docs(db): Phase 5 close-out — measurement baselines, staging parity, and D4 settled to fact (#316)

[BigSimmo]

Summary

Discharges the last remaining follow-on on #316 (Phase 5 of the database remediation programme), brings staging back to parity, and corrects the D4 documentation to the dashboard fact. Documentation, one staging-only migration apply, and local environment cleanup — no product code changed.

• Phase 5 close-out recorded in docs/audit/live-drift-forensics-2026-08.md. Like-for-like end-to-end production probes in the same style as §1.3, so the before/after table is comparable: semantic text fast path 31,610 → 955 ms (33× better than the incident, 1.6× better than the 2026-08-14 post-restore reading) and hybrid 21,757 → 6,720 ms. Nothing measured worse than the 2026-08-17 healthy baseline, so nothing was escalated.
• A new EXPLAIN forward baseline, captured on the healthy system, which §1.3 never had — all four RPCs that public.explain_retrieval_rpc supports, --analyze with buffers, three samples each, zero errors across twelve samples. The new slowest path is match_document_table_facts_text (1.72 s unprimed, 1,070 unprimed shared_read), recorded as the outlier to watch.
• §1.3's two pending items closed: missing-index sizing is moot (0 missing), and the rag_retrieval_logs miss-scan baseline is now recorded, with the reading that sequential scans are correct and cheap at this scale and the growth signal to watch is seq_tup_read.
• Two instrument limits stated rather than papered over.explain_retrieval_rpc EXPLAINs select * from public.<rpc>(…), so only an outer Function Scan is visible and plan flips are not observable through it; and it raises 22023 Unsupported retrieval RPC for the _v2 family, proven against production. Extending it is production DDL under an enabled auto-deploy toggle, so it was deliberately not written during a read-only phase and is queued instead.
• Finding, escalated rather than absorbed: all 22 indexes restored by the incident response report idx_scan = 0 against statistics that have never been reset (pg_stat_database.stats_reset is NULL, while 163/210 indexes show scans and the total is 344,747,815). That includes both trigram indexes credited with fixing the incident, whose OIDs are unchanged since 2026-08-14. Retrieval is actually served by the GIN tsvector and HNSW indexes. This retracts the attribution — the co-administered ANALYZE is the better-supported explanation — not the repair, and it changes triage order for the next latency incident. Queued as its own ledger item; the indexes are repo-defined and must not be dropped.
• Staging parity closed.20260820120000 applied to ikoiolksxqxfxgiyqpnu by real db push (never migration repair), after confirming the pending set was exactly one version with zero remote-only. Staging now reads 211 rows with migration_history_versions() present and stmt_count 3, matching production exactly.
• The alarm is observed clear, not merely believed clear.live-drift run 32514326022 on main is green: No unexpected schema drift between live and supabase/schema.sql, Remote migration versions: 211 (read via rpc), Remote-only (Preview blockers): 0, every step success. That is the first green live-drift since 2026-07-19T19:37:29Z — of the last 60 runs only four succeeded — ending a 33-day red streak, and pinned issue Live drift check failing #1963 auto-closed at 2026-08-21T18:38:42Z.
• D4 corrected to fact in both documents. The coordination board and the forensics dossier said the "Deploy to production" toggle had never been read and gave a hedged safe-either-way rule. It has since been read: the toggle is ENABLED with production branch main, and automatic branching is ON (limit 3, "Supabase changes only"). Both documents now carry the fact and its date and defer to AGENTS.md for the operative rule; the superseded reasoning is retained and marked as superseded rather than deleted.
• Two §5.1 deliverables are explicitly OPEN, not claimed as done (raised by Codex review and corrected in 9646a7dbd): there is no query-specific plan-flip evidence — cumulative idx_scan aggregates every workload and is a weaker, different signal, not a substitute — and the document_index_units path has no EXPLAIN baseline at all, because match_document_index_units_hybrid_v2 delegates to match_document_index_units_hybrid_scoped over a table none of the four supported RPCs touches. Only document_chunks has a usable v1 sibling. Both need production DDL and are queued; Phase 5 status reads "COMPLETE, two deliverables explicitly OPEN".
• Five ledger inbox requests queued, no reconcile run (PR docs(issues): reconcile 38 queued ledger requests into the canonical ledger #2229 owns the in-flight serialized reconcile): three adds (uncapped Branching Compute cost; the explain_retrieval_rpc_v2 gap; the zero-scan attribution finding), one update to #231 recording that Phase 5.2 is confirmed satisfied and flagging that its recommended-queue row still contradicts its own P2 re-grade, and one close of #316.

Verification

• npm run verify:pr-local

PR-local verification summary:
- completed: check:runtime, check:installed-lock-parity, format:changed, sitemap:check,
docs:check-index, docs:check-inventory, docs:check-scripts, docs:check-links,
check:branch-review-ledger, check:outstanding-issues, check:ledger-write-discipline
- failed: (none)
- not reached: (none)

• npm run check:production-readiness

[Production Readiness]
Project: Clinical KB Database (sjrfecxgysukkwxsowpy)
PASS (9): … Node runtime 24.19.0 … Supabase project config points to Clinical KB Database.
READY: no blocking production-readiness failures.

• npm run format (whole tree, committed)

UI verification not run: no UI, routing, styling, browser, reduced-motion, or forced-colors behaviour changed — this PR touches only Markdown documentation and ledger inbox JSON.

Verification not run — npm run eval:retrieval:quality, eval:rag, eval:quality, verify:release: no retrieval, ranking, selection, chunking, scoring, or answer-generation behaviour changed, and paid evals were explicitly not authorized for this task.

Risk and rollout

• Risk: Low. No product code, no schema change to production, no RAG surface touched. The only mutation anywhere is one migration applied to the staging project, which was already applied to production on 2026-08-20 and is the migration the repository chain has commanded since then. The documentation risk is the opposite of the usual one: this PR removes a hedged rule that told operators to skip a step, and replaces it with the stricter rule AGENTS.md already carries.
• Rollback:git revert restores both documents and removes the five inbox request files; nothing has been reconciled into docs/outstanding-issues.md, so no ledger state depends on it. The staging migration is not rolled back by reverting this PR and should not be — it brings staging into agreement with production and with the chain. If it ever had to be undone, it is a single security definer function that can be dropped on staging alone.
• Provider or production effects: Explicitly authorized and scoped. (1) A read-only production window against Clinical KB Database (sjrfecxgysukkwxsowpy) — baseline verification, explain_retrieval_rpc profiling, index/table statistics reads, and two /api/search probes. Zero production writes and zero production DDL. (2) One staging-onlysupabase db push to ikoiolksxqxfxgiyqpnu. (3) One npm run check:production-readiness. (4) One live-drift workflow dispatch on main. The dedicated worktree carried the Supabase link, the main checkout was left on its staging link throughout, the ref was re-verified immediately before every call, and the worktree was supabase unlinked at the end.
• RAG impact: no retrieval behaviour change — read-only measurement, a staging-only migration apply, documentation, and local environment cleanup; no ranking, selection, or ordering surface touched

Clinical Governance Preflight

• Source-backed claims still require linked source verification before clinical use
• No patient-identifiable document workflow was introduced or expanded without explicit governance approval
• Supabase target remains Clinical KB Database (sjrfecxgysukkwxsowpy)
• Service-role keys and private document access remain server-only
• Demo/synthetic content remains clearly separated from real clinical sources
• Source metadata, review status, and outdated/unknown-source behavior remain conservative
• Deployment classification/TGA SaMD impact was checked when clinical decision-support behavior changed

Notes on the preflight: no clinical decision-support behaviour changed, so the TGA SaMD classification is unaffected — the check was made and the answer is "no change", not "not applicable". The Supabase target was verified positively rather than assumed: check:production-readiness reports Project: Clinical KB Database (sjrfecxgysukkwxsowpy), and every hosted call in this task carried an explicit --project-ref. Service-role access stayed server-side: explain_retrieval_rpc is revoked from public/anon/authenticated and was reached only through the repo's own admin-client tooling and the Supabase management API.

Notes

• issues:reconcile was deliberately not run. A serialized reconcile of the queued backlog is owned by PR docs(issues): reconcile 38 queued ledger requests into the canonical ledger #2229; a second one would collide. The five requests here are immutable inbox files and are merge-safe.
• One item could not be completed and is not being reported as done. An empty leftover directory at D:\Repos\Database\.claude\worktrees\phase-4-index-restoration-b0f4ea is still on disk. It is confirmed empty (zero entries) and is not a registered git worktree, but both rmdir and PowerShell Remove-Item fail with "being used by another process" — a live session still holds it as its working directory. It will clear when that session exits; no process was killed to force it.
• Environment note for whoever picks this up next: gh is no longer slow on this machine (0.20 s / 0.26 s / 0.28 s on three consecutive gh --version runs, versus the 97 s measured 2026-08-20). node --version moved 17 s → 0.08 s over the same period, which shows the earlier slowness was machine-wide process-spawn starvation rather than anything about gh; a reboot cleared it. No security settings were changed.

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📥 Commits

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📒 Files selected for processing (8)

• docs/audit/live-drift-forensics-2026-08.md
• docs/branch-review-records/eecaf3f51b0f4d8dad88a76dbb9c162887d5067cd48bdde0bbaa87a410f4701a.record.md
• docs/database-remediation-coordination.md
• docs/outstanding-issues-inbox/05bd88ac-f24f-464a-8853-5d7ff55b375b.json
• docs/outstanding-issues-inbox/0a0ab127-0cc1-4b14-b4ce-fd839a98386c.json
• docs/outstanding-issues-inbox/1c89922d-3d01-4811-a255-ed78e2ed11c3.json
• docs/outstanding-issues-inbox/3c71ce2a-b752-4f1b-a8ef-4870f8027bf7.json
• docs/outstanding-issues-inbox/98e6ae7f-4190-49f3-a64d-fbf632ef6643.json

📝 Walkthrough

Walkthrough

The PR documents Phase 5 completion, production measurements, confirmed deploy-on-merge behavior, staging parity, successful live-drift validation, issue closure, and remaining database and infrastructure follow-up work.

Changes

Phase 5 close-out

Layer / File(s)	Summary
Measurements and completion records docs/audit/live-drift-forensics-2026-08.md, docs/database-remediation-coordination.md, docs/branch-review-records/...	The records capture production health checks, retrieval latency, EXPLAIN and index-usage baselines, readiness results, staging parity, and Phase 5 completion.

Deployment and validation

Layer / File(s)	Summary
Deploy-on-merge confirmation and staging validation docs/audit/live-drift-forensics-2026-08.md, docs/database-remediation-coordination.md	The documentation replaces D4 inference with dashboard confirmation, records staging migration catch-up, and records a successful live-drift run with zero schema drift and zero preview blockers.

Issue follow-up records

Layer / File(s)	Summary
Resolved findings and residual work docs/outstanding-issues-inbox/*.json	The issue records document retrieval improvements, generation-side timeout residuals, _v2 EXPLAIN limitations, trigram index scan findings, issue #316 closure, and preview-branch compute cost decisions.

Estimated code review effort: 2 (Simple) | ~10 minutes

Merge Risk:🟡 Moderate · up to 67ab9

The PR is documentation and ledger-only, but the current text still contains a conflicting production migration instruction, inconsistent evidence dates, and an attribution claim that needs qualification. Merge should wait for these corrections or explicit owner acceptance; the remaining issues are minor.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0 files. (8 skipped: 8 unsupported.)
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title clearly summarizes the main changes: Phase 5 close-out, measurement baselines, staging parity, and corrected D4 documentation.
Description check	✅ Passed	The description follows the repository template and provides complete summary, verification, risk, rollout, governance, and notes sections.

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• Create PR with unit tests
• Commit unit tests in branch claude/phase-5-closeout

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Inline comments:
In `@docs/audit/live-drift-forensics-2026-08.md`:
- Line 1761: Update the four fenced code blocks identified near the existing
fences to include a suitable language identifier, such as text, preserving their
captured-output content.
In
`@docs/branch-review-records/da9eadddac4befebc995b1000caa73f1fa0ced0d25d52b5789223410bac06c08.record.md`:
- Line 1: Update the Phase 5 close-out verification record to include the
decisive output line from verify:pr-local alongside the existing 11/11 summary,
preserving the recorded pass status and using the actual gate output rather than
a paraphrase.
In `@docs/database-remediation-coordination.md`:
- Around line 179-180: Update the “Next dispatches” guidance to remove the
requirement that every future migration have its own production db push, while
retaining the approved-window, merge-to-main deployment, and green live-drift
verification requirements. State that db push is reserved for explicitly
authorized staging or recovery procedures.
In `@docs/outstanding-issues-inbox/0a0ab127-0cc1-4b14-b4ce-fd839a98386c.json`:
- Around line 8-9: Align the records with the August 21, 2026 review date:
update the `#231` detail and source date in
docs/outstanding-issues-inbox/0a0ab127-0cc1-4b14-b4ce-fd839a98386c.json lines
8-9, update the `#316` closure date in
docs/outstanding-issues-inbox/98e6ae7f-4190-49f3-a64d-fbf632ef6643.json line 8,
and update the production measurement date before recording the attribution
finding in
docs/outstanding-issues-inbox/3c71ce2a-b752-4f1b-a8ef-4870f8027bf7.json line 10;
alternatively defer each corresponding update rather than asserting measurements
completed after the review date.
Apply the same fix in `@docs/audit/live-drift-forensics-2026-08.md` around lines
1687 - 1692: Make the record date consistent with the staging event timestamp.
In `@docs/outstanding-issues-inbox/3c71ce2a-b752-4f1b-a8ef-4870f8027bf7.json`:
- Line 10: Revise the detail text to retain the zero-scan observation but remove
the claim that index counters “have never been reset,” since database-level
stats_reset does not exclude per-table or per-index resets. Qualify the
attribution accordingly: where PostgreSQL 18 is available, reference
pg_stat_all_indexes.stats_reset for the affected indexes; otherwise defer to
available reset or audit records before concluding that ANALYZE caused the
recovery.

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• docs/database-remediation-coordination.md
• docs/outstanding-issues-inbox/0a0ab127-0cc1-4b14-b4ce-fd839a98386c.json
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• docs/outstanding-issues-inbox/98e6ae7f-4190-49f3-a64d-fbf632ef6643.json
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