chore: reconcile outstanding repository work

[BigSimmo]

Summary

• reconcile maintained task and planning docs so completed or superseded work is no longer presented as active
• update the codebase index for the current DSM/specifier route and mode structure
• prune redundant Knip configuration while retaining intentional server-only and operational ignores
• remove the unused default export from the signed-image component

Why

The repository had a small set of stale task documents, index entries, and dead-code configuration left after recently merged work. This commit resolves the locally actionable items and explicitly records the work that remains provider-gated or requires product/security decisions.

Areas touched

• maintained documentation and review ledger
• knip.json
• src/components/clinical-dashboard/signed-image.tsx

Verification

• npm run verify:pr-local -- --dry-run --files <changed files> — selected runtime, format, lint, typecheck, full unit tests, and production build
• runtime, Prettier, ESLint, and TypeScript phases passed
• full Vitest run: 2,456 passed, 1 skipped; two architecture-graph tests hit the default 30-second timeout under local contention, with no assertion failures
• npm run test -- tests/architecture-boundaries.test.ts --reporter=verbose --testTimeout=120000 — 6/6 passed
• npm run build — passed
• git diff --check — passed

Checks not run

• no live OpenAI, Supabase, Railway, ingestion, answer-generation, or other provider-backed checks
• no browser/UI gate because the only source change removes an unused export and does not alter rendering or behavior

Risk and governance

Low runtime risk. The source change is export-surface cleanup only. Provider-gated operational tasks and product/security decisions remain explicitly deferred in their owning documents rather than being silently marked complete.

Summary by CodeRabbit

• Breaking Changes

  • The SignedImage component is now exported only as a named export (default export removed), requiring import updates.

• Documentation

  • Refreshed planning/status and ledger materials with updated completion and reconciliation dates, and clearer “historical vs active” guidance.
  • Updated the codebase index with additional app modes, DSM-related route groups, and module mappings.
  • Refreshed ingestion concurrency fix, redesign deferred items, threat model status messaging, and related alignment notes.

• Maintenance

  • Improved codebase consistency-check configuration by adjusting entry/ignore patterns and narrowing ignored binaries.

[supabase]

This pull request has been ignored for the connected project sjrfecxgysukkwxsowpy because there are no changes detected in supabase directory. You can change this behaviour in Project Integrations Settings ↗︎.

---

Preview Branches by Supabase.
Learn more about Supabase Branching ↗︎.

[coderabbitai]

📝 Walkthrough

Walkthrough

The changes reconcile project-status documentation, refresh the ingestion workorder, expand the codebase index for DSM routes and data, narrow Knip configuration, and remove the SignedImage default export.

Changes

Repository reconciliation

Layer / File(s)	Summary
Reconcile project status records docs/README.md, docs/branch-review-ledger.md, docs/production-readiness-checklist.md, docs/project-alignment-cleanup.md, docs/rag-injection-threat-model.md, docs/redesign/*	Living and historical indexes, review records, readiness guidance, threat-model status, and redesign records are updated to reflect completed, resolved, maintained, or blocked work.
Refresh ingestion workorder state docs/ingestion-concurrency-fix-workorder.md	The workorder records live migration verification, database-function provenance, applied migration items, and remaining operator redeployment work.
Update application and clinical indexes docs/codebase-index.md	The index documents twelve app modes, additional DSM routes, the DSM clinical data module, and the corresponding clinical knowledge-base count.
Align static analysis and component exports knip.json, src/components/clinical-dashboard/signed-image.tsx	Knip entry, ignore, and binary settings are narrowed, and SignedImage remains available only as a named export.

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

Possibly related PRs

• BigSimmo/Database#652: Also modifies docs/branch-review-ledger.md by adding a review record.
• BigSimmo/Database#677: Also appends a dated review record to docs/branch-review-ledger.md.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title matches the main change: reconciling stale repository work across docs and cleanup tasks.
Description check	✅ Passed	The description is mostly complete and clearly covers summary, verification, scope, and deferred work, though it doesn't follow the template headings exactly.
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/outstanding-work-cleanup

---

_{Comment @coderabbitai help to get the list of available commands.}

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit:8d63f13755

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[BigSimmo]

@copilot resolve the merge conflicts on this branch.

[Copilot]

@copilot resolve the merge conflicts on this branch.

Merge conflicts resolved. The only conflict was in docs/branch-review-ledger.md at the end of the review table — both sides had appended new rows. The resolution keeps all rows from both sides (this branch's codex/outstanding-work-cleanup entry plus codex/design-polish-pass and codex/documents-closed-default from main). Committed in fix: remove conflict markers from branch-review-ledger.md.

[coderabbitai]

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 `@docs/codebase-index.md`:
- Line 63: Update the route index entry to distinguish the nested routes under
both `/specifiers/...` and `/formulation/...`, so `/builder`, `/compare`, and
`/map` are not presented as shared top-level URLs; preserve the existing
ownership mapping for `/specifiers` and its slug route.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro Plus

Run ID: 403ef85c-fb55-4e94-afcd-9327746b3152

📥 Commits

Reviewing files that changed from the base of the PR and between eccfb2e and 62e5d3c.

📒 Files selected for processing (1)

• docs/codebase-index.md