Cover repository migrations and settings cache invalidation (codex)

[numnx]

🧩 Task: Cover repository migrations and settings cache invalidation

Automated task PR opened by Code UX for T03.

📋 Summary

Sprint: Sprint 143 · QS: Coverage Observability and CI Reliability Audit · Task: T03

Strengthen Code UX coverage observability and CI reliability through enforceable tests, workflow hardening, structured observability guarantees, security validation, and aligned operational documentation without lowering coverage thresholds.

📝 Full Task Prompt

## Objective
Close persistence coverage gaps by enforcing repository migration idempotency, scoped settings defaults, and cache invalidation guarantees.

## Scope
- `src/repositories/db/app-db-migrations.ts`
- `src/repositories/db/app-db-schema.ts`
- `src/repositories/app-db-storage.ts`
- `src/repositories/settings-repository.ts`
- `tests/backend/repositories/db/app-db-schema.test.ts`
- `tests/backend/repositories/app-db-storage.test.ts`
- `tests/backend/repositories/settings-repository.test.ts`
- `docs/development/testing-and-quality.md`
- Current verification gap: schema/index and settings tests exist, but this sprint needs explicit audit coverage for migration replay, legacy rows, and scoped cache invalidation edge cases.
- Desired guarantee: migrations can run repeatedly on existing databases, legacy data is preserved, and effective settings caches invalidate after system, project, and sprint mutations.

## Implementation Requirements
1. Add migration replay tests that initialize a DB, run migrations multiple times, and assert expected columns/indexes/tables still exist without duplicate or destructive changes.
2. Add a legacy-shape test for at least one existing migration path, such as `guardrail_ledger` foreign key rebuild or token accounting backfill, proving data survives migration.
3. Extend settings repository tests to cover partial persisted settings, default fallback preservation, and invalidation after system/project/sprint resets or mutations.
4. Ensure all new tests use in-memory DB or the existing temp-home cleanup helpers and close SQLite handles before removing temp paths.
5. Update `docs/development/testing-and-quality.md` with the focused persistence verification commands and the migration idempotency expectation.

## Constraints
- Do not change schema semantics unless a test exposes a real bug; preserve existing data and indexes.
- Do not lower coverage thresholds or skip repository tests to satisfy coverage.
- Do not use real `~/.code-ux/app.db` in tests.
- Keep assertions behavioral rather than tied to incidental SQL formatting.

## Verification
- `pnpm run test:backend -- tests/backend/repositories/db/app-db-schema.test.ts tests/backend/repositories/app-db-storage.test.ts tests/backend/repositories/settings-repository.test.ts`
- `pnpm run test:backend:coverage`
- `pnpm run lint`
- Success means migration replay is idempotent, legacy rows survive, settings defaults remain backward compatible, and SQLite temp artifacts are cleaned up.

✅ QA Review

⏳ QA review runs after this PR is opened. Check the task card in the dashboard for the outcome once it lands.

🤖 Model & Provider

Provider	Codex CLI
Model	gpt-5.5

⏱️ Timing

Started	2026-07-06 19:02:59 UTC
Finished	2026-07-06 19:10:31 UTC
Duration	7m 32s

📊 Token Usage

Metric	Value
Input tokens	206,890
Cached input tokens	1,640,320
Output tokens	10,661
Total tokens	1,857,871
Invocations	1
Tool calls	48
Active time	6m 20s

Included usage estimate (subscription/local login): $2.17

🌿 Branch Info

Base: feature/CODUX-143-qs-coverage-observability-and-ci-reliability-audit-3
Head: task/feature-codux-143-qs-coverage-observability-and--t03-codex-mr9l84x6

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🤖 Generated by Code UX