fix(native): make Retry work after a turn start cut off once Codex recorded the turn (#20516)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A native Codex run sends `turn/start` through its runner. A
control-plane restart can kill the runner and Codex while that request
is in flight
> - #20507 lets the runner resume by itself when Codex's thread history
proves the turn was never created. When Codex did record the turn, the
turn may have done work, so the runner still fails closed and nothing
replays it
> - That branch must still end in a Retry that works. The next run on
the same conversation is refused at the runner-state fence before it
asks for a runner. #20507 let Retry continue after that run by matching
the refusal's error text
> - Driving that branch end to end with the real runner exposed a second
dead end. When the owner's runner dies, its provider-session close
cannot prove suspension, so this server process can keep an
operator-required cleanup quarantine for the task. Retry was then
refused outright ("Send a new message")
> - This pull request replaces the text match with a server-authored
run-log event, lets Retry take the same verified-stop path as a new
message, and adds a real-runner test of the whole branch: the cut-off
owner fails closed, the follow-up is refused with structured proof,
Retry is admitted, and the fresh Retry run completes
> - The benefit is that this restart window cannot strand a task, and
the Retry gate no longer depends on error wording

## Linked Issues or Issue Description

**What happened?**
Follow-up to #20507 (restart-chaos wave `w-20261110T033426-s108`, t03).
#20507 left one item open: prove that a person's Retry produces a
working run when the restart cut off `turn.start` after Codex recorded
the turn. It also matched the fence refusal by its error text.

**Expected behavior**
After that cut-off, the owner stays failed closed and the turn is never
started again by itself. A person's Retry starts a new run that
completes. It never fails with `quarantine_owner_unverified` and never
returns 202 with no run.

**Steps to reproduce**
1. Run `pnpm --filter @paperclipai/server exec vitest run
src/services/native-runtime/native-cut-turn-start-retry.integration.test.ts`.
2. Without the new event, the test fails: the refused follow-up has no
proof that it never launched, so Retry after it would wait on
`process_identity_missing`.

## What Changed

- `native-session-executor.ts`: when the runner-state fence refuses a
run before launch (`prior_owner_*` or `legacy_prior_owner_*`), the
executor records the server-authored event
`native.prior_owner_fence_refused` with the closed refusal `reason`,
then fails the run as before. A failed write leaves the run held (the
safe side).
- `native-local-process-stop.ts`: `nativeRunNeverLaunched` accepts a
failed run that has this event (and still no launch, identity,
`adapter.invoke` or runner-sourced event). It no longer reads the error
text.
- `explicit-native-continuation.ts`: when the task's in-process cleanup
quarantine is operator-required, a Retry no longer returns
`cleanup_quarantined` at once. Like a new message, it must first pass
`verifyStoppedNativeSessionForContinuation`, which releases the
quarantine and records `native.stopped_conversation_verified`. A native
Retry always starts a fresh conversation (`forceFreshSession`), so it
never resumes the interrupted turn. If the proof fails, Retry still
returns `cleanup_quarantined`.
- `verifyStoppedNativeSessionForContinuation`
(`native-session-executor.ts`), three narrow additions:
- a run with `native.prior_owner_fence_refused` may stand in for the
saved state's owner, like a run refused by the cleanup quarantine (both
were refused before launch);
- when the session root is gone, it reads the fence's single
`identity_indeterminate` quarantined copy of the owner's state (several
copies stay ambiguous);
- a provider startup attempt in phase `initialization_failed` whose
direct child exited and whose process and process group are gone no
longer blocks the proof. A same-run restore that fails closed leaves
exactly this record. Those PIDs are also re-checked before the
quarantine is released.
- New real-runnerd integration test
`native-cut-turn-start-retry.integration.test.ts` (real runnerd and fake
Codex with `--hang-turn-start after`):
1. The owner run's `turn/start` hangs after Codex recorded the turn; the
runner and Codex are killed. The owner's provider state keeps the
ambiguous start, and the thread history keeps the turn.
2. The same-run resume restores the runner and fails closed with "cannot
safely recover an ambiguous Codex turn start". Codex saw exactly one
`turn/start`.
3. A follow-up on the same conversation is refused with `prior_owner_*`,
never `quarantine_owner_unverified`. It records
`native.prior_owner_fence_refused`, launches nothing, and
`nativeRunNeverLaunched` is true for it.
4. The owner's operator-required in-process cleanup quarantine is pinned
(whether the real close lands there is timing-dependent; about half of
the local runs did).
5. Retry of the refused follow-up passes
`admitExplicitNativeContinuation` (not a dry run) with no block reason,
releases the quarantine and records
`native.stopped_conversation_verified`.
6. The Retry run, prepared with a fresh conversation as task Retry does
(`forceFreshSession`), uses a different runner-state root and completes
with exit code 0. Codex saw one new `thread/start` and one new
`turn/start`; the cut-off turn was never started again.
- `explicit-native-continuation.test.ts`: the fence rows now insert the
event. A new row shows that the refusal text alone keeps the run held.
The "worker loss (retry)" case now expects a verified Retry to be
admitted like a new message.
- `native-recovered-owner-followup.test.ts`: a fixture event moves to a
free sequence number, because the refused follow-up now writes its own
event.
- Docs: `doc/run-log-events.md` (new event) and
`packages/paperclip-runner/docs/durable-recovery.md`.

## Verification

- Red/green:
- Without the event write, the integration test fails (no fence event,
so the follow-up is not proven unlaunched).
- Without the gate and proof changes, it fails with `expected [
'cleanup_quarantined' ] to deeply equal []`: Retry is refused while the
owner's quarantine is held.
  - With all changes, it passes.
- `vitest run` of `native-recovered-owner-followup`,
`explicit-native-continuation` (427 tests), `quarantined-task-retry`,
`issue-confirm-run-stopped-routes`, `native-finalization-recovery`,
`task-interruption-query`, `execution-projection`,
`chat-run-publications`, `closed-native-receipt-accounting`,
`agent-live-run-routes` and the new integration test pass.
- Server `tsc --noEmit` passes.
- Runner code and the pack `contractDigest` do not change.

## Risks

- Low-medium risk. The new event is written only on the fence refusal
path, which already fails the run. It is local run-log data (no
Telemetry or OpenTelemetry).
- Retry after an operator-required cleanup quarantine is a behaviour
change: it was always refused, and now it is admitted only after the
same exact stop proof a new message needs. That proof checks the owner's
runner stop record, every recorded provider and startup PID and process
group, and the unchanged state fingerprint before it releases the
quarantine.
- A run refused by a build between #20507 and this change has only the
error text. It stays held on `process_identity_missing` until a person
sends a new message or the board confirms the stop. #20507 has not
shipped in a release yet.
- The test models the restart in-process: it kills the runner and Codex
and calls the executor again. It does not drive the HTTP Retry route;
the route's own behaviour (fresh conversation, admission gate) is
covered by existing tests and by `nativeRunNeverLaunched` here.
- Open decision, unchanged: a turn Codex recorded before the restart is
never replayed or adopted. Continuing is a person's decision.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), via Claude Code with tool use
(shell, file edits, test execution).

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

Refs #20507

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude <noreply@anthropic.com>

scripts/__tests__/run-vitest-stable-shard.test.mjs

@@ -329,6 +329,7 @@ const pluginEvictionSuitePath = "server/src/services/native-runtime/plugin-runne
 const dotRunnerSuitePath = "server/src/__tests__/dot-runner.test.ts";
 const restartRecoverySuitePath =
   "server/src/services/native-runtime/native-runner-restart-recovery.integration.test.ts";
+const cutTurnStartRetrySuitePath = "server/src/services/native-runtime/native-cut-turn-start-retry.integration.test.ts";
 const restartWaitSuites = ["lease-renewal", "preparation", "checkpoint-cost", "diskless"]
   .map(name => `server/src/services/native-runtime/native-runner-restart-${name}.integration.test.ts`);
 
@@ -372,12 +373,13 @@ test("12 PR without-chat shards plus the dedicated chat and native-runner lanes
   assert.ok(!files.includes(ingressRetrySuitePath));
   assert.ok(!files.includes(dotRunnerSuitePath));
   assert.ok(!files.includes(restartRecoverySuitePath));
+  assert.ok(!files.includes(cutTurnStartRetrySuitePath));
   assert.ok(!files.includes(usageDeliverySuitePath));
   assert.ok(!files.includes(warmCheckpointOwnershipSuitePath));
   assert.ok(!files.includes(pluginWarmOwnerSuitePath));
   assert.ok(!files.includes(pluginReleaseResumeSuitePath));
   assert.ok(!files.includes(pluginEvictionSuitePath));
-  assert.deepEqual([...files, chatSuitePath, nativeRunnerSuitePath, ingressRetrySuitePath, dotRunnerSuitePath, restartRecoverySuitePath, ...restartWaitSuites, usageDeliverySuitePath, warmCheckpointOwnershipSuitePath, pluginWarmOwnerSuitePath, pluginReleaseResumeSuitePath, pluginEvictionSuitePath, "server/src/services/native-runtime/plugin-runner-probe.test.ts"].sort(), full.selectedGeneralServerSuites.sort());
+  assert.deepEqual([...files, chatSuitePath, nativeRunnerSuitePath, ingressRetrySuitePath, dotRunnerSuitePath, restartRecoverySuitePath, ...restartWaitSuites, cutTurnStartRetrySuitePath, usageDeliverySuitePath, warmCheckpointOwnershipSuitePath, pluginWarmOwnerSuitePath, pluginReleaseResumeSuitePath, pluginEvictionSuitePath, "server/src/services/native-runtime/plugin-runner-probe.test.ts"].sort(), full.selectedGeneralServerSuites.sort());
   assert.equal(new Set(files).size, files.length);
   const defaultRun = dryRunJson([], prEnv);
   assert.ok(defaultRun.generalServerSuiteCount === full.generalServerSuiteCount);
@@ -432,6 +434,7 @@ test("the native-runner lane runs exactly the cargo-dependent suites", () => {
     dotRunnerSuitePath,
     restartRecoverySuitePath,
     ...restartWaitSuites,
+    cutTurnStartRetrySuitePath,
     usageDeliverySuitePath,
     warmCheckpointOwnershipSuitePath,
     pluginWarmOwnerSuitePath,

scripts/run-vitest-stable.mjs

@@ -103,6 +103,7 @@ const nativeRunnerSuites = [
   "server/src/services/native-runtime/native-runner-restart-preparation.integration.test.ts",
   "server/src/services/native-runtime/native-runner-restart-checkpoint-cost.integration.test.ts",
   "server/src/services/native-runtime/native-runner-restart-diskless.integration.test.ts",
+  "server/src/services/native-runtime/native-cut-turn-start-retry.integration.test.ts",
   "server/src/services/native-runtime/native-usage-delivery.integration.test.ts",
   "server/src/services/native-runtime/native-warm-checkpoint-ownership.integration.test.ts",
   "server/src/services/native-runtime/plugin-runner-task-warm.integration.test.ts",