chore(issues): ledger doc hygiene + canonical reference cleanup (#142 #154 #156 #186 #187 #232) - #1835
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📝 WalkthroughWalkthroughThe PR adds capacity and scale-readiness audit documents, updates references to relocated audit and archive documents, strengthens CI and issue-tracking safeguards, and records review-policy and ledger updates. ChangesAudit and governance updates
Estimated code review effort: 3 (Moderate) | ~20 minutes Possibly related PRs
Suggested reviewers: 🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✨ Finishing Touches🧪 Generate unit tests (beta)
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Updates to Preview Branch (codex/clean-up-ledger-documentation-and-references) ↗︎
Tasks are run on every commit but only new migration files are pushed.
View logs for this Workflow Run ↗︎. |
CI triageCI failed on this PR. Automated classification of the 2 failed job(s):
Compared with main CI run #9803 (failure). Classification is evidence routing, not permission to ignore a failure. Exact quarantined Playwright identities remain governed by the flake ledger. |
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💡 Codex Review
Database/docs/archive/operator-apply-july8-batch.md
Lines 15 to 16 in a2258eb
Rebase companion links after archiving the runbook
After this file moves from docs/ to docs/archive/, these targets resolve to nonexistent files under docs/archive/, so both companion links return 404 instead of opening the maintained reconciliation and workorder documents. npm run docs:check-links -- --all reports both paths as missing; prefix the targets with ../ to preserve the links.
Rebase proof links after moving the tenancy audit
Once the audit lives under docs/audit/, ../scripts/check-owner-scope-api.mjs resolves to the nonexistent docs/scripts/ directory; the test link on line 286 similarly resolves under docs/tests/. The all-doc link check reports both failures, so these proof links need ../../scripts/... and ../../tests/... paths.
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@codex resolve actionable Codex review findings for this pull request and current head using the repository instructions. This is the pull request's single automatic repair pass: do not perform a fresh review, create new standalone findings, or request another review. Work only the existing unresolved Codex threads on the current head. The only repository destination is BigSimmo/Database, and the only branch destination is the pull request head branch codex/clean-up-ledger-documentation-and-references at starting commit a2258eb; never publish fixes to a detached or synthetic work branch and never create a stacked pull request. Use the authenticated GitHub connector to commit each approved fix to BigSimmo/Database:codex/clean-up-ledger-documentation-and-references, then verify that the pull request head contains the published commit before reporting success. Always fix P0 and P1 findings. For P2 and lower findings, fix only clear, scoped, low-risk issues; otherwise disposition them with a concise reason. For a fixed thread, reply with as the first line and as the second line. For a no-code disposition, use followed by . These result markers authorize the workflow to close that exact thread only after it verifies a fixed commit is the pull request head; a local-only commit is not a fix. If publication or verification fails, do not use either result marker, do not claim success, and leave the thread open with the blocker. If human input or new authorization is required, do the same. Finish only after every actionable thread is fixed or dispositioned and closed, or explicitly left open for a human decision. Do not update the branch from main, address unrelated reviews, broaden scope, or create more than one scoped fix commit. Do not use external APIs, paid services, credentials, dependency changes, or broad refactors unless explicitly authorized. Add targeted tests where behavior changes and run the narrowest relevant validation. |
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💡 Codex Review
Database/docs/archive/operator-apply-july8-batch.md
Lines 15 to 16 in a2258eb
Preserve companion links after archiving the runbook
After this file moves from docs/ to docs/archive/, these relative targets resolve to nonexistent files under docs/archive/, so readers following the runbook's two companion links receive 404s. Update both targets to traverse back to docs/ (for example, ../supabase-migration-reconciliation.md); the default docs link check excludes archived files, so this regression is not caught unless the historical sweep is run.
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Pull request overview
Reorganizes historical documentation into canonical audit/archive locations and updates ledger guidance and records.
Changes:
- Moves dated reviews/runbooks and updates references.
- Archives completed issue-ledger entries and adds superseding review evidence.
- Adds durable CI fallback and ledger-verification guidance.
Reviewed changes
Copilot reviewed 37 out of 40 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
.claude/agents/clinical-governance-reviewer.md |
Updates tenancy-review path. |
AGENTS.md |
Adds CI and ledger safeguards. |
SECURITY.md |
Updates tenancy-review link. |
docs/README.md |
Indexes relocated documents. |
docs/archive/operator-apply-july8-batch.md |
Updates capacity-review reference. |
docs/audit/audit-handover-2026-07-14.md |
Updates tenancy-review references. |
docs/audit/audit-remediation-plan-2026-07-14.md |
Updates remediation file path. |
docs/audit/capacity-review.md |
Relocates capacity audit. |
docs/audit/latency-audit-2026-07-28.md |
Updates capacity references. |
docs/audit/scale-readiness-review.md |
Relocates scale audit. |
docs/audit/tenancy-defense-in-depth-review.md |
Relocates tenancy audit and runbook links. |
docs/auth-connection-cap-runbook.md |
Updates capacity references. |
docs/branch-review-ledger.md |
Appends superseding PR-J record. |
docs/codebase-index.md |
Updates documentation map. |
docs/deploy-corrector-public-titles.md |
Updates related-document paths. |
docs/deployment-architecture.md |
Updates capacity references. |
docs/ingestion-concurrency-fix-workorder.md |
Updates audit and archive paths. |
docs/ingestion-state-machine.md |
Updates scale-review path. |
docs/launch-operator-runbook.md |
Updates operator and capacity links. |
docs/operator-backlog.md |
Updates runbook links. |
docs/outstanding-issues.md |
Revises and archives ledger entries. |
docs/privacy-impact-assessment.md |
Updates tenancy-review link. |
docs/process-hardening.md |
Updates archived runbook link. |
docs/prompts/codex-data-database-safety-ultra-review.md |
Updates review input path. |
docs/prompts/codex-performance-reliability-ultra-review.md |
Updates audit input paths. |
docs/staging-setup.md |
Updates capacity references. |
docs/supabase-migration-reconciliation.md |
Updates archived runbook link. |
docs/worker-deploy-runbook.md |
Updates archived runbook link. |
scripts/archive/check-july8-live-batch.ts |
Updates failure guidance path. |
scripts/check-owner-scope-api.mjs |
Updates tenancy-review references. |
scripts/check-retrieval-owner-migration.ts |
Updates remediation path. |
scripts/soak-test.ts |
Updates capacity-review references. |
src/lib/owner-scope.ts |
Updates tenancy-review comment. |
supabase/migrations/20260708160000_ingestion_jobs_one_open_per_document.sql |
Updates archived runbook comment. |
supabase/migrations/20260708160001_retrieval_owner_matches_fail_closed.sql |
Updates tenancy-review comment. |
supabase/migrations/20260708170000_ingestion_jobs_one_open_per_document.sql |
Updates archived runbook comment. |
supabase/migrations/20260717120000_corrector_public_titles_only.sql |
Updates tenancy-review comment. |
supabase/migrations/20260724120000_table_facts_plpgsql_execute.sql |
Updates scale-review comment. |
supabase/schema.sql |
Updates archived runbook comment. |
tests/owner-scope-guard.test.ts |
Reads the relocated tenancy review. |
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@copilot Fix the code for all comments in this review thread. When a review comment includes a suggested change, apply the suggestion exactly. Do not make changes beyond what is described in the linked review thread. |
fix #186 archive - Restore #156 (read-modify-write race + Update-branch corruption) from archive back to the open issues section with its original full text; the underlying allocation race is not resolved by the conservative architecture decision described in the previous commit. - Re-add #156 to the recommendations priority table as row 51 (between #101 and #172, consistent with its original ordering). - Correct #101 to credit only metadata and memory parallelisation (hydrateCandidatesWithMetadataAndMemory) from PR #1474; visual hydration (attachPageVisualEvidence) is still called serially after hydration on all six call sites and is explicitly listed as a remaining candidate. - Update #186 archive text to reflect that only metadata+memory were updated in #101, not visual hydration. Co-authored-by: BigSimmo <87357024+BigSimmo@users.noreply.github.com>
Fixed in commit
Regarding the Clinical Governance Preflight finding: the migration file in this PR is a performance-only change (switching from a generic cached plan to |
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Actionable comments posted: 4
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@docs/audit/capacity-review.md`:
- Around line 153-154: Align the non-429 error-rate gate with the documented
acceptance threshold: require less than 1% and fail runs at or above 1%,
updating both the executable check and acceptance table consistently.
- Around line 129-163: The soak-test documentation currently claims broader
capacity coverage than the driver provides and uses a 5% failure threshold
instead of the documented <1% criterion. Either update scripts/soak-test.ts to
model authentication bursts, two searches and one document open per answer, and
enforce a non-429 error rate below 1%, or explicitly scope this documentation to
search-and-answer traffic and revise its success criteria accordingly.
In `@docs/audit/scale-readiness-review.md`:
- Around line 55-62: Update the RPC fan-out statement in the scale-readiness
review to distinguish the base cold-request range from the higher retry-expanded
maximum, explicitly accounting for OR-relaxation and trigram-correction retries.
Revise the F6 connection and throughput planning reference to use the
retry-expanded peak rather than the 10–14 base range alone.
In `@docs/ingestion-concurrency-fix-workorder.md`:
- Line 25: Correct the Markdown link paths relative to their containing files:
in docs/ingestion-concurrency-fix-workorder.md:25,
docs/ingestion-state-machine.md:21, and docs/privacy-impact-assessment.md:494
use audit/scale-readiness-review.md or audit/tenancy-defense-in-depth-review.md
as appropriate; in docs/prompts/codex-data-database-safety-ultra-review.md:67
use ../audit/tenancy-defense-in-depth-review.md.
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.claude/agents/clinical-governance-reviewer.mdAGENTS.mdSECURITY.mddocs/README.mddocs/archive/operator-apply-july8-batch.mddocs/audit/audit-handover-2026-07-14.mddocs/audit/audit-remediation-plan-2026-07-14.mddocs/audit/capacity-review.mddocs/audit/latency-audit-2026-07-28.mddocs/audit/scale-readiness-review.mddocs/audit/tenancy-defense-in-depth-review.mddocs/auth-connection-cap-runbook.mddocs/branch-review-ledger.mddocs/codebase-index.mddocs/deploy-corrector-public-titles.mddocs/deployment-architecture.mddocs/ingestion-concurrency-fix-workorder.mddocs/ingestion-state-machine.mddocs/launch-operator-runbook.mddocs/operator-backlog.mddocs/outstanding-issues.mddocs/privacy-impact-assessment.mddocs/process-hardening.mddocs/prompts/codex-data-database-safety-ultra-review.mddocs/prompts/codex-performance-reliability-ultra-review.mddocs/staging-setup.mddocs/supabase-migration-reconciliation.mddocs/worker-deploy-runbook.mdscripts/archive/check-july8-live-batch.tsscripts/check-owner-scope-api.mjsscripts/check-retrieval-owner-migration.tsscripts/soak-test.tssrc/lib/owner-scope.tssupabase/migrations/20260708160000_ingestion_jobs_one_open_per_document.sqlsupabase/migrations/20260708160001_retrieval_owner_matches_fail_closed.sqlsupabase/migrations/20260708170000_ingestion_jobs_one_open_per_document.sqlsupabase/migrations/20260717120000_corrector_public_titles_only.sqlsupabase/migrations/20260724120000_table_facts_plpgsql_execute.sqlsupabase/schema.sqltests/owner-scope-guard.test.ts
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Actionable comments posted: 4
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@docs/audit/capacity-review.md`:
- Around line 153-154: Align the non-429 error-rate gate with the documented
acceptance threshold: require less than 1% and fail runs at or above 1%,
updating both the executable check and acceptance table consistently.
- Around line 129-163: The soak-test documentation currently claims broader
capacity coverage than the driver provides and uses a 5% failure threshold
instead of the documented <1% criterion. Either update scripts/soak-test.ts to
model authentication bursts, two searches and one document open per answer, and
enforce a non-429 error rate below 1%, or explicitly scope this documentation to
search-and-answer traffic and revise its success criteria accordingly.
In `@docs/audit/scale-readiness-review.md`:
- Around line 55-62: Update the RPC fan-out statement in the scale-readiness
review to distinguish the base cold-request range from the higher retry-expanded
maximum, explicitly accounting for OR-relaxation and trigram-correction retries.
Revise the F6 connection and throughput planning reference to use the
retry-expanded peak rather than the 10–14 base range alone.
In `@docs/ingestion-concurrency-fix-workorder.md`:
- Line 25: Correct the Markdown link paths relative to their containing files:
in docs/ingestion-concurrency-fix-workorder.md:25,
docs/ingestion-state-machine.md:21, and docs/privacy-impact-assessment.md:494
use audit/scale-readiness-review.md or audit/tenancy-defense-in-depth-review.md
as appropriate; in docs/prompts/codex-data-database-safety-ultra-review.md:67
use ../audit/tenancy-defense-in-depth-review.md.
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📒 Files selected for processing (40)
.claude/agents/clinical-governance-reviewer.mdAGENTS.mdSECURITY.mddocs/README.mddocs/archive/operator-apply-july8-batch.mddocs/audit/audit-handover-2026-07-14.mddocs/audit/audit-remediation-plan-2026-07-14.mddocs/audit/capacity-review.mddocs/audit/latency-audit-2026-07-28.mddocs/audit/scale-readiness-review.mddocs/audit/tenancy-defense-in-depth-review.mddocs/auth-connection-cap-runbook.mddocs/branch-review-ledger.mddocs/codebase-index.mddocs/deploy-corrector-public-titles.mddocs/deployment-architecture.mddocs/ingestion-concurrency-fix-workorder.mddocs/ingestion-state-machine.mddocs/launch-operator-runbook.mddocs/operator-backlog.mddocs/outstanding-issues.mddocs/privacy-impact-assessment.mddocs/process-hardening.mddocs/prompts/codex-data-database-safety-ultra-review.mddocs/prompts/codex-performance-reliability-ultra-review.mddocs/staging-setup.mddocs/supabase-migration-reconciliation.mddocs/worker-deploy-runbook.mdscripts/archive/check-july8-live-batch.tsscripts/check-owner-scope-api.mjsscripts/check-retrieval-owner-migration.tsscripts/soak-test.tssrc/lib/owner-scope.tssupabase/migrations/20260708160000_ingestion_jobs_one_open_per_document.sqlsupabase/migrations/20260708160001_retrieval_owner_matches_fail_closed.sqlsupabase/migrations/20260708170000_ingestion_jobs_one_open_per_document.sqlsupabase/migrations/20260717120000_corrector_public_titles_only.sqlsupabase/migrations/20260724120000_table_facts_plpgsql_execute.sqlsupabase/schema.sqltests/owner-scope-guard.test.ts
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docs/audit/capacity-review.md (2)
129-163: 🚀 Performance & Scalability | 🟠 Major | 🏗️ Heavy lift
🧩 Analysis chain
🏁 Script executed:
#!/bin/bash set -euo pipefail rg -n -C 4 -- 'search|answer|document|auth|bearer|think|error|429' scripts/soak-test.tsRepository: BigSimmo/Database
Length of output: 8326
🏁 Script executed:
#!/bin/bash set -euo pipefail printf '%s\n' '--- applicable guidance ---' find .. -name AGENTS.md -print printf '%s\n' '--- capacity model and criteria ---' sed -n '1,190p' docs/audit/capacity-review.md printf '%s\n' '--- soak-test structure ---' sed -n '1,285p' scripts/soak-test.tsRepository: BigSimmo/Database
Length of output: 20006
🏁 Script executed:
#!/bin/bash set -euo pipefail cat AGENTS.md python3 - <<'PY' from pathlib import Path import re script = Path("scripts/soak-test.ts").read_text() doc = Path("docs/audit/capacity-review.md").read_text() endpoints = sorted(set(re.findall(r'endpoint:\s*"([^"]+)"', script))) request_paths = sorted(set(re.findall(r'`/api/\$\{endpoint\}`', script))) has_bearer = "authorization: `Bearer ${args.bearer}`" in script has_auth_endpoint = bool(re.search(r'/api/(auth|sign[-_]?in|login)', script, re.I)) has_document_endpoint = bool(re.search(r'/api/[^`"]*(document|doc)', script, re.I)) gate_lines = [line.strip() for line in doc.splitlines() if "Non-429 error rate" in line or "gate:" in line or "FAIL: non-429" in script] print("script endpoint union:", endpoints) print("script constructs only parameterized /api/{endpoint} requests:", bool(request_paths)) print("bearer header present:", has_bearer) print("authentication endpoint present:", has_auth_endpoint) print("document endpoint present:", has_document_endpoint) print("success/gate lines:") for line in gate_lines: print(" " + line) PYRepository: BigSimmo/Database
Length of output: 50374
Align the soak test with the capacity model and success criteria.
The model includes authentication bursts, two searches per answer, and one document open per answer. The driver sends only
/api/searchand/api/answerrequests, and--bearerreuses an existing session. It cannot measure authentication or document-read capacity. Its 5% non-429 failure gate also conflicts with the documented<1%success criterion. Add the missing phases and enforce the<1%gate, or scope the documentation to search and answer traffic.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@docs/audit/capacity-review.md` around lines 129 - 163, The soak-test documentation currently claims broader capacity coverage than the driver provides and uses a 5% failure threshold instead of the documented <1% criterion. Either update scripts/soak-test.ts to model authentication bursts, two searches and one document open per answer, and enforce a non-429 error rate below 1%, or explicitly scope this documentation to search-and-answer traffic and revise its success criteria accordingly.
153-154: 🩺 Stability & Availability | 🟠 Major | ⚡ Quick win
Make the executable error gate match the acceptance threshold.
Line 153 allows a non-429 error rate below 5%, while Line 171 requires less than 1%. A run with a 4% error rate can exit successfully and still fail the documented success criteria. Align the script and the acceptance table. If
<1%is the gate, fail at>=1%.Proposed documentation correction
- Exits non-zero if the non-429 error rate exceeds 5 %. + Exits non-zero if the non-429 error rate reaches 1 % or more.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@docs/audit/capacity-review.md` around lines 153 - 154, Align the non-429 error-rate gate with the documented acceptance threshold: require less than 1% and fail runs at or above 1%, updating both the executable check and acceptance table consistently.docs/audit/scale-readiness-review.md (1)
55-62: 🚀 Performance & Scalability | 🟠 Major | 🏗️ Heavy lift
Include retry fan-out in the RPC capacity budget.
The calculation reaches 14 RPCs before the OR-relaxation and trigram-correction retries described on Lines 59-60. A retrying request can therefore exceed the stated 10–14 RPC range. F6 reuses that range for connection and throughput planning, which underestimates peak pool occupancy. Report the base fan-out and the retry-expanded maximum separately.
Proposed wording correction
- A single cold request can issue 10–14 RPCs, of which the table-facts trio alone is ~3 × 6.75 s of parallel DB CPU. + A single cold request issues 10–14 base RPCs. OR-relaxation and trigram-correction retries add further RPCs; budget their maximum separately.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@docs/audit/scale-readiness-review.md` around lines 55 - 62, Update the RPC fan-out statement in the scale-readiness review to distinguish the base cold-request range from the higher retry-expanded maximum, explicitly accounting for OR-relaxation and trigram-correction retries. Revise the F6 connection and throughput planning reference to use the retry-expanded peak rather than the 10–14 base range alone.
Checked all 12 open PRs and mapped them to ledger rows. Twenty-four open rows are actively being fixed right now — #1835 (7 rows), #1840 (4), #1842 (6), #1841 (4), #1836 (2), #1837 (1), #1839 (1) — and none of those rows said so. This is the #292 failure mode with the safety off: a queued row that reads as unclaimed while a PR is open against it is how the same conversion shipped twice on 2026-08-09. Each row now names its PR and says not to start until that PR merges. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_017paT42ZVMf8jaLtkjFxdy5
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@copilot please resolve all issues for me including the merge failure and then have it ready to merge and babysit this PR |
Head branch was pushed to by a user without write access
Head branch was pushed to by a user without write access
Done. Here's what was resolved:
The branch is now pushed and CI should be running. Once CI completes green, the PR will be ready to merge. Note: per AGENTS.md "Stop when the pull request is open" policy, I'm stopping here — the CI results and merge decision are yours. |
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Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@PR_POLICY_BODY.md`:
- Around line 17-19: Update the verification entries in PR_POLICY_BODY.md to
include the decisive success-output line for every listed command, including
formatting, issue, ledger, documentation, design-system, migration-role, and
diff checks. Replace unsupported “passed” or exit-code-only claims with the
exact gate output while preserving the existing command coverage.
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# Conflicts: # docs/outstanding-issues.md
Summary
docs/audit/anddocs/archive/locations and repair every affected repository reference.#101so it no longer proposes the metadata and memory hydration already shipped by PR perf(rag): parallelise independent retrieval hydration #1474.Verification
npm run drift:manifest— passed; scratch PostgreSQL replay completed and regeneratedsupabase/drift-manifest.jsonfor the changed schema source.npm run verify:pr-local— partial: runtime, installed-lock parity, changed-file formatting, sitemap/docs checks, ledger guards, workflow/policy guards, lint, and typecheck passed. The full unit stage failed in unrelated Windows/baseline areas (bundle-budget,pr-handoff-stop, worker-observability timing, and document-viewer virtualization timing), so build and offline RAG evaluation were not reached.npm run check:outstanding-issues,npm run check:branch-review-ledger,npm run docs:check-links,npm run docs:check-inventory,npm run docs:check-index,npm run check:migration-role, andnpm run format— passed.npm run test -- tests/drift-detection.test.ts— 12/12 passed.UI verification not run: this PR does not change UI, routing, styling, browser behavior, reduced motion, or forced-colors behavior.
RAG impact: no retrieval, ranking, candidate-selection, source-rendering, or answer-contract behavior changes. The ledger text only records that PR #1474 already shipped metadata and memory hydration parallelisation; the remaining candidates stay behind their existing RAG flag and canary requirements.
Risk and rollout
force_custom_planperformance hint; it does not change result sets, RLS, schema shape, or clinical logic.Clinical Governance Preflight
Clinical KB Database(sjrfecxgysukkwxsowpy)Notes
docs/audit/; current repository policy says historical audit records are superseded rather than rewritten.