Save Codex local changes - #50
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Pull request overview
This PR aggregates a broad set of “local Codex changes” spanning worker ingestion/indexing behavior, Supabase schema hardening (health checks, indexes, dedup), clinical output formatting, UI accessibility/table rendering, and process/CI guardrails (verification scripts + Playwright coverage + production readiness preflight).
Changes:
- Add embedding-field dedup support (
content_hash+ trigger + unique index), expand schema health/index validation, and refresh table stats post-ingestion. - Improve RAG/clinical UX output: smarter bottom-line selection, clipboard/note formatting, evidence passage compaction, and safety finding text cleanup.
- Harden process: new verification commands, CI Playwright Chromium smoke, production-readiness preflight, security headers, and new Playwright UI/accessibility tests.
Reviewed changes
Copilot reviewed 107 out of 120 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| worker/main.ts | Adds embedding-field content_hash, larger insert batching, and post-job analyze_rag_tables refresh. |
| worker/embedding-fields.ts | Formatting-only adjustment to addField call. |
| tests/ward-output.test.ts | Updates assertions for new clipboard/ward-note formatting and section merging behavior. |
| tests/ui-tools.spec.ts | Adds Playwright coverage for /tools launcher usability. |
| tests/ui-smoke.spec.ts | Stabilizes selectors and updates upload drawer interactions for new UI structure. |
| tests/ui-accessibility.spec.ts | Adds reduced-motion + forced-colors Playwright smoke coverage. |
| tests/supabase-schema.test.ts | Loosens grants regex to accommodate new schema items. |
| tests/private-access-routes.test.ts | Formatting-only change to route handler invocation. |
| tests/ingestion.test.ts | Formatting-only change to long error string literal. |
| tests/evidence.test.ts | Formatting-only change to array expectation. |
| tests/embed-texts-integrity.test.ts | Formatting-only change to mock embedding data creation. |
| tests/deep-memory.test.ts | Formatting-only tweaks; removes stray whitespace. |
| tests/clinical-safety.test.ts | Updates expectations for cleaned safety finding labels/text; adds new test. |
| tests/bulk-import.test.ts | Formatting-only tweak to expected array literal. |
| tests/answer-verification.test.ts | Formatting-only change to function call layout. |
| tests/accessible-table-normalization.test.ts | Adds a source-based regression test for updated AccessibleTable structure. |
| supabase/migrations/20260623014639_finalize_embedding_fields_hnsw_health.sql | Finalizes schema-health expectations and adds embedding-fields HNSW index + health RPC update. |
| supabase/migrations/20260622000000_reconcile_schema_health_vector_privileges.sql | Adds index reconciliation, embedding-field hash trigger + dedup index, RPC hardening, and analyze_rag_tables. |
| src/lib/ward-output.ts | Major rework of clipboard/ward-note output structure and bottom-line selection logic. |
| src/lib/supabase/health.ts | Formatting-only adjustments in type signatures and HTML title extraction. |
| src/lib/rag.ts | Adds additional retrieval telemetry counters and minor formatting fixes. |
| src/lib/openai.ts | Formatting-only adjustment to PublicApiError construction. |
| src/lib/ingestion.ts | Formatting-only refactor of retryable-error regex check. |
| src/lib/ingestion-recovery.ts | Formatting-only change to boolean expression layout. |
| src/lib/image-filtering.ts | Formatting-only refactor of condition wrapping. |
| src/lib/extractors/document.ts | Formatting-only change to warning string push. |
| src/lib/env.ts | Changes default worker runtime parameters (polling, batch size, concurrency, attempts, stale window). |
| src/lib/deep-memory.ts | Increases batch sizes for deep-memory inserts and minor formatting. |
| src/lib/clinical-vocabulary.ts | Expands formatting for readability of vocabulary entries. |
| src/lib/clinical-safety.ts | Cleans/compacts extracted safety finding text using sanitizer helpers. |
| src/lib/bulk-import.ts | Formatting-only change to normalized key assignment. |
| src/lib/answer-ranking.ts | Comment whitespace cleanup. |
| src/lib/answer-formatting.ts | Adds semicolon-list splitter helper and standardizes fallback text. |
| src/components/DocumentViewer.tsx | Improves mobile actions UX (sheet), table rendering behavior, and copy changes (“Open source”). |
| src/components/DashboardFloatingFab.tsx | Minor string quoting and SR live-region formatting adjustments. |
| src/components/clinical-dashboard/use-theme.ts | Adds a client theme hook using useSyncExternalStore. |
| src/components/clinical-dashboard/source-actions.tsx | Adds source action row + link helpers for dashboard usage. |
| src/components/clinical-dashboard/relevance.tsx | Adds relevance badges/chips utilities and components. |
| src/components/clinical-dashboard/index.ts | Exports the clinical-dashboard module surface. |
| src/components/clinical-dashboard/ClinicalDashboard.tsx | Provides compatibility export for ClinicalDashboard. |
| src/components/clinical-dashboard/badges.tsx | Adds status/strength badge components. |
| src/components/clinical-dashboard/answer-status.tsx | Adds empty/skeleton/copy UI helpers for dashboard answer states. |
| src/components/AccessibleTable.tsx | Reworks mobile table presentation to keep a single semantic table + adds expand dialog + row actions. |
| src/app/page.tsx | Switches to importing ClinicalDashboard from the new module entrypoint. |
| src/app/api/search/route.ts | Adds rag_retrieval_logs insert diagnostics with failure metrics tracking. |
| src/app/api/ingestion/jobs/[id]/retry/route.ts | Formatting-only change to JSON error field layout. |
| scripts/supabase-recovery-status.ts | Formatting-only refactor of safeCount calls. |
| scripts/reindex-health.ts | Formatting-only refactor of safeCount calls. |
| scripts/production-readiness.ts | Adds an executable production readiness preflight script. |
| scripts/playwright-base-url.ts | Increases local identity probe timeout. |
| scripts/import-documents.ts | Formatting-only console.log line wrapping changes. |
| scripts/eval-search.ts | Adds retry/backoff on rate limits + spacing delay between cases. |
| scripts/eval-retrieval.ts | Formatting-only change to a long numeric expression. |
| scripts/ensure-local-server.mjs | Improves project identity probing robustness (retries + timeout). |
| scripts/enrich-documents.ts | Adds retry/backoff on rate limits and better enrichment completion stamping. |
| scripts/check-indexing.ts | Adds paginated document loading + ordering and more readiness reporting. |
| scripts/backfill-smart-index.ts | Adds embedding-field md5 hash inclusion and small formatting fixes. |
| scripts/audit-tables.ts | Formatting-only change to .or(...) usage. |
| scratch/update-health-check.sql | Adds a scratch SQL version of search_schema_health updates. |
| scratch/show-samples.ts | Adds a scratch script to print sample documents. |
| scratch/queue-queued-docs.ts | Adds a scratch script to enqueue ingestion jobs for queued documents. |
| scratch/fix-indexes.ts | Adds a scratch script stub for index fixes. |
| scratch/create-hnsw-indexes.sql | Adds scratch SQL for creating HNSW indexes via dashboard/editor. |
| scratch/count-status.ts | Adds scratch script to count document/job statuses. |
| scratch/count-files.ts | Adds scratch script with local Windows paths for file counting. |
| scratch/check-queued-docs.ts | Adds scratch script to inspect active ingestion jobs. |
| scratch/check-indexes.ts | Adds scratch script attempting to query system indexes via Supabase. |
| scratch/audit-guidelines.ts | Adds scratch script with local Windows paths for auditing guideline coverage. |
| README.md | Documents new verification/readiness commands. |
| playwright.config.ts | Expands test match to include accessibility/tools and increases timeout. |
| package.json | Adds verify and production-readiness scripts plus workflow helpers. |
| next.config.ts | Adds security headers (CSP, COOP/COEP, HSTS, etc.) and disables powered-by header. |
| eslint.config.mjs | Ignores scratch/**. |
| docs/redesign/06-verification.md | Records verification steps and results for redesign/process pass. |
| docs/redesign/05-changelog.md | Adds June 23 process hardening notes. |
| docs/redesign/04-deferred.md | Updates deferred items to reflect tools page coverage resolution. |
| docs/redesign/03-decision-log.md | Adds decisions D7–D10 related to scope, upload drawer, viewer actions, evidence hint. |
| docs/redesign/02-design-direction.md | Adds June 20 scoped direction notes. |
| docs/redesign/01-audit.md | Adds audit notes emphasizing scoped run exclusions. |
| docs/production-readiness-checklist.md | Adds executable production readiness checklist/runbook. |
| docs/process-hardening.md | Adds verification gating plan and phases. |
| docs/clinical-governance.md | Adds PR preflight guidance for governance-sensitive changes. |
| AGENTS.md | Adds process-hardening guidance and verification gates for future agents. |
| .vscode/extensions.json | Adds recommended dev extensions. |
| .tmp-visual/stream-headers.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/stream-capture.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/query-smoke.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/query-final.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/query-disabled-state.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/query-ask.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/query-ask-submit.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/query-api-trace.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/query-answer-stream.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/inspect-home.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/inspect-ask-controls.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/check-search-api.mjs | Adds local visual/debug helper script (repo-local). |
| .tmp-visual/capture.mjs | Adds local visual/debug helper script (repo-local). |
| .prettierignore | Ignores .tmp-visual/ and scratch/. |
| .github/workflows/codeql.yml | Formatting-only YAML cleanup. |
| .github/workflows/ci.yml | Adds production-readiness CI check + installs/runs Playwright Chromium smoke. |
| .github/pull_request_template.md | Adds verification checklist + clinical governance preflight section. |
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| top_rrf_score: topResult?.rrf_score ?? null, | ||
| mean_hybrid_score: meanScore || null, | ||
| selected_chunk_ids: args.results |
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| selected_chunk_ids: args.results | ||
| .slice(0, 12) | ||
| .map((r) => r.id) | ||
| .filter((id) => /^[0-9a-f-]{36}$/i.test(id)), | ||
| selected_document_ids: Array.from(new Set(args.results.slice(0, 12).map((r) => r.document_id))).filter((id) => | ||
| /^[0-9a-f-]{36}$/i.test(id), | ||
| ), | ||
| selected_count: Math.min(args.results.length, 12), |
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| WORKER_POLL_MS: z.coerce.number().int().positive().default(1500), | ||
| WORKER_BATCH_SIZE: z.coerce.number().int().positive().default(25), | ||
| WORKER_CONCURRENCY: z.coerce.number().int().positive().default(8), | ||
| WORKER_MAX_ATTEMPTS: z.coerce.number().int().positive().default(5), | ||
| WORKER_STALE_AFTER_MINUTES: z.coerce.number().int().positive().default(5), |
BigSimmo pushed a commit
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Jul 20, 2026
…rank score The 2026-07-20 post-merge golden run (eval-canary #50, 35/36) showed the #982 tie-break regressing alcohol-ciwa-threshold: keying saturated ties on the boost-laden rankScore let generic clinicalSignalBoost stacking promote screening/monitoring chunks over the chunk containing the queried terms — the same failure mode the clamped-score contract exists to prevent. The tie-break key is now the clinical rank's lexicalCoverageScore (query-term coverage, immune to boost stacking), renamed contentCoverageScore; ties on coverage still fall back to the stable chunk-id order. The saturated-tie contract test now pins coverage winning against a HIGHER rankScore, and the fast-path CIWA guard adds the screening-chunk shape from run #50. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EXsJcLrbZUXwnBeG91cVo9
BigSimmo pushed a commit
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Jul 20, 2026
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EXsJcLrbZUXwnBeG91cVo9
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BigSimmo added a commit
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Jul 20, 2026
…rank score (#987) * fix(rag): break saturated selection ties by query-term coverage, not rank score The 2026-07-20 post-merge golden run (eval-canary #50, 35/36) showed the #982 tie-break regressing alcohol-ciwa-threshold: keying saturated ties on the boost-laden rankScore let generic clinicalSignalBoost stacking promote screening/monitoring chunks over the chunk containing the queried terms — the same failure mode the clamped-score contract exists to prevent. The tie-break key is now the clinical rank's lexicalCoverageScore (query-term coverage, immune to boost stacking), renamed contentCoverageScore; ties on coverage still fall back to the stable chunk-id order. The saturated-tie contract test now pins coverage winning against a HIGHER rankScore, and the fast-path CIWA guard adds the screening-chunk shape from run #50. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EXsJcLrbZUXwnBeG91cVo9 * docs(ledger): record run-#50 finding and coverage tie-break review row Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EXsJcLrbZUXwnBeG91cVo9 --------- Co-authored-by: Claude <noreply@anthropic.com>
BigSimmo pushed a commit
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Jul 20, 2026
…ck, WebKit focus/forced-colors/stale-style, Firefox tab order, CIWA term alias Seven fixes from the run-4012 triage, each root-caused: - playwright.config.ts: serviceWorkers 'block' suite-wide (+ ui-pwa.spec.ts 'allow' opt-in). In production builds public/sw.js registers in every test, claims the page (clients.claim) and serves every navigation — probe-proven to bypass route interception for navigations on Chromium and to wedge Playwright-Firefox's reload path under an active route (both ui-smoke reload hangs). Only ui-pwa exercises the worker itself; its offline/CacheStorage journey passes under the opt-in. - master-search-header.tsx: close the desktop mode menu on Tab from the trigger (APG menu-button pattern). WebKit's sequential focus navigation can fail to deliver a wrapper-escaping focusout (links excluded from its Tab order; backward wrap into the menu), leaving the menu open. - ui-accessibility.spec.ts: webkit skip for the forced-colors token test — WebKit has no forced-colors implementation, so the media remap under test cannot engage there. - ui-formulation.spec.ts: pin the step-nav Previous button enabled with opacity 1 before the axe scan — WebKit can serve a stale :disabled computed style whose 0.4 opacity axe folds into a phantom contrast violation for a WCAG-1.4.3-exempt state. - ui-smoke.spec.ts: step over Firefox's scrollable-container tab stop (the sheet body sits between Close and 'New chat' in DOM order). - scripts/eval-retrieval.ts: ciwa -> ciwa-ar content alias. The matcher is whitespace-delimited, so the bare fixture term can never match the scale's hyphenated written name; canary runs #50/#51 ranked the CIWA-Ar dosing-table region top-5 yet the gate reported a miss. - tests/helpers/zero-touch.ts: shared stubZeroTouchPoints helper replacing the six inline copies from #995 (review follow-up). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EXsJcLrbZUXwnBeG91cVo9
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Saves local Codex changes for review.