fix(store): persist periodic SQLite cleanup and retry failed deletes

[DeliciousBuding]

Summary

• Persist SQLite's periodic retention deletes instead of removing runs and evidence only from memory.
• Keep failed cleanup commits pending for the next timer tick, even when no more runs expire; preserve the existing in-memory-on-write-failure contract and LastPersistError reporting.
• Stop and join both constructor-owned background loops before final shutdown persistence/database close.
• Reuse the existing persistence machinery and fixture helpers; update the stable store lifecycle documentation. No new constructor seam, schema or storage abstraction.

Closes #2343

Verification

Four focused tests use real SQLite with testing/synctest virtual time to drive the constructor's unchanged production cadence: durable deletion before close, retry after SQL trigger failure, close flushing pending cleanup and close waiting for owned work. The reopen helper deliberately bypasses final Close/Flush persistence, so shutdown cannot conceal a missing background commit. Unrelated queued run/checkpoint data is retained.

Three temporary negative controls each failed for the intended behavioral reason and were restored byte-for-byte:

• Disable periodic persistence: six expired rows survive and reappear after reopen.
• Discard pending retry state: next tick leaves the six rows and the observed persist error.
• Remove shutdown join: close returns and the DB closes before owned work is released.

Passed locally using Go 1.26.5:

• Windows, CGO_ENABLED=0: go test -p 2 ./internal/store ./internal/api -count=1 -cpu=4 -timeout=10m.
• Linux, CGO_ENABLED=1: go test -race -p 2 ./internal/store ./internal/api -count=1 -cpu=4 -timeout=10m.
• go vet -p 2 ./internal/store ./internal/api; staticcheck ./internal/store ./internal/api; gofmt clean.
• Existing verify-doc-ssot.py, verify-project-skills.py, verify-real-e2e-contract.py, OpenAPI YAML parse and git diff --check. Skills-specific checks report their existing absent-root skip/trivial-pass boundary; this is not real E2E.

Boundaries / pending

The 5-minute cadence, 24-hour terminal TTL, 50-per-thread cap, terminal states, cascade membership, public API, SQL/schema, connection pool, PRAGMAs and WAL policy are unchanged. No runtime configuration, deployment, restart or real workspace-file deletion. This is local SQLite durability/fault-injection evidence, not a production-load, real process-kill, live-login or packaged Desktop claim. All seven required checks passed on df01b0e1cc8eefba209e6125af2205407233cd66; checks workflow 34034111396 completed successfully. Frontend-only lanes were intentionally path-filtered. CodeRabbit reported Review skipped; this is not an automated review approval.

[coderabbitai]

Important

Review skipped

Auto reviews are disabled on this repository. Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Team

Run ID: 09a5371a-d173-4a98-8267-3c4c42e819ee

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

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