spec` |
 | 36 | `session-lineage` |
@@ -70,10 +70,10 @@ Generated by `python3 scripts/docs/catalog_lineage_docs.py --write-catalog`.
 | `docs/lineage/plans/open/2026-05-07-parthenon-ingestion-templates-phase-4-plan-6-fhir-bulk-data-reader.md` | Parthenon Ingestion Templates — Phase 4, Plan 6: HL7 FHIR Bulk Data reader (streaming claims) | 62 | yes | `docs/lineage/plans/open/2026-05-07-parthenon-ingestion-templates-phase-4-plan-6-fhir-bulk-data-reader.md` |
 | `docs/lineage/plans/open/2026-05-07-parthenon-ingestion-templates-phase-4-plan-7-federated-mapping-spike.md` | Parthenon Ingestion Templates — Phase 4, Plan 7: Federated mapping review spike | 61 | yes | `docs/lineage/plans/open/2026-05-07-parthenon-ingestion-templates-phase-4-plan-7-federated-mapping-spike.md` |
 | `docs/lineage/plans/open/2026-05-07-parthenon-ingestion-templates-phase-4-plan-8-upstream-diff-workflows.md` | Parthenon Ingestion Templates — Phase 4, Plan 8: Quarterly upstream-diff workflows (ARTEMIS + NAACCR) | 53 | yes | `docs/lineage/plans/open/2026-05-07-parthenon-ingestion-templates-phase-4-plan-8-upstream-diff-workflows.md` |
-| `docs/lineage/plans/open/2026-06-18-application-completion-plan.md` | Parthenon Application Completion Plan | 467 | yes | `docs/lineage/plans/open/2026-06-18-application-completion-plan.md` |
+| `docs/lineage/plans/open/2026-06-18-application-completion-plan.md` | Parthenon Application Completion Plan | 479 | yes | `docs/lineage/plans/open/2026-06-18-application-completion-plan.md` |
 | `docs/lineage/plans/open/2026-06-19-production-readiness-roadmap.md` | Parthenon Production-Readiness Roadmap | 351 | yes | `docs/lineage/plans/open/2026-06-19-production-readiness-roadmap.md` |
 | `docs/lineage/plans/open/README.md` | Open Plan Backlog | 47 | yes | `docs/lineage/plans/open/README.md` |
-| `docs/lineage/plans/open/protocol-to-publication-implementation-plan.md` | Abby — Protocol-to-Publication Pipeline: Implementation Plan | 371 | yes | `docs/lineage/plans/open/protocol-to-publication-implementation-plan.md` |
+| `docs/lineage/plans/open/protocol-to-publication-implementation-plan.md` | Abby — Protocol-to-Publication Pipeline: Implementation Plan | 380 | yes | `docs/lineage/plans/open/protocol-to-publication-implementation-plan.md` |
 
 ### active-spec
 
@@ -309,7 +309,7 @@ Generated by `python3 scripts/docs/catalog_lineage_docs.py --write-catalog`.
 |---|---|---:|---|---|
 | `docs/compliance/audit-controls.md` | Parthenon Audit Controls Documentation | 311 | yes | `docs/compliance/audit-controls.md` |
 | `docs/compliance/compliance-remediation-plan.md` | Parthenon Compliance Remediation Plan | 855 | yes | `docs/compliance/compliance-remediation-plan.md` |
-| `docs/compliance/disaster-recovery-plan.md` | Parthenon Disaster Recovery Plan | 382 | yes | `docs/compliance/disaster-recovery-plan.md` |
+| `docs/compliance/disaster-recovery-plan.md` | Parthenon Disaster Recovery Plan | 395 | yes | `docs/compliance/disaster-recovery-plan.md` |
 | `docs/compliance/evidence/breach-log.md` | Parthenon HIPAA Breach Log | 35 | yes | `docs/compliance/evidence/breach-log.md` |
 | `docs/compliance/incident-response-plan.md` | Parthenon Incident Response Plan | 345 | yes | `docs/compliance/incident-response-plan.md` |
 | `docs/compliance/risk-assessment.md` | Parthenon Risk Assessment | 242 | yes | `docs/compliance/risk-assessment.md` |
@@ -477,7 +477,7 @@ Generated by `python3 scripts/docs/catalog_lineage_docs.py --write-catalog`.
 | `docs/README.md` | Documentation Map | 76 | yes | `docs/README.md` |
 | `docs/lineage/README.md` | Developer Lineage | 147 | yes | `docs/lineage/README.md` |
 | `docs/lineage/archive/README.md` | Lineage Archive | 26 | yes | `docs/lineage/archive/README.md` |
-| `docs/lineage/catalog.md` | Documentation Lineage Catalog | 1128 | yes | `docs/lineage/catalog.md` |
+| `docs/lineage/catalog.md` | Documentation Lineage Catalog | 1129 | yes | `docs/lineage/catalog.md` |
 | `docs/lineage/design/README.md` | Design Lineage | 27 | yes | `docs/lineage/design/README.md` |
 | `docs/lineage/document-authoring-governance.md` | Document Authoring Governance | 136 | yes | `docs/lineage/document-authoring-governance.md` |
 | `docs/lineage/plans/README.md` | Plan Lineage | 32 | yes | `docs/lineage/plans/README.md` |
@@ -518,7 +518,7 @@ Generated by `python3 scripts/docs/catalog_lineage_docs.py --write-catalog`.
 | `docs/lineage/modules/analyses/2026-04-15-ohdsi-full-parity-shiny-supersession-runtime-guardrails.md` | OHDSI Full Parity - Shiny Supersession and Runtime Guardrails | 331 | yes | `docs/lineage/modules/analyses/2026-04-15-ohdsi-full-parity-shiny-supersession-runtime-guardrails.md` |
 | `docs/lineage/modules/analyses/2026-05-09-hades-parity-managed-ohdsi-shiny-runtime.md` | HADES Parity and Managed OHDSI Shiny Runtime | 657 | yes | `docs/lineage/modules/analyses/2026-05-09-hades-parity-managed-ohdsi-shiny-runtime.md` |
 | `docs/lineage/modules/analyses/2026-05-09-managed-ohdsi-shiny-followup-devlog.md` | Managed OHDSI Shiny Follow-Up Devlog | 695 | yes | `docs/lineage/modules/analyses/2026-05-09-managed-ohdsi-shiny-followup-devlog.md` |
-| `docs/lineage/modules/analyses/2026-06-20-hades-sidecar-readiness-verification.md` | HADES / Darkstar Sidecar Readiness Verification | 106 | yes | `docs/lineage/modules/analyses/2026-06-20-hades-sidecar-readiness-verification.md` |
+| `docs/lineage/modules/analyses/2026-06-20-hades-sidecar-readiness-verification.md` | HADES / Darkstar Sidecar Readiness Verification | 172 | yes | `docs/lineage/modules/analyses/2026-06-20-hades-sidecar-readiness-verification.md` |
 | `docs/lineage/modules/analyses/afib-anticoagulation-study-design.md` | AFib Anticoagulation Study Design | 109 | yes | `docs/lineage/modules/analyses/afib-anticoagulation-study-design.md` |
 | `docs/lineage/modules/analyses/analyses-hardening-audit.md` | Analyses Hardening Audit | 94 | yes | `docs/lineage/modules/analyses/analyses-hardening-audit.md` |
 | `docs/lineage/modules/analyses/analyses-hardening-v1.md` | Analyses Hardening v1 — API Envelope Fixes & Defensive Numeric Formatting | 77 | yes | `docs/lineage/modules/analyses/analyses-hardening-v1.md` |
@@ -665,6 +665,7 @@ Generated by `python3 scripts/docs/catalog_lineage_docs.py --write-catalog`.
 | `docs/lineage/modules/solr/vector-explorer-3d-visualization.md` | Vector Explorer — 3D Embedding Visualization for Chroma Studio | 86 | yes | `docs/lineage/modules/solr/vector-explorer-3d-visualization.md` |
 | `docs/lineage/modules/studies-module-s10-s13.md` | Studies Module — Phases S10–S13 Devlog | 117 | yes | `docs/lineage/modules/studies-module-s10-s13.md` |
 | `docs/lineage/modules/studies-ux-enhancements.md` | Studies Module — Next-Gen UX Enhancements Devlog | 112 | yes | `docs/lineage/modules/studies-ux-enhancements.md` |
+| `docs/lineage/modules/studies/2026-06-21-protocol-to-publication-closeout.md` | Protocol-to-Publication (ADR-0020) — Implementation Closeout | 79 | yes | `docs/lineage/modules/studies/2026-06-21-protocol-to-publication-closeout.md` |
 | `docs/lineage/modules/synpuf-enrichment-2026-04-04.md` | SynPUF 2.3M Enrichment — Complete | 100 | yes | `docs/lineage/modules/synpuf-enrichment-2026-04-04.md` |
 | `docs/lineage/modules/templates-laravel-integration-2026-05-02.md` | Templates Laravel Integration — 2026-05-02 | 67 | yes | `docs/lineage/modules/templates-laravel-integration-2026-05-02.md` |
 | `docs/lineage/modules/ui/2026-04-12-light-mode-rollout.md` | Light / Dark Mode Rollout — Where We Are (2026-04-12) | 230 | yes | `docs/lineage/modules/ui/2026-04-12-light-mode-rollout.md` |
@@ -700,6 +701,7 @@ Generated by `python3 scripts/docs/catalog_lineage_docs.py --write-catalog`.
 | `docs/lineage/operations/2026-06-11-grant-adr0020-study-tables.md` | Migration: grant ADR-0020 study tables to `parthenon_app` | 56 | yes | `docs/lineage/operations/2026-06-11-grant-adr0020-study-tables.md` |
 | `docs/lineage/operations/2026-06-11-manuscript-publisher-bridge.md` | Migration + bridge: seed a /publish draft from the composed manuscript | 67 | yes | `docs/lineage/operations/2026-06-11-manuscript-publisher-bridge.md` |
 | `docs/lineage/operations/2026-06-11-study-results-projection.md` | Migration + backfill: project analysis executions into `study_results` | 165 | yes | `docs/lineage/operations/2026-06-11-study-results-projection.md` |
+| `docs/lineage/operations/2026-06-21-dr-restore-runbook.md` | PostgreSQL Backup & Restore Runbook (DR drill verified 2026-06-21) | 125 | yes | `docs/lineage/operations/2026-06-21-dr-restore-runbook.md` |
 | `docs/lineage/operations/README.md` | Operations Lineage | 22 | yes | `docs/lineage/operations/README.md` |
 | `docs/lineage/operations/process/2026-04-24-care-bundles-migration-fixes.md` | Care Bundles Workbench — Migration & Permission Fixes | 49 | yes | `docs/lineage/operations/process/2026-04-24-care-bundles-migration-fixes.md` |
 | `docs/lineage/operations/process/2026-04-24-care-bundles-tier-a.md` | CareBundles Tier A — Methodology card, DQ flags, Stratification | 56 | yes | `docs/lineage/operations/process/2026-04-24-care-bundles-tier-a.md` |

docs/lineage/modules/studies/2026-06-21-protocol-to-publication-closeout.md

@@ -0,0 +1,79 @@
+---
+doc_type: lineage
+status: historical
+date: 2026-06-21
+owner: acumenus
+module: studies
+lineage_anchor: false
+supersedes: []
+superseded_by: null
+related_prs: []
+related_code:
+  - docs/lineage/decisions/adr/adr-0020-protocol-to-publication-pipeline.md
+  - docs/lineage/plans/open/protocol-to-publication-implementation-plan.md
+  - backend/app/Support/Hashing/DefinitionHasher.php
+  - backend/app/Services/Analysis/Calibration/CalibrationService.php
+  - backend/app/Services/Studies/Gates/StudyGateService.php
+  - backend/app/Services/Studies/Gates/GateThresholdEvaluator.php
+  - backend/app/Support/EstimationResultNormalizer.php
+  - backend/app/Services/Analysis/CohortDiagnosticsService.php
+  - backend/app/Services/Publication/ManuscriptComposer.php
+  - backend/app/Http/Controllers/Api/V1/StudyOrchestratorController.php
+  - ai/app/orchestrator/state_machine.py
+  - darkstar/api/calibration.R
+  - backend/tests/Feature/Studies/HypertensionV3RegressionTest.php
+  - backend/tests/Feature/Studies/ManuscriptComposerTest.php
+  - backend/tests/Unit/Services/Analysis/Calibration/CalibrationServiceTest.php
+  - ai/tests/test_orchestrator.py
+---
+
+# Protocol-to-Publication (ADR-0020) — Implementation Closeout
+
+This closeout records the shipped evidence for each phase of the ADR-0020
+protocol-to-publication pipeline. All seven phases (P0–P6) landed in code with
+passing tests between 2026-06-19 and 2026-06-21. It satisfies the
+`docs/lineage/plans/open/2026-06-18-application-completion-plan.md` Phase 3
+acceptance "Protocol-to-publication has shipped closeout evidence for each
+phase." The implementation plan
+(`docs/lineage/plans/open/protocol-to-publication-implementation-plan.md`)
+**remains open** for the one outstanding acceptance: the live gated re-run of
+the golden regression study (`app.studies.id = 114`).
+
+## Per-phase shipped evidence
+
+| Phase | Deliverable | Code | Test | Commit |
+|---|---|---|---|---|
+| **P0** | Regression harness for the golden study-114 failures | `backend/tests/Feature/Studies/HypertensionV3RegressionTest.php` | Load-bearing cases un-skipped: S5 gate-fail + blinding, S6 calibration-fail, incidence-rate CIs (green). 3 cases remain `markTestSkipped` as explicitly-scoped future discrete rules (design-lint, 100%-Unknown DQ-flag, connection-retry), documented in-test. | `8fd842c70` |
+| **P1** | Provenance spine (SHA-256 over definitions) | `backend/app/Support/Hashing/DefinitionHasher.php`; consumed by `CohortDefinition`, `ConceptSet`, `AnalysisExecution`, `StudyPackageService`, `Console/Commands/Provenance/BackfillProvenanceHashes` | Provenance asserted in `ManuscriptComposerTest` (`study_diagnostics=overridden`) | — |
+| **P2** | Empirical calibration service + R endpoint | `backend/app/Services/Analysis/Calibration/CalibrationService.php`; `darkstar/api/calibration.R` (`POST /analysis/calibrate`) | `CalibrationServiceTest` (payload contract, insufficient-controls refusal, error fallback — green) | `f9b208182` |
+| **P3** | Gate ledger, blocking gates, estimate blinding | `StudyGateService::blindEstimationIfGated()`, `GateThresholdEvaluator`, `EstimationResultNormalizer::blind()` | `HypertensionV3RegressionTest` S5 (blind strips estimates — green) | — |
+| **P4** | Missing/inclusion cohort diagnostics | `backend/app/Services/Analysis/CohortDiagnosticsService.php::getInclusionAttrition()` (emits `severe_inclusion_attrition`) | Live-verified cohort 68 → 29,204 entry → 27,702 final | `5b4c39a95` |
+| **P5** | Abby orchestration via python-ai with recoverable job state | `ai/app/orchestrator/{state_machine,guards,tools}.py`; Laravel relay `StudyOrchestratorController` (`POST /orchestrate`, scoped Sanctum token); channel `abby.study.{study}` | `ai/tests/test_orchestrator.py` — 7 passed in the python-ai container (study-114 halts at S5 with estimates blinded, full-pass, S6 halt, guards) | `40cb5c3ab` |
+| **P6** | Manuscript synthesis with provenance-linked sections | `backend/app/Services/Publication/ManuscriptComposer.php` | `ManuscriptComposerTest` — gate-aware compose, withholds estimates when gate uncleared, never prints a fabricated effect number (green) | `ed6ca4eaf` |
+
+## Adjacent verified evidence
+
+- **HADES sidecar readiness** (Phase 3): 40/40 HADES packages installed, 0
+  required missing, real end-to-end compute; recorded in
+  `docs/lineage/modules/analyses/2026-06-20-hades-sidecar-readiness-verification.md`.
+- **Sidecar contract tests** (Phase 3): `backend/tests/Unit/Services/RServiceTest.php`
+  covers all four runners across success / invalid-input / legacy
+  `not_implemented` / empty-non-JSON / connection-failure.
+- **`r_not_implemented` decision** (Phase 3): retained as a defensive fallback for
+  unconfigured deployments (decision recorded in commit `cc3faba17`).
+
+## Remaining before the implementation plan can close
+
+1. **Live gated re-run of study 114** with `execute=true`, confirming the
+   orchestrator halts at S5 with estimates blinded against real analytics
+   (offline + dry-walk already proven; the full live run is ~90 min of prod
+   analytics and is the last acceptance).
+2. **UI diagnostics** (Phase 3 sub-item, not P0–P6): the dedicated
+   `EstimationResults.tsx` / `PredictionResults.tsx` sidecar-pending branch still
+   renders generic copy rather than package/environment-specific diagnostics.
+3. **Frontend contract coverage** for the resolved phenotype-validation behavior
+   (the backend contract — 17 cases, 0 skips — is shipped).
+
+Once item 1 lands, move
+`docs/lineage/plans/open/protocol-to-publication-implementation-plan.md` to
+`plans/closed/` with `status: shipped` and link this closeout.

docs/lineage/operations/2026-06-21-dr-restore-runbook.md

@@ -7,6 +7,7 @@ module: infrastructure
 lineage_anchor: false
 supersedes: []
 superseded_by: null
+related_prs: []
 related_code:
   - scripts/pg-host-logical-backup.sh
   - scripts/pg-host-basebackup.sh