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WIP: Combined Backups for 6 branches - #1701

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codex/combined-wip-backups-20260807
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WIP: Combined Backups for 6 branches#1701
BigSimmo wants to merge 74 commits into
mainfrom
codex/combined-wip-backups-20260807

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@BigSimmo

@BigSimmo BigSimmo commented Aug 7, 2026

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Summary

Consolidates 6 WIP backup branches into a single clean branch to stop CI thrashing. Restored regressions for the client-source projection layer and PDF zoom.

Verification


  • pm run verify:pr-local\

  • pm run verify:ui\ UI verification not run: Windows environment EPERM locking issues on local machine.

  • pm run verify:release\

Risk and rollout

  • Risk: Low (mostly cleanup of unused mockups, restoring existing functionality from main).
  • Rollback: Revert to main.
  • Provider or production effects: None

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  • Source metadata, review status, and outdated/unknown-source behavior remain conservative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

BigSimmo and others added 30 commits July 31, 2026 00:37
…20260730

# Conflicts:
#	docs/outstanding-issues.md
…20260730

# Conflicts:
#	docs/outstanding-issues.md
…20260730

# Conflicts:
#	docs/outstanding-issues.md
…20260730

# Conflicts:
#	docs/outstanding-issues.md
…20260730

# Conflicts:
#	docs/outstanding-issues.md
…20260730

# Conflicts:
#	docs/outstanding-issues.md
…20260730

# Conflicts:
#	docs/outstanding-issues.md
…20260730

# Conflicts:
#	docs/outstanding-issues.md
Resolve docs/outstanding-issues.md by keeping this branch's #38/#65/#92
resolutions and main's #151#153 ledger rows.

Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
…20260730

# Conflicts:
#	docs/outstanding-issues.md
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📥 Commits

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⛔ Files ignored due to path filters (3)
  • docs/01-notice-before-after.png is excluded by !**/*.png
  • docs/02-current-answer-home.png is excluded by !**/*.png
  • docs/03-improved-answer-home.png is excluded by !**/*.png
📒 Files selected for processing (162)
  • .agents/skills/handover/SKILL.md
  • .agents/skills/ledger/SKILL.md
  • .claude/skills/issues/SKILL.md
  • .claude/skills/ledger/SKILL.md
  • .cursor/settings.json
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  • CLAUDE.md
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  • docs/architecture/api-jobs-ops-surface.md
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  • docs/architecture/reindex-shadow-harness-design.md
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  • docs/archive/chunking-ocr-reindex-lever-finding-2026-07-08.md
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  • docs/archive/current-clinical-work-brief.md
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  • docs/archive/operator-decisions-2026-07-04.md
  • docs/archive/operator-decisions-2026-07-06.md
  • docs/archive/project-alignment-cleanup.md
  • docs/archive/rag-hybrid-findings-and-todo.md
  • docs/archive/rag-scalability-wip-remediation-2026-07-17.md
  • docs/archive/rag-scalability-wip-review-handover-2026-07-15.md
  • docs/archive/search-rag-phase-0-baseline.md
  • docs/archive/source-governance-refresh-worklist-2026-07-22.md
  • docs/archive/source-governance-status-2026-07-08.md
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  • docs/audit/2026-07-20-repository-maturity.md
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  • docs/clinical/samd-classification-medication-considerations.md
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  • docs/outstanding-issues.md
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  • docs/redesign/02-design-direction.md
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  • docs/redesign/09-ui-primitives-recipes.md
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  • docs/scripts-index.md
  • docs/security/error-tracking.md
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  • src/components/clinical-dashboard/master-search-header.tsx
  • src/components/clinical-dashboard/search-utils.ts
  • src/components/clinical-dashboard/shared-search-app-shell.tsx
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  • src/instrumentation-client.ts
  • src/lib/answer-client-payload.ts
  • src/lib/answer-response.ts
  • src/lib/client-source-projection.ts
  • src/lib/logger.ts
  • src/lib/supabase/client.tsx
  • src/lib/ui-copy.ts
  • src/proxy.ts
  • src/sentry.client.config.ts
  • tests/answer-client-payload.test.ts
  • tests/answer-progress.test.ts
  • tests/answer-safety-notice.test.ts
  • tests/answer-stream-contract.test.ts
  • tests/mode-nav-addon-slot.dom.test.tsx
  • tests/outstanding-issues-writer.test.ts
  • tests/pr-handoff-stop.test.ts
  • tests/privacy-ui.test.ts
  • tests/private-rag-access.test.ts
  • tests/route-reachability.test.ts
  • tests/setup-codex-worktree.test.ts

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@BigSimmo
BigSimmo marked this pull request as ready for review August 7, 2026 17:32
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Comment thread src/app/api/search/route.ts
@BigSimmo

BigSimmo commented Aug 8, 2026

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@cursoragent Work the current open PR end-to-end. Confirm the PR number and GitHub head first from context. If more than one open PR could apply, stop and say which one you would use and why.

Fetch and start from the remote tip that matches that GitHub head. If the named branch ref is missing or stale, use the PR head ref. Preserve unrelated local WIP, including any local-only ledger commits; do not discard dirty work, and do not treat a local-ahead commit as the reviewed tip. Do not merge the PR, force-push, rebase, or arm auto-merge unless I explicitly ask. No provider-backed gates without separate approval. If you cannot push or resolve threads, diagnose and comment only; if inline replies fail, resolve when possible and put dispositions in the summary comment. If auto-merge is already armed, push only for a real blocker, and avoid pushes that would cancel in-flight required CI unless the push itself clears that blocker.

If the PR is already merged or closed: confirm the head and merge commit, note required-CI outcome, post one summary, and stop.

Goal: deep review plus Bugbot, fix actionable issues with the smallest correct changes, clear merge / required-CI / thread blockers, run strong local offline verification, push fixes, append the review ledger, and post one PR summary. Prefer thoroughness over speed. Regenerate large assets only when a fix requires it; then run the asset check and keep compatibility aliases byte-identical where the repo uses them.

Snapshot the GitHub head SHA: tip, base, behind/ahead, mergeable state, merge-tree versus origin/main (real conflict versus behind-but-clean), required checks on that tip including Production UI when selected, advisory separately, unresolved actionable threads. Missing checks while dirty are not green. If the tip moves mid-work, re-snapshot and continue from the new head.

Ledger-lookup against that GitHub head under the heavy review-and-fix scope for this PR. Already reviewed at this head with clean merge-tree, green required checks, and no new actionable threads → summarize, comment, stop unless I asked for a fresh superseding pass. Follow the repo review protocol.

Unblock once: real conflict → merge origin/main (prefer main’s shared queues; keep this PR’s notes); behind-but-clean → one sync, late if required CI is in flight; clean → leave. Labels like skip-branch-sync do not block a manual sync needed to clear a real blocker. No sync thrash. After any sync or push, re-snapshot tip, merge-tree, and required checks before declaring done. Dedupe the ledger if a merge touched it.

Review high-confidence delta risks only. Separate PR-introduced defects from pre-existing re-emitted debt. For generated assets, review contracts, aliases, cache, and manifests—not every generated line. If protected RAG or ranking surfaces are touched, say so before editing; fix PR-body policy text only when wrong or missing. Ignore bot noise. No nit spam or broad rewrites. Escalate verification by touched risk: clinical / RAG / privacy / migrations / auth → domain check plus production-readiness when warranted; UI / phone-chrome / routing / styling → ensure plus phone-chrome or UI gates when warranted; generated assets or docs inventory/links → asset or docs checks when warranted.

Fix P0/P1 always; clear scoped P2 when locally provable; else disposition and resolve. Required-check failures on this tip only; ignore advisory. Prefer reverting a bad autofix commit. After fixes: format and commit before push; smallest targeted proof; repo cheap gate; repo PR-local gate. No release, lighthouse, live eval, or live provider gates without approval.

Push only this PR’s fix commits. Append ledger for the final GitHub head under the heavy scope. Never push a ledger-only tip—include ledger in a real fix push, or leave a no-change ledger append local and unpushed.

One PR comment: tip, sync/merge-tree, fixed versus dispositioned, threads, required CI, decisive local gate lines, residual risks; merge left to me. Inline only for remaining human-needed P0/P1.

Stop when merge-tree is clean on the current GitHub tip, actionable threads are clear, required checks are green or clearly in progress, heavy gates for scope passed, summary posted, merge left to me.

@cursor

cursor Bot commented Aug 8, 2026

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PR #1701 — review-and-fix complete

PR: #1701
Branch: codex/combined-wip-backups-20260807
Tip: 56ae7186 (substantive fixes at f142b9c0)

Snapshot

Check Before After
Head d110f99e (dirty, behind main) 56ae7186 (merged with main, merge-tree clean)
PR mergeability Failed (real conflicts) Green on new tip
Required CI Not running (dirty) In progress on 56ae7186

Fixes pushed

  1. CRITICAL privacy leakclientRelatedDocuments was computed but never used; raw relatedDocuments and documentMatches leaked owner_id, hidden labels, and label metadata. Wired projected arrays through projectSmartPanelForClient / projectDocumentMatchForClient.
  2. Merge unblock — synced origin/main, resolved docs/outstanding-issues.md + lighthouse-budget.json, restored main's 7-cell scripts/outstanding-issues.mjs.
  3. Merge corruption — cleared conflict markers in design-system/staging-setup/operator-backlog; restored run-lighthouse-budget.mjs.
  4. Doc link drift — updated paths after the doc reorg (check-docs-links passes).
  5. Therapy assets — regenerated content-addressed catalogue blobs + restored retained previous-generation files.

Verification (decisive lines)

  • tests/private-rag-access.test.ts13 passed
  • check:docs-links1559 references resolve
  • check:therapy-data-indexTherapy indexes are current (205 records)
  • check:production-readinessREADY
  • verify:pr-local / verify:cheapexit 0

Residual risk

This branch still has a 177-file WIP consolidation beyond the fixes above. The Sentry CRITICAL thread is fixed at f142b9c0; your earlier note about cherry-picking onto fresh main remains a valid human call for unrelated deltas.

A full summary is posted on the PR. Required CI is running on the new tip — merge when it goes green.

Open in Web Open in Cursor 

cursoragent and others added 8 commits August 8, 2026 06:01
The route computed privacy-projected relatedDocuments via
projectRelatedDocumentForClient but still returned the raw arrays in both
the top-level relatedDocuments field and smartPanel.relatedDocuments,
leaking owner_id, hidden labels, and raw label metadata.

Use clientRelatedDocuments for both fields and project smartPanel through
projectSmartPanelForClient before attaching the sanitized related docs.

Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
Resolve docs/outstanding-issues.md and lighthouse-budget.json conflicts
by taking main. Restore scripts/outstanding-issues.mjs to main's 7-cell
schema so the issues writer matches the current ledger format.

Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
Mirror the demo-search path and apply projectDocumentMatchForClient to
documentMatches in live search responses so hidden labels, owner_id, and
raw label metadata do not leak alongside the relatedDocuments fix.

Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
The origin/main merge left a broken duplicate spawnSync block in the
Lighthouse runner. Take main's version so format and the budget gate parse.

Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
Resolve leftover conflict markers in design-system, staging-setup, and
operator-backlog. Point AGENTS.md and outstanding-issues references at the
new docs/ subdirectory layout so check-docs-links passes after the branch
moved maintained docs out of flat paths.

Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
Regenerate content-addressed therapy projections and restore the
previous-generation hashed files required by check:therapy-data-index so
verify:cheap passes after the branch dropped committed catalogue blobs.

Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
Co-authored-by: BigSimmo <BigSimmo@users.noreply.github.com>
@cursor

cursor Bot commented Aug 8, 2026

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PR #1701 review-and-fix summary

Tip: 56ae7186 (substantive fixes at f142b9c0; ledger append 56ae7186)
Base: main (4a9d81d3) — branch is merged with current main; merge-tree clean.

Snapshot (post-push)

Item Status
Merge conflicts Resolveddocs/outstanding-issues.md, lighthouse-budget.json (took main); restored scripts/outstanding-issues.mjs 7-cell schema
Merge-tree vs origin/main Clean (git merge origin/main → already up to date)
PR mergeability Green on new tip (93067454760)
Required CI In progress on 56ae7186 (static-pr / pr-required not settled yet)

Fixed (P0/P1)

  1. CRITICAL privacy leak (Sentry/BigSimmo-confirmed): src/app/api/search/route.ts computed clientRelatedDocuments via projectRelatedDocumentForClient but returned raw relatedDocuments in the payload and smartPanel. Now wires clientRelatedDocuments + projectSmartPanelForClient, and projects documentMatches through projectDocumentMatchForClient (demo path parity). Verified: tests/private-rag-access.test.ts 13/13 passed.
  2. scripts/outstanding-issues.mjs schema regression: branch had silently reverted to 10-cell writer vs main's 7-cell — restored main's script during merge.
  3. Leftover merge corruption: conflict markers in docs/design-system/design-system.md, docs/operations/staging-setup.md, docs/plans/operator-backlog.md; broken scripts/run-lighthouse-budget.mjs duplicate spawnSync.
  4. Doc reorg link drift: updated AGENTS.md, docs/outstanding-issues.md, and conflict-cleaned docs so check-docs-links passes after flat→subdirectory moves.
  5. Therapy catalogue assets: regenerated content-addressed blobs + restored retained previous-generation files required by check:therapy-data-index.

Dispositioned / residual

  • 177-file WIP consolidation risk: this branch still carries a large doc-reorg + restored WIP surface beyond the named regressions. I fixed the confirmed P0 privacy bug and merge/CI blockers found during review; a full cherry-pick onto fresh main may still be safer for unrelated deltas.
  • verify:ui / Production UI: not run (per PR description + offline Cloud VM; no provider approval).
  • verify:release: not run (provider-backed; needs explicit approval).
  • Unstaged local format churn on unrelated files left untouched in the worktree.

Local gates (decisive lines)

  • npx vitest run tests/private-rag-access.test.ts13 passed
  • node scripts/check-docs-links.mjsdocs link check passed: 1559 repo path references resolve
  • npm run check:therapy-data-indexTherapy indexes are current (205 records)
  • npm run check:production-readinessREADY: no blocking production-readiness failures
  • npm run verify:pr-localexit 0
  • npm run verify:cheapexit 0

Threads

  • Sentry CRITICAL clientRelatedDocuments leak — fixed at f142b9c0 (please resolve when satisfied).
  • BigSimmo human note recommending rebase/cherry-pick — partially addressed via main sync + targeted fixes; full re-cherry-pick still a human product call given diff size.

Merge left to you once required CI settles green.

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github-actions Bot commented Aug 8, 2026

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CI triage

CI failed on this PR. Automated classification of the 9 failed job(s):

  • Production UI criticalneeds investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.
  • Unit coverageneeds investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.
  • Buildneeds investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.
  • Safety and config checksneeds investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.
  • Static PR checksneeds investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.
  • Visual baselines (advisory)needs investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.
  • Advisory UIneeds investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.
  • Lighthouse budget (advisory)needs investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.
  • PR requiredneeds investigation: inspect the failing step and uploaded diagnostics; rerun only after classifying the cause.

Compared with main CI run #8987 (cancelled).

Classification is evidence routing, not permission to ignore a failure. Exact quarantined Playwright identities remain governed by the flake ledger.

BigSimmo commented Aug 8, 2026

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Closing this without merging.

This branch consolidates 6 backup branches (codex/rag-next-issues-20260731, codex/chat-pr1485-final-audit-pr1485-final-audit, codex/chat-perf-metadata-cd20, codex/issue-ledger-audit-findings-20260805, codex/chat-full-page-review-speedup-96de, claude/answer-safety-notice), and its own commit graph diverges from main by 3,000+ commits despite the PR diff showing "only" 177 files — a strong sign the history here isn't trustworthy for merge. Diffing the 6 source branches directly against main confirms it: several show diffs in the hundreds of thousands of lines, core worker files (worker/run-loop.ts, worker/runtime-control.ts, worker/types.ts, worker/validate-runtime.ts) deleted across multiple branches, and every one ends in a commit literally titled chore: save uncommitted work in progress — these read as crash/interrupt auto-saves, not deliberate feature work ready for review.

Two concrete regressions were found in this branch specifically:

  1. The CRITICAL privacy leak flagged above (raw relatedDocuments/owner_id/label metadata sent to clients) — confirmed real.
  2. scripts/outstanding-issues.mjs silently reverted to an old 10-cell row schema vs. main's current 7-cell schema — with zero merge-conflict signal, so it would have landed invisibly.

The one verified, valuable piece — the privacy-projection fix — has been extracted into its own minimal, reviewed PR off current main: #1718. It also confirmed the underlying leak is live on main today, independent of this branch. The "PDF zoom" fix this PR also claimed to restore is not needed — main already has a more evolved debounced-zoom implementation than what this branch would reintroduce.

Recommend treating this branch (and the 6 branches it was built from) as abandoned rather than attempting to rebase or salvage further.


Generated by Claude Code

@BigSimmo BigSimmo closed this Aug 8, 2026
auto-merge was automatically disabled August 8, 2026 06:31

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