fix(plugin): keep resolved checkpoint deferrals closed

[rohanpoudel2]

Summary

Fixes #741.

Interim scan checkpoints intentionally preserve deferred coverage so later writers cannot erase unfinished work by omission. That preservation also restored a linked deferral after the final draft had explicitly given every referenced surface a terminal disposition. The restored row downgraded otherwise complete coverage to partial and made the canonical result contradict the final draft.

Treat a deferral linked through surfaceIds as resolved only when every referenced surface has an unambiguous terminal outcome in the current draft. Historical checkpoint files remain unchanged.

Changes

• Reconnect workbench-owned historical surface IDs to terminal semantic surfaces when the current draft omits derived IDs.
• Drop an earlier linked deferral and its stale needs_follow_up surface only when all of the deferral's surface references resolve.
• Preserve unlinked, missing, partially resolved, and duplicate-ambiguous surface work.
• Cover successful terminal reconciliation, immutable checkpoint history, and the ambiguous duplicate-surface control through the real scan artifact writer.

Testing

• pnpm --dir plugins/codex-security/mcp-app exec node --test tests/test_artifact_scan_draft.mjs — passed.
• pnpm --dir sdk/typescript run test:mcp — 23 passed, 0 failed.
• pnpm run types from sdk/typescript/ — passed; Node 25 emitted the repository's unsupported-engine warning.
• pnpm run format from sdk/typescript/ — passed.
• uv run --no-project --with ruff==0.16.1 python -m ruff check --config plugins/codex-security/pyproject.toml .github/scripts/check_plugin_source_compatibility.py .github/scripts/test_check_plugin_source_compatibility.py plugins/codex-security — passed.
• uv run --no-project --with ruff==0.16.1 python -m ruff format --check --config plugins/codex-security/pyproject.toml .github/scripts/check_plugin_source_compatibility.py .github/scripts/test_check_plugin_source_compatibility.py plugins/codex-security — 137 files already formatted.
• python .github/scripts/check_plugin_source_compatibility.py — passed.
• git diff --check — passed.
• pnpm run test --seed 12345 was attempted on unsupported Node 25 and was not used as passing validation. It reported seven failures in unchanged deduplication-review fixture cases, one unchanged workflow-fixture parse failure, and one ZIP-path stress test exceeded 30 seconds but passed in an isolated rerun. The broader run later stopped producing output and was interrupted. Focused reruns reproduced the first two unrelated failures; supported Node 22, 24, and 26 remain covered by hosted CI.

Risk and rollout

The reconciliation rule is limited to deferred rows with a nonempty surfaceIds list whose every reference resolves to one terminal surface. Missing references, follow-up outcomes, and duplicate semantic surfaces remain deferred, so the existing loss-prevention behavior stays in place. No public CLI, schema, stored-artifact format, dependency, or migration changes are required.

Public disclosure review

• No customer, partner, prospect, or user identities, data, or identifying details are included.
• No credentials, personal data, private source, scan findings, or nonpublic links or tickets are included.
• I reviewed the branch name, title, description, commits, changes, comments, logs, screenshots, attachments, and links for public disclosure.

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-01T03:26:29.465958Z	bbbaca4	Manual request
🔒 Security Review	✅ Completed 2026-09-01T04:18:51.124324Z	e896031	New commits

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