docs: record RAG merge closure and fix route index

[BigSimmo]

Summary

• Record the completed RAG recovery and merge-closure review.
• Correct the stale /applications codebase-index target to its redirect route handler.

Verification

• npm run test — 301 files and 2,779 tests passed.
• npm run eval:rag:offline — 36 golden cases, 21 suites, and 294 tests passed.
• npx prettier --check docs/codebase-index.md docs/branch-review-ledger.md — passed.
• npm run docs:check-links — 892 references passed.
• npm run docs:check-scripts — 296 script references passed.
• git diff --check — passed.
• Verification not run: npm run verify:cheap was blocked twice at lint by active heavyweight jobs in other registered worktrees; the check was not retried.
• Verification not run: no Supabase, OpenAI, live retrieval, production-readiness, deployment, or hosted-CI command was run.

Risk and rollout

• Docs-only change; no clinical behavior, source data, privacy boundary, provider configuration, or schema changes.
• The recovered RAG implementation was compared with fresh origin/main; source-scoped grounding, blocked-only extractive recovery, generic LAI recovery, latency diagnostics, and agitation retrieval protections are already present there.
• The branch-only source delta was proven unreachable and intentionally not reintroduced.

Summary by CodeRabbit

• Documentation
  • Updated the codebase index to accurately reference the applications route.
  • Added a review record documenting verification of RAG protections and local quality checks.
  • Noted that some hosted or provider-backed validation checks were unavailable or not run.

[supabase]

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[coderabbitai]

📝 Walkthrough

Walkthrough

Updates the branch review ledger with a 2026-07-18 verification record and corrects the /applications implementation reference in the codebase index.

Changes

Documentation updates

Layer / File(s)	Summary
Review ledger record docs/branch-review-ledger.md	Adds a record documenting RAG fix verification, the unreachable residual diff, and local check results.
Applications route index docs/codebase-index.md	Changes the /applications routing entry to reference src/app/applications/route.ts.

Estimated code review effort: 1 (Trivial) | ~3 minutes

Possibly related PRs

• BigSimmo/Database#591: Updates related /applications routing documentation.
• BigSimmo/Database#830: Updates the same dated review ledger entry.
• BigSimmo/Database#652: Adds a related review record to the same ledger.

Suggested labels: codex

Suggested reviewers: copilot, claude

🚥 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.
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 states the two main changes: RAG merge closure documentation and the route index fix.
Description check	✅ Passed	The summary, verification, and risk sections are present and detailed; only non-critical template sections like Notes and Clinical Governance Preflight are omitted.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/rag-merge-final-20260718-655a

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