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Nicky LeachandClaude Opus 5.5 d95fdd8d79 feat(observability): span the unnamed gaps in run preparation (#20396)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Before a task reaches the agent, the server prepares the run: it
reads the task, the workspace and the configuration, and then hands the
run to the native controller
> - With an OTLP endpoint, each preparation step emits a
`heartbeat.prepare.<phase>` or `native.controller.<phase>` span
> - On a hosted test deployment, 0.3 to 0.5 s of each `task.prepare`
sits between those spans, and about 0.5 s more sits between
`execution.dispatch_admission` and `native.coordinator.claim`
> - Nobody can say which step is slow in that time, so latency work in
this area is guesswork
> - This pull request adds spans around the existing awaited work in
those gaps, with the existing timing helpers and naming conventions
> - The benefit is that a trace of a slow preparation now names the step
that used the time

## Linked Issues or Issue Description

**What existing behavior does this improve?**
The OpenTelemetry trace of task preparation. Today it has unnamed gaps
between the named preparation spans.

**Subsystem affected**
Server: heartbeat run preparation and the native controller
(`server/src/services/heartbeat.ts`,
`server/src/services/native-runtime/native-session-executor.ts`).

**Current behavior**
On a hosted test deployment (8 runs per group), `task.prepare` takes 2.6
to 3.4 s. Between `heartbeat.prepare.runtime_state` and
`heartbeat.prepare.run_identity`, about 0.25 s has no span. Between
`execution.dispatch_admission` and `native.coordinator.claim`, about 0.5
s has no span, and in one pair of runs it was 1.4 s. Nobody can tell
which step used that time.

**Proposed behavior**
Spans name the existing awaited reads and writes in those gaps. The
change adds no reads and records no content. The operator endpoint gate
and the no-operation behaviour stay.

**Reason and benefit**
Latency work in this area needs a measurement. With these spans, a trace
of a slow preparation names the step that used the time, so a fix can be
confirmed or rejected after deployment.

**Breaking changes**
None. The change adds span names to the closed list. It changes no API,
schema or behaviour.

**Additional context**
The server uses postgres.js, which the auto-instrumentation does not
cover, so database spans do not fill these gaps.

## What Changed

- `server/src/services/execution-preparation-timing.ts`: add the new
closed phase names.
- `server/src/services/heartbeat.ts`: add `heartbeat.prepare.*` spans
for `chat_retry_admission`, `workspace_selection`,
`dependency_readiness`, `issue_checkout`, `instance_settings`,
`workspace_context`, `project_context`, `plan_wake_routing`,
`routine_environment`, `responsible_user` and `execution_start`. The
re-reads of the issue after a checkout use the existing `issue_context`
name.
- `server/src/services/native-runtime/native-session-executor.ts`: add
`native.controller.*` spans for `attachment_staging`, `warm_restore`,
`span_persistence` (persistence of the preparation spans to the run log)
and `state_migration` before the coordinator claim.
- `doc/observability.md`: list the new spans.
- `server/src/__tests__/heartbeat-preparation-gap-spans.test.ts`: run a
real heartbeat through native preparation with an in-memory span
exporter. Check that each new span is emitted and that the new
preparation spans are children of `task.execution_attempt`.

## Verification

- `pnpm --filter @paperclipai/server typecheck`
- `npx vitest run src/__tests__/heartbeat-preparation-gap-spans.test.ts`
(fails without the source change, passes with it)
- `npx vitest run
src/services/heartbeat/preparation-timing-context.test.ts
src/services/execution-preparation-timing.test.ts
src/services/native-runtime/native-session-executor.test.ts
src/__tests__/heartbeat-context-compaction-execution.test.ts`

## Risks

- Low risk. The change only wraps existing awaited calls. Values and
errors pass through the timing helper unchanged, and a checkout conflict
still reaches the same `catch`.
- Phases of 50 ms or more inside `heartbeat.prepare.*` are also written
to the run log, as for the existing phases. This adds a few run-log rows
on slow runs.
- Without an OTLP endpoint, the helpers keep their current no-operation
behaviour.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude
Code with tool use (shell, file edits, test runs) and extended thinking.

## 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 15:27:58 -08:00
DottaandPaperclip 0e325e8d52 fix(runner): settle saved handoffs after verified shutdown (#20336)
## Thinking Path

> - Paperclip manages AI agents and their work.
> - An agent can save a question or approval handoff before its provider
stops.
> - A missing provider terminal notification does not prove that the
saved work failed.
> - Runner already verifies provider exit, event drain, tool settlement
and suspension.
> - This change uses that proof to settle the same saved handoff.
> - Unproven shutdown holds continuation and explains that the work is
saved.
> - Recovery must never repeat the completed work or allow overlapping
execution.

## Linked Issues or Issue Description

Refs #20330. That PR extends the Codex terminal drain window. This
change handles the separate case where no terminal arrives but the owned
shutdown can prove stopped execution.

**What happened?**

A native run saved a human handoff, accepted cancellation, and later
stopped its provider. The missing terminal notification still made the
attempt fail and show “Couldn’t finish this attempt.”

**Expected behavior**

Keep the saved handoff. Accept its yielded result after either an
authoritative provider terminal or verified shutdown of the exact
execution. If shutdown remains uncertain, retain the handoff and explain
the hold without offering a duplicate Retry.

**Steps to reproduce**

Save a governed wait, acknowledge interruption, and omit the provider
terminal. The new regression uses the real Runner binary and a
controlled Codex process. The old runtime rejects the handoff instead of
asking the existing shutdown owner to settle it.

**Deployment mode**

Native Runner with Codex. Local verification used macOS arm64 and Node
26.4.0. Hosted sandbox recovery has not been qualified.

## What Changed

- Add an optional driver shutdown-settlement operation. Runner returns
proof only after its existing stop, drain, tool settlement and
suspension barrier passes.
- Bind the receipt to the run, normalized session and turn. Persist it
with the saved wait and validate it during recovery.
- Complete the same yielded handoff after verified shutdown. Retire the
stopped session from warm reuse. Do not invent a provider terminal or
complete usage.
- Retain a named shutdown-pending condition under the existing bounded
same-run recovery policy. Preserve actual provider failures and
integrity failures.
- Show saved-work shutdown guidance in task and inbox presentation. Keep
genuine approvals authoritative and disable duplicate Retry.
- Document the completion and restart contract. The checkpoint field is
additive; older checkpoints retain the terminal-or-shutdown path.

## Verification

- Red: the new runtime regression failed against the original
implementation because verified shutdown was never requested. Server
presentation and error-classification regressions also failed before the
fix.
- Red: both inbox shutdown states showed generic text before the inbox
change.
- Green: Runner runtime, shutdown and harness-backend suites pass 301
tests. Tests cover missing terminals, failed stop proof, wrong identity,
cancellation, late proof, genuine provider failure, and restart after
receipt persistence. Recovery completes once without another model turn.
- Green: the native executor and task-presentation suites pass 1,371
tests. Execution projection, inbox and blocker presentation pass 125
tests. Two test-authoring mistakes were corrected: an integrity-error
text expectation and an assertion for a nonexistent projection field.
Their initial failures remain in local logs.
- Runner TypeScript and full server layered type checks pass. Token
gates and diff whitespace checks pass.
- Live provider acceptance: real Runner and Codex with gpt-6.1-sol, one
disposable local workspace, one tool call, and one deliberately dropped
terminal notification. The saved file, bound settlement receipt, one
accepted yielded result, one provider turn, confirmed provider exit and
suspended Runner all passed. The tool handler and persistence port were
controlled. This does not claim a full server or hosted journey.
- The full browser question-and-answer cell stopped before execution
because OPENAI_API_KEY was absent. No model work ran in that attempt.
Hosted sandbox recovery and the full browser continuation journey remain
unverified.
- `pnpm verify` returned exit 2 because the execution-spec change
requires broad CI. Required CI will supply that coverage; a full local
repository suite was not repeated.

- Review correction in `8553da244e`: a failed trailing-event write could
hide a provider failure. A new regression reproduced red, then passed
after all ordinary drain errors retained the named pending condition. No
settlement receipt or result can be accepted after that error. The live
missing-terminal check passed again on the corrected runtime.
- The real PostgreSQL control-plane regression and three existing
governed-wait controls pass. The new case persists one accepted yielded
result, a bound shutdown receipt, and the original pending human
question without a provider terminal.
- First CI revision `7c2cb9b1`: test-program typecheck found a missing
`PrpEvent` annotation in the new fixture. The annotation is fixed and
the Runner test-program typecheck passes. Runner support also timed out
in the unchanged `registered roots remain protected even when equal to
genuine public static bytes` case after 30 seconds. One unchanged local
diagnostic passed in 3.69 seconds overall. The hosted timeout cause
remains unknown; no timeout, fixture, or assertion was weakened.
[Original failed support
job](https://github.com/paperclipai/paperclip/actions/runs/42670851821/job/129346900133).

- Rebased onto the merged #20330 and current recovery changes. The
combined branch passes 1,402 executor/presentation tests. Both prompt
and 18-second provider terminals still pass. A warm session with no
terminal passes after the full 30-second drain and verified
stop/suspension. Its initial overly broad assertion rejected a
nonterminal turn event; the corrected assertion rejects every terminal
type. The rebased CI gate was cancelled before any runner or step
started; its cause is unconfirmed and it supplies no validation credit.
Final revision `b49ec5a144` starts fresh CI and review.

- Final-head CI attempt 1 failed before creating jobs. GitHub reports an
internal server error (correlation
`2c576b07-b67f-4179-a69f-74f7d99cd926`), followed by empty
runner-selection outputs for the aggregate jobs. One unchanged-commit
retry was requested; the initial admission failure remains recorded. [CI
run](https://github.com/paperclipai/paperclip/actions/runs/42673159868).

- **Current blocker:** final head
`b49ec5a144e94e41e96e2508a79bd9aec91fe45a` has a fresh 5/5 Greptile
review and zero unresolved threads, but required CI is not complete.
GitHub reports an active [Actions and Checks API
incident](https://www.githubstatus.com/incidents/tp8cghg7tlc4). Attempt
2 ran only part of the full selected graph. Build, canary, Rust, sandbox
providers, admitted browser shards and other completed test jobs passed.
The E2E aggregate correctly failed because `policy` and `e2e_shards` had
`abandoned` results. Server shard 5/12 received a runner shutdown signal
at 18:36:55 UTC and its test step was cancelled; its job still reports
in progress. The shutdown cause is not established. The separate review
workflow had the same pre-execution internal-error class and passed one
bounded retry. No further retry was submitted during the incident.
Resume with the missing/cancelled coverage after GitHub recovers; do not
count the absent typecheck, Runner or support jobs as passes. [Failed
coverage
gate](https://github.com/paperclipai/paperclip/actions/runs/42673159868/job/129354318236),
[interrupted server
shard](https://github.com/paperclipai/paperclip/actions/runs/42673159868/job/129350854174).

## Risks

- A missing terminal can use one additional bounded shutdown interval.
Unknown shutdown still blocks continuation.
- Provider terminal and usage accounting keep their separate meaning.
The receipt proves stopped execution and settled tool outcomes, not
model success.
- Recovery rejects a foreign receipt, a later turn, an active turn with
a settled receipt, and an actual failed provider terminal.
- There is no database migration. Older checkpoint shapes remain
readable. Drivers without this optional proof retain a named pending
state.
- This PR does not deploy the fix or repair an existing hosted task.

## Model Used

OpenAI Codex, GPT-6 family, with reasoning, repository tools and local
code execution. The exact serving model ID and context window are not
exposed in this session. Live test inference used gpt-6.1-sol.

## 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
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-09 13:46:16 -06:00
Dotta a3e7e63330 Guard Native recovery with process-space proof and explicit containment (#19813)
## Thinking Path

> - Paperclip manages agents and their work.
> - Recovery must preserve execution ownership and accepted results.
> - A saved PID proves nothing outside its recorded process namespace.
> - Uncertain unfinished work must stay held until its original owners
stop.
> - Operators need a source-bound containment action and a separate
ordinary Retry.
> - Accepted results must use the existing finalizer without another
provider turn.
> - This PR keeps those paths safe, recoverable, and quiet between real
obligations.

## Linked Issues or Issue Description

Refs: #19713

Refs: #19591

Recovery could use a local PID to release or replace a controller from
another process namespace. Connected-chat Retry also rejected successful
containment on a task in `todo`. The new containment action used a
broader permission than the existing owner-stop action. A later review
found that result-less guards also rejected the existing accepted-result
confirmation action.

## What Changed

- Record and verify the controller's kernel/PID namespace. Keep unknown
and foreign unfinished ownership held. Preserve independent durable stop
evidence and the existing remote lease fences.
- Use the shared accepted-result ownership reconciler. Bind settlement
to the observed lease token, generation, boot, PID, namespace and
process birth. Retain finalizer, cleanup, current-controller, live-owner
and remote exclusions.
- Share the remote-owner reader across recovery consumers. Scope runner
leases to the same company, task and run. Do not make local PID probes
for remote accepted-result ownership.
- Gate original-host containment on `runtime:confirm_owner_stop`. Bind
it to the current task, source, assignee, original expiry, lease and
Stop state. Audit separate controller/provider containment and reviewed
action outcomes.
- Keep containment separate from ordinary Retry. Use one canonical
committed receipt and the normal admission, budget, workspace and
lineage checks. Preserve the recorded external-action outcomes.
- Keep the controller-only confirmation actionable for both result-less
work and accepted results. Result-less work gets its next source-bound
attention in the same transaction. Accepted results keep their original
result and use normal shared settlement/finalization.
- Keep identity inspection quiet. Preserve the original foreign-owner
expiry and use the existing scoped finalizer in accepted-result recovery
controls.
- Update the recovery card, validators, execution projection, docs and
access maps. Reuse existing canonical columns; add no migration or
ownership backfill.

## Verification

Current publication head: `71ea76b568de09d6313d8992e803131d9d5c54f3`.

**The current fix has a causal red/green check.** On the test-only
revision, both foreign-local stopped/fenced controller cases failed
because recovery probed saved runner, process-group and provider PIDs in
this host's namespace. This measured the wrong probes; it did not run
duplicate providers. After the fix, the same two cases passed every
no-probe, no-claim, no-controller-stamp, no-stop-receipt and
unchanged-authority assertion. Three existing remote preparation, grace
and fenced-controller progress cases also passed. Total: **5 passed, 0
failed;170 filtered rows excluded**. All three normal affected App
TypeScript programs passed on this head (660,681 and428 roots).

The fix separates a controller wait from execution stop proof.
Independent live/grace evidence still schedules recovery. A
stopped/fenced foreign controller can pass this namespace guard only for
remote execution, which keeps its later checkpoint and never-launched
checks. Foreign local execution stays held before runner or provider PID
inspection.

Earlier source-scoped results remain evidence, not fresh executions on
the current head:

- On `c86dd741`, the complete failed-owner file passed **25/25**, with
no skips or filters. Empty scans wrote no controller stamps. Foreign
ownership kept its original expiry. Normal returned-claim settlement and
attention at the exact deadline passed.
- On `c86dd741`, **15 selected accepted-result/restart controls
passed**. The81 filtered rows are excluded. Both completion cases used
the existing scoped finalizer and kept their accepted result without
another provider turn.
- Trusted CI at synthetic merge `50d072a5` (actual master `1b7fe334`
plus `c86dd741`) passed the complete **17-case maintenance-server
file**. This includes the original90-real-second quiet observation and
two qualified hourly windows. The quiet case took118,918ms. The four
jobs that failed on the earlier publication all passed on that synthetic
merge.
- On `6243b32c`, the complete ownership-report file passed **29/29**.
Native NULL namespace stayed unprovable and generic compatibility
remained. Three selected recovery controls passed;170 filtered rows are
excluded.
- On `f81f2c3c`,356 business cases passed: whole ownership-route221,
recoveryUI70, owner-proof38 and controller-confirmation8; selected
accepted-result authority18; and one real connected-chat containment,
separate authorized Retry, useful Native result and downstream reply
case. The2,024 filtered rows are excluded. A separate earlier
accepted-result causal case kept the original result and completed after
restart without replay.

Normal Shared exports, App programs, UI typecheck, token gates and map
checks passed on their recorded revisions. Unchanged DB, adapter, Eval
and Runner inputs/outputs have explicit carry proofs. The clean normal
merge with fetched master `8fe524f7` preserves all31 exclusive owned
paths and14,827 unrelated master entries. The nine overlapping paths
were reviewed, including the upstream unidentified-run stop action.
Fresh CI must validate that actual merge composition.

PG cases used existing external PG17, fresh owned databases, pools at
most4, one worker and no SQL observer during cases. Registered clients
and recorded process groups closed. Independent final SQL audits found
zero campaign sessions before normal database cleanup. Original failing
fixtures remain retained.

Original failures are preserved. One new test first failed compilation
due to a missing getter import; an import-only correction passed its
full owning programs before the causal red/green check. A local quiet
attempt stopped in the normal prerequisite hook before any business case
and its collector rejected two normal build markers. The later17-case CI
pass establishes quiet recovery; it does not turn that failed local
collector into a pass. An earlier useful case passed before its private
cleanup collector failed on an owned read-only directory; normal cleanup
completed after all owners closed. Earlier runner-shutdown cancellation
and a separate private whole-suite failure remain unexplained.

Current-head checks are complete:57 success,1 neutral and3 skipped,
including the successful aggregate CI gate. The legacy status passed.
Greptile is5/5 and Ponytail gives an explicit5/5 Ship verdict for this
head. All seven review threads are resolved. Full recursive typecheck,
the full test suite and release build were not repeated locally. No
result here proves deployed suspension, a live provider or termination
on another host.

## Risks

- Unknown physical ownership can require an owner/admin action. A false
containment statement can be unsafe.
- New work, reassignment, Stop, renewed authority, accepted results or
pending cleanup can invalidate an action. The operator must refresh.
- Controller confirmation does not prove provider/tool containment.
Completed external actions must not be replayed.
- Generic legacy and child-process compatibility remains separate from
the strict Native controller policy.
- Existing saved state and canonical schema are preserved. Permanent
safety refusals remain held with their normal named recovery path.

## Model Used

OpenAI `gpt-6.1-sol` agents implemented and tested the changes with
reasoning, repository tools and code execution. A GPT-6-based Codex
managing agent reviewed and integrated them. The host does not expose
the manager's exact build or the context-window sizes.

## 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 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge
2026-11-09 12:06:11 -06:00
DottaandClaude Opus 5.5 8fe524f796 fix(issues): let the board confirm an unidentified run stopped instead of an endless Retry wait (#20310)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Before a new attempt can start on a task, Paperclip must prove the
previous run's agent stopped, so two agents never work the same task at
once
> - A local native run can be interrupted after it asked to start the
runner but before it recorded the runner's process. The runner may have
saved state and started a provider, and provider processes can outlive
it, so the existing check (#19694) rightly refuses to assume the run
stopped
> - Today that case has no way out: every Retry is accepted and then
waits forever as `process_identity_missing` (storage chaos ST1, t02/t03)
> - This pull request makes the wait explicit and actionable. The task
explains why it waits, and a board operator who has checked can confirm
the run stopped; the parked Retry then starts at the click
> - A second shape from the Daytona storage baseline (t06) parked a
Retry with no reason at all: a follow-up was interrupted by a graceful
shutdown while it was still restoring its workspace. No provider ran,
but the restore hold kept the same agent held, so the Retry never
started
> - The benefit is that no Retry stays accepted-and-waiting with nothing
anyone can do

## Linked Issues or Issue Description

Refs #19831. Storage chaos wave `w-20261109T145628-s9902` (ST1), tasks
t02 and t03.

**What happened (CHA-3, run `3c3f6241`):**
- The run requested a runner launch (`native.process_start_requested`),
and a K2 restart hit before its process identity was recorded.
- After the restart, the resumed attempt failed on the storage outage.
The task was blocked.
- The board's Retry (202) was parked as `executionWait.reason =
process_identity_missing`: "The previous run has no verified stop
record."
- `recordUnidentifiedLocalRunnerStop` cannot prove the stop because this
run's runner saved control-plane state. Once that exists, a provider may
have started (#19694), and a provider is not guaranteed to carry
`--run-id` or `PAPERCLIP_RUN_ID` (the Codex provider env omits it on
purpose). The shared owner prover needs a PID, which the run never
recorded.
- Nothing could ever clear the wait.

**Daytona storage baseline `w-20261109T154810-s9911`, task t06:**
- The run succeeded. The follow-up was cancelled
(`continuation_task_ownership_changed`), and the next run was
interrupted by a graceful shutdown (`server_shutdown_interrupted`) 3 s
into `preparing`. It was restoring the saved remote workspace and had
launched no provider.
- Restore recovery saved the files (`workspaceRecovery.status:
recovered`, system recovery `complete`). But the
`legacy_execution_requires_reconciliation` restore hold releases only
for a different owner, or for a native Stop fenced before any provider
turn, so it kept the same agent held.
- The UI Retry returned 202 and parked with `executionWait.reason:
execution_recovery`, the generic wait, so the task showed a Retry that
never started.

Automatic proof needs the runner to record its identity before saving
state and to group provider processes under it. That is follow-up runner
work; this PR removes the endless wait now.

## What Changed

- `server/src/services/native-local-process-stop.ts`: new
`confirmUnidentifiedLocalRunnerStopped`. It accepts only a finished
native run of the task with no recorded process and whose latest launch
evidence is an unconfirmed launch on this host in a local environment.
It still refuses while a runner with `--run-id <run>` is running. It
records `native.local_process_stopped` with `basis: "operator_attested"`
and the attesting user. That is the receipt the existing continuation
gate already accepts.
- `server/src/routes/issues.ts`: `POST
/issues/:id/recovery-actions/confirm-run-stopped` (`runId`,
`stopEvidence` of 20 to 12,000 characters). It is board-only and
requires issue read plus `runtime:confirm_owner_stop`, like the other
stop attestations. It logs `issue.run_stop_confirmed` with the evidence,
promotes deferred intents for the issue, and resumes each parked task
Retry, so work starts at the click. Refusals return 409 with a code.
- `packages/shared`: `confirmRunStoppedSchema`, and the presentation
user action `confirm_run_stopped`.
- `server/src/services/task-interruption-presentation.ts`: a Retry
parked as `process_identity_missing` for a native run that recorded no
process now presents as waiting for the user (`canRetry: false`,
`userAction: "confirm_run_stopped"`), with a message explaining why and
who can act. A run with a recorded process keeps the existing
verification wait.
- UI:
- `ExecutionBlockerNotice` shows the explanation and, for users who can
confirm a stop, "Confirm it stopped" with a short evidence form.
- It reuses `PreviousServerStopConfirmation`, now with optional
`action`, explicit `runId` and `formId`, and a custom button label.
  - The Inbox names the action.

- `server/src/services/execution-blocker.ts`:
`interruptedPreparationBeforeProviderWorkCondition`. The restore hold
also releases for the same agent when the stopped run was a
system-interrupted preparation (legacy runtime never resolved, still
`preparing`) with no process identity, no runner or provider events, no
finalization or result, and every lease released with a confirmed stop.
It mirrors the existing interrupted-preparation proof and still requires
the completed workspace-recovery receipt. Auto-replay is unchanged; this
only lets the user's Retry or message start.
- Review fixes:
- `unidentifiedLocalLaunchRefusal` holds the endpoint's launch, host and
lease checks, and the presentation offers `confirm_run_stopped` only
when it passes.
  - The attested stop wakes cost accounting in the same transaction.
  - The confirmation form is keyed by task and run.
  - The route is registered in OpenAPI.

## Verification

Red/green (each new test fails against master and passes with this PR):
- `server/src/__tests__/issue-confirm-run-stopped-routes.test.ts`:
- The parked Retry presents `confirm_run_stopped` with the explanation.
- Confirming records the operator-attested stop and the activity entry,
satisfies the stop check, and resumes the parked Retry: its receipt is
coalesced into a newly started run.
  - It refuses with 409 while a runner for the run is running.
  - Agents and viewers get 403.
-
`ui/src/components/ExecutionBlockerNotice.confirm-run-stopped.test.tsx`:
the notice offers "Confirm it stopped" (and no dead Retry) and posts the
run and evidence. A viewer sees the explanation without the action.

- `server/src/__tests__/interrupted-preparation-restore-retry.test.ts`
(t06 shape):
  - The restore hold no longer blocks.
- A Retry is accepted and resumed into a started run, and the audit hold
keeps `replay: blocked`.
- The hold stays when a provider turn started, when a runner event was
recorded, when an operator stopped the run, or when the sandbox has no
stop receipt.
- `issue-confirm-run-stopped-routes.test.ts`:
- A case per refusal code checks the presentation keeps the generic wait
and the endpoint returns 409.
  - An `alreadyStopped` case.
  - An accounting-wake assertion.
- The UI test switches targets with stale evidence.

Regression and static checks:
- `ExecutionBlockerNotice`, `WorkspaceExportRecovery` and its control
tests: 74 passed.
- `tsc --noEmit` passes for `packages/shared`, `server` and `ui/src`.
`pnpm check:token-gates` is clean.

## Risks

- A board operator can now attest that an unidentified run stopped. The
attestation is permission-gated, requires written evidence, is
activity-logged, and is refused while a runner for the run is visibly
running. A wrong attestation could start a second agent beside an
orphaned provider, the same trust model as the existing previous-server
attestations.
- The confirmation component now accepts a run without a recovery
action. Existing callers pass the action as before.
- No schema migration.

## Model Used

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

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 11:36:41 -06:00
DottaandClaude Opus 5.5 6459488984 fix(native): open a remote replacement as a new runner after archiving the reattached one (#20242)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - After a restart, a remote (Daytona) run can resume by reattaching to
its surviving sandbox runner. If provider recovery fails and the
checkpoint allows it, the run opens a replacement provider session
instead.
> - Before a replacement, the executor archives the local controller
state and the remote session root as a continuity break, then opens a
new session.
> - On a reattach backend, the replacement still adopted the archived
runner and asked for its old authority, so it failed. The archive had
already moved the remote state, so the next retry could not verify the
runner and the issue waited 17 minutes on an unconfirmed stop.
> - Review showed that a reattach backend fixes many launch inputs once
at creation (runner binary, provider pack and companions, artifacts,
live-recovery mode, authority, spawn barrier), so resetting them after
the archive does not scale.
> - This pull request builds the replacement on a new backend for the
same run, created under a `bootstrap_incomplete` claim after the
archive, so every launch input resolves through the ordinary fresh path.
> - The benefit is that a failed reattach after a restart falls back to
a working replacement instead of a stuck issue.

## Linked Issues or Issue Description

**What happened?**
In restart-chaos Daytona K13 storm wave seed 9503, task t36 graded R1
(no rest within budget). A K2 drain suspended run a53dd948's sandbox
runner (pid 589) during startup. On restart the run claimed
`reattach_remote_runner`. The adopted runner authenticated and restored,
then its connection closed, and provider recovery failed. The runtime
opened a replacement: `provider.session.archive_before_replacement`
archived the local and remote state, then the replacement failed with
"PRP provider resume state is unavailable". The same-run retry at
10:25:50 then failed with `runner_remote_state_unavailable: exit=1` (the
remote `runner-state.json` had moved), and file preservation deferred on
`agent_stop_unconfirmed` until the wave ended.

**Expected behavior**
After the continuity archive, the replacement opens a new runner for
this run, as it does for every other claim kind.

**Steps to reproduce**
1. Run a remote (Daytona) native run and restart the server so the run
claims `reattach_remote_runner`.
2. Make provider recovery fail on the adopted runner with a checkpoint
that allows replacement.
3. See the replacement open on the adopted runner's authority and fail
after the archive.

**Paperclip version or commit**
master at 465da4227a

## What Changed

- `native-session-executor.ts` `openReplacementSession`, on a
`reattach_remote_runner` backend: archives the continuity state (local
and remote, as before), then calls
`createRunnerdBackendWithinSessionClaim` for the same run with the claim
re-kinded to `bootstrap_incomplete` (minus `remote` and
`stagedAttachment`) and without warm recovery, and opens the replacement
on that backend. Root migration then quarantines the empty archived root
(the #20241 rule) and every launch input resolves fresh.
- A backend that adopts only through warm recovery (no claim to re-kind)
throws `native_runner_replacement_requires_fresh_launch` **before**
archiving, so its saved state stays intact.
- Tests: a classic Daytona reattach backend for `codex` and `acpx`
(Claude). The replacement comes from a second backend: the original
backend's `openSession` is never called, and the new transport has no
adopted runner, uses `turn-<runId>`/`item-<runId>`, has a new
still-pending spawn barrier, and (for `acpx`) carries the packaged
provider paths. The bundled-image replacement test now expects a new
backend and its own pack admission, not the recovered session's cold
admission.

## Verification

- Red before the fix: both new replacement tests fail on master. They
pass with the fix.
- `native-session-executor.test.ts`,
`native-recovered-owner-followup.test.ts`,
`native-harness-filesystem-independence-continuation.integration.test.ts`:
1,398 passed.
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` in `server`: passes.

## Risks

- Medium. The replacement now constructs a second backend inside the
same session claim. The new backend's tool-authority epoch supersedes
the reattach backend's, which is being abandoned anyway.
- A warm-recovery-only replacement now fails with a named error instead
of archiving and then failing. Its saved state stays intact for the next
recovery.
- Previous-release story: no saved state or schema changes.
- Not covered: why provider recovery on the suspended, adopted runner
failed in t36 in the first place. This PR makes the fallback work.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, via Claude Code with
tool use and code 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 08:12:24 -06:00
DottaandClaude Opus 5.5 68253e3175 fix(recovery): continue a run refused by an inert cleanup quarantine with no click (#20260)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - When a native session's cleanup fails unrecoverably, the runtime
quarantines it in process. The next run for that task is refused with
`native_session_cleanup_quarantined`.
> - A board Retry or a new message already recovers from this.
`verifyStoppedNativeSessionForContinuation` proves that the old runner
and providers stopped, releases the quarantine and starts a fresh
session.
> - Without a click nothing recovers. The automatic safe-replacement
sweep proves stopped sessions only with the Codex replacement verifier,
which needs the failed run's own active turn. A run refused before
launch never has one, so the sweep skips it on every pass.
> - Restarts must recover on their own. This pull request lets the sweep
use the same continuation proof for a cleanup-quarantined run.
> - The benefit is that an inert quarantine turns into a fresh-session
continuation with no click, and an unproven one still keeps its board
Retry.

## Linked Issues or Issue Description

**What happened?**
In restart-chaos wave seed 9802 (local, G1, Claude), task t02's run
71f03e16 succeeded, but its runner cleanup could not prove it drained
and was quarantined. Follow-up run 0b4b404f was refused before launch
with `native_session_cleanup_quarantined`, and the task showed
"Automatic recovery stopped" until someone pressed Retry.

**Expected behavior**
When the quarantined session's owner run and every provider process are
proven stopped, recovery continues the task by itself in a fresh
session, without charging an attempt. When that cannot be proven, the
board Retry stays available.

**Steps to reproduce**
1. Have a native run succeed while its runner cleanup is quarantined.
2. Let the next run for the task be refused with
`native_session_cleanup_quarantined` before it launches.
3. Stop the old runner and provider processes, then run the
safe-replacement sweep. No successor is created.

**Paperclip version or commit**
master at 8eb11fa8aa

## What Changed

- `native-session-executor.ts`: new
`verifyStoppedNativeSessionForAutomaticReplacement`. It returns the
existing replacement proof, or, for a
`native_session_cleanup_quarantined` run with no replacement proof, the
continuation proof that the board Retry already uses (Codex and ACPX,
including an inherited owner run).
- `server/src/index.ts`: the safe-replacement sweep uses that verifier.
- The existing sweep then retires the quarantine, records
`native.stopped_text_turn_verified` and queues a successor with
`forceFreshSession: true` at the failed run's attempt number, so no
attempt is charged.
- `quarantined-task-retry.test.ts`: "recovers a quarantined $provider
source that never launched with no click…" for Codex and ACPX (Claude).
A stopped owner makes the sweep queue one fresh-session successor at the
same attempt. A running owner (Codex) or a live ACPX agent process
queues nothing and leaves the board Retry in place.

## Verification

- Red before the fix: with the replacement-only proof, the stopped case
queues no successor. It passes with the fallback, and the running-owner
case passes on both.
- `quarantined-task-retry` (35), `native-safe-replacement`,
`native-replacement-evidence`: pass.
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` in `server`: passes.

## Risks

- Low to medium. The fallback applies only to
`native_session_cleanup_quarantined` runs. It uses the stricter
continuation proof that already gates the board Retry: owner run
settled, local leases released, runner and every recorded provider pid
absent, and an unchanged retained state. The sweep keeps every other
gate (task ownership, failure-block receipt, attempt limit, effect
inventory).
- Previous-release story: no schema or saved-state change.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, via Claude Code with
tool use and code 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 07:12:07 -06:00
DottaandClaude Opus 5.5 3374ca54f5 fix(runner): record a runner exit mid-turn as runner loss, and stop the lineage sampler panicking (#20259)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The native runner (`runnerd`) runs each provider turn, and the
server records why a run stopped and what the person can do next
> - When `runnerd` exits during a provider turn, the server saved the
run as `native_provider_terminal_failed`: "The provider session is
permanently unusable", with automatic retries stopped
> - The real cause was the runner process, and the transport already
names it (`native_runner_process_exited`) at the start of the
closed-stream message
> - Separately, the process-lineage sampler added in #19727 panicked on
Linux debug builds when a provider tool started its own session, and
that panic text became the run's visible failure
> - This pull request records a runner exit mid-turn as runner loss, and
reads session IDs without the assertion that panicked
> - The benefit is that a person sees the true cause of a stopped run,
and recovery treats a lost runner like every other runner exit

## Linked Issues or Issue Description

Refs #19727

**What happened**

A chat eval killed only the owned `runnerd` process (SIGKILL) while a
provider tool was running. The run failed with `errorCode:
native_provider_terminal_failed` and the next action "The provider
session is permanently unusable". The error text was `Notification
transport failed closed: native_runner_process_exited: runnerd exited
unexpectedly: paperclip-runnerd panic: panicked at
rustix-1.1.4/src/pid.rs:61:9: assertion failed: raw > 0`. The panic came
from the lineage sampler thread before the kill. It called
`rustix::process::getsid`, which asserts a nonzero session. A kernel
thread, or a process whose session leader is outside the PID namespace,
reports session 0.

**Expected behavior**

A runner process exit is recorded as `native_runner_process_exited`, the
same cause the server already uses for a runner exit outside a turn.
Recovery then applies its normal runner-loss rules (checkpoint evidence,
bounded attempts, cleanup quarantine). The lineage sampler does not
panic, and its diagnostics do not replace the real failure text.

**Steps to reproduce**

1. Start a native OpenCode run on Linux with a debug `runnerd`.
2. Let the agent run a shell tool that starts its own session (for
example a long `node -e` command).
3. Send SIGKILL to the `runnerd` PID only.
4. Read `GET /api/heartbeat-runs/<runId>`: `errorCode` is
`native_provider_terminal_failed` and the error names the rustix panic.

## What Changed

- `nativeSessionFailureSourceCode` returns
`native_runner_process_exited` for a `NativeProviderTerminalFailure`
with code `notification_transport_failed` when its message starts with
`Notification transport failed closed: native_runner_process_exited: `.
Only the runner transport writes that prefix. Other closed-stream causes
stay `native_provider_terminal_failed`.
- `paperclip-process-table` has a new `session(pid)` function. Linux
reads the session field of `/proc/<pid>/stat`. macOS calls `getsid`. A
session of 0 or an error gives `None`.
- `process_lineage` reads sessions through
`paperclip_process_table::session` instead of rustix `getsid`.
- Regression tests: the runner-loss classification (attempts 1 and 3,
and three negative shapes), the stat session parser with a kernel-thread
line, and a live read of this process's session.

## Verification

- `cd server && npx vitest run
src/services/native-runtime/native-session-executor.test.ts -t "runner
process exit that closed|preserves stable provider and runner|model
rejection from a provider terminal|operator-owned through terminal"` (8
passed)
- `cd packages/paperclip-runner/runner && cargo test -p
paperclip-process-table` (macOS: 3 passed; the Linux-only parser tests
run in CI)
- `cd packages/paperclip-runner/runner && cargo test -p
paperclip-runner-core --lib process_lineage` (6 passed)
- End to end: the `recovery.*` chat eval cells that kill `runnerd` are
run against this change on a separate eval branch.

## Risks

- Behavior shift: a runner exit during a turn now follows runner-loss
recovery instead of stopping as a permanent provider failure. Recovery
still decides from durable evidence. Ambiguous state stays terminal, and
an unverified cleanup stays quarantined.
- Previous-release story: no persisted shape changes. Runs saved earlier
with `native_provider_terminal_failed` keep that code. Only new failures
are classified with the new rule.
- The session read on Linux now uses `/proc` instead of a syscall. It
gives the same value, and it reports 0 (now `None`) in the same cases.

## Model Used

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

## 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

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 06:38:24 -06:00
DottaandClaude Opus 5.5 3f2a940d5b fix(runner): answer held Paperclip tool calls after a local restart before the next turn (#20227)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - When a restart interrupts a turn, the Runner keeps each Paperclip
tool call the model made as "held" until Paperclip answers it, and it
refuses to start the next turn while any call is held
> - Paperclip answers held calls after a reattach through its tool
recovery path. That path was wired only for remote runners
> - In restart chaos wave `w-20261109T084023-s9403`, t101 (local codex,
K2 then K1) held a `read_document` call that nothing answered, so the
continuation's `turn.start` failed and the task needed a Retry
> - This pull request wires held-call recovery for local runners too,
and makes `turn.start` answer or wait for held calls first
> - The benefit is that a turn lost to a restart no longer strands the
run behind one unanswered call

## Linked Issues or Issue Description

Refs #19831. Restart chaos wave `w-20261109T084023-s9403` (master
`fc5c79a327`), task t101 (codex C1, K2, local).

**What happened:**
- Run `4b5810d5` called `read_document` (`exec-ac8fa9b4`) around the K2
drain at 09:08:18. A K1 then killed the next server start.
- At 09:08:36 the third controller reattached. The Runner restored the
conversation and reported the old turn lost
(`provider_turn_lost_on_restore`, recoverable). The held call stayed
pending, by design: a held call accepts a late result.
- The controller had the call: the quarantine detail lists
`exec-ac8fa9b4` under `semanticTools.pending`. But
`recoverPendingSemanticInputs()` returned at once: for a local run
`controllerPersistence` is unset, so `recoverSemanticToolInput` was
`undefined`.
- At 09:08:46 the continuation's `turn.start` failed with "cannot
prepare the next provider turn while tool calls are active (pending: 1
[read_document:exec-ac8fa9b4…])". The run ended
`native_session_interrupted`.

## What Changed

- `server/src/services/native-runtime/native-session-executor.ts`: the
runnerd transport now always gets `recoverSemanticToolInput`, not only
when `controllerPersistence` (remote) is set. It uses the same epoch
check and `SessionAuthorityEpoch.recover`. Recovery re-authorizes and
re-runs reads, and replays receipts for mutations; it never repeats an
uncertain mutation.
- `packages/paperclip-runner/src/live/runnerd-codex-transport.ts`
(`#startTurnWork`): when the control plane has unsettled semantic
inputs, it runs `recoverPendingSemanticInputs()` before queueing
`turn.start`, and waits for that pass, bounded by the turn-start
deadline. Recovered results are queued as commands ahead of
`turn.start`, and the Runner applies commands in order. If recovery has
not finished by the deadline, the turn start fails with
`native_turn_start_held_tool_calls_unresolved` instead of sending
`turn.start` behind it. When everything is settled there is no wait, so
a normal turn start is unchanged. Live calls of a turn being replaced
are not waited on; the replaced start still rejects them.
-
`packages/paperclip-runner/src/control-plane/durable-prp-control-plane.ts`:
`recoverPendingSemanticInputs()` passes are serialized. A call made
while the startup pass is still answering a held call waits for that
pass, then runs its own, so the turn-start gate cannot finish early by
skipping a call that is already being recovered.

## Verification

Red/green:
- `native-session-executor.test.ts` "answers a local run's held
Paperclip tool calls after a restart (restart chaos t101)". On master
`recoverSemanticToolInput` is `undefined` for a local run; with this PR
it is wired.
- `runnerd-codex-transport.test.ts` "answers a held call before starting
the next turn (restart chaos t101)", against real runnerd and fake
Codex, with a slow startup recovery pass already in flight when
`turn/start` arrives. On master `turn/start` never ran recovery, and
without the serialization `turn.start` is queued before the held call's
result. With this PR the held call is recovered once and its result is
queued before `turn.start`.

Regression and static checks:
- `runnerd-codex-transport.test.ts`,
`durable-prp-control-plane.test.ts`,
`runnerd-codex-transport-adoption.test.ts`: 510 passed.
- `native-session-executor.test.ts` and `native-session-resume.test.ts`:
1368 passed, 1 failed. The failing case, "archives a damaged prior epoch
… with real runnerd", fails identically on master on this Mac (`ENOENT …
authority-epochs`), so CI is its reference.
- `tsc --noEmit` passes for `packages/paperclip-runner` and `server`.

## Risks

- Local runs now recover held calls after a reattach, as remote runs
already did. Reads re-run under current authority. A mutation without a
saved receipt still returns no result and stays held, as before.
- `turn.start` may now wait up to its existing deadline while a recovery
pass runs, then fails clearly if it has not finished. It never waits
when nothing is unsettled, so normal turns get no added latency before
`turn.start`.
- No schema change and no change to persisted run state formats.

## Model Used

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

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 05:26:12 -06:00
DottaandClaude Opus 5.5 bd83715a6e fix(recovery): bootstrap a remote follow-up again when a restart cut it off after retiring its finished owner (#20241)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A restart must resume in-progress runs on its own. Restart recovery
classifies each claimed native run and the executor acts on that claim.
> - A C1 follow-up on a remote sandbox first retires the finished owner
of the previous turn (it archives the previous controller state), then
launches a new runner.
> - A restart in that window left the run with an inherited session
checkpoint but no runner for this run. Recovery read the inherited
checkpoint as proof of a live remote runner and claimed reattach. The
executor then found no runner identity and failed with
`durable_identity_unreadable`, so the user had to press Retry.
> - This pull request makes recovery recognize that nothing reached a
runner for this run, and makes the executor bootstrap again over the
empty root.
> - The benefit is that this restart window resumes the follow-up by
itself.

## Linked Issues or Issue Description

**What happened?**
In restart-chaos Daytona K13 storm wave seed 9503, task t03 (codex, C1)
graded R3 retry_needed. Follow-up run 0d8b7258 retired its previous
owner at 10:07:32.988 ("Run 4ee1c19a finished without a saved runner
checkpoint; starting a new runner"). A K1 kill at 10:07:34 cut it off
before any runner start was requested. On restart, recovery claimed
`reattach_remote_runner` and the executor failed with
`runner_state_identity_mismatch: durable_identity_unreadable`. The run
ended with `native_continuation_requires_reconciliation` and a Retry
offer.

**Expected behavior**
Recovery sees that no runner was ever requested for this run, claims
`bootstrap_incomplete`, and the executor starts the new runner the first
attempt was about to start.

**Steps to reproduce**
1. Run a remote (Daytona) C1 follow-up whose previous turn finished.
2. Kill the server after the follow-up retires the finished owner and
before it records `native.process_start_requested`.
3. Restart the server. See the `reattach_remote_runner` claim and the
`durable_identity_unreadable` failure.

**Paperclip version or commit**
master at 3963d38560

## What Changed

- `native-restart-recovery.ts`: the `remote_runner_never_launched` proof
also holds when the run carries only its continued session. That means a
session checkpoint with a matching identity and no projected provider
event, active turn, semantic result, terminal or pending runtime
request, plus the predecessor's `sessionIdBefore`. The proof still
requires no `native.process_start_requested`, no controller checkpoint
for this run, no runner process identity and no `sessionIdAfter`. The
classifier then sees no checkpoint for this run.
- `native-session-executor.ts`: a `bootstrap_incomplete` claim over a
root with no runner identity and no controller state quarantines that
root and bootstraps again for a remote target too. Previously only a
local target with no live runner process could do this. Such a root was
never authenticated by a controller on this host.
- Tests: four classifier cases (restart; a requested runner start, a
pending runtime request and a projected provider event stay held). Two
executor cases (created and replacement sandbox) restart the exact state
the kill left after the retire.

## Verification

- Red before the fix: the classifier test got a non-bootstrap claim. The
executor tests failed with `runner_state_identity_mismatch:
durable_identity_unreadable`, the error from the wave. Both pass after
it.
- `native-runner-restart-recovery.integration.test.ts` and
`native-recovered-owner-followup.test.ts`: 239 passed.
- `native-session-executor.test.ts`: 1,310 passed.
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` in `server`: passes.

## Risks

- Low to medium. The proof widens only for a claimed remote run with
none of its own start, checkpoint, runner or provider evidence. A
pending runtime request in the inherited checkpoint still holds the run,
as in #20226.
- The quarantined root keeps the archived previous owner for inspection.
The usual quarantine retention applies.
- Previous-release story: no saved state or schema changes. A run that
an older build left in this state is classified with the new rule at its
next claim.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, via Claude Code with
tool use and code 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 05:17:15 -06:00
DottaandClaude Opus 5.5 fe72bc5f81 fix(native): roll back a warm rotation cut off before its new control plane once its runner is proven dead (#20218)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A warm follow-up rotates authority before it attaches. It archives
the previous epoch (suspended runner state and settled controller) under
`authority-epochs/`, then writes its own control plane
> - #20146 taught recovery to roll back a rotation whose new control
plane held only an undelivered `run.attach`, once its runner was proven
dead
> - A hard kill can land one step earlier, after the archive and before
the new control plane exists. The root then holds only the archive, with
no active control plane and no runner state. The executor read "no
durable identity" and failed with `runner_state_identity_mismatch:
durable_identity_unreadable`
> - This pull request applies the same proven rollback to that earlier
point of the rotation
> - The benefit is that a hard kill anywhere in the rotation window
resumes the follow-up from the previous turn

## Linked Issues or Issue Description

Refs #20146

**What happened?**
Local mixed restart-chaos wave w-20261109T081456-s9901 (master
09e24dd12c), t15 (codex M1):
- Run `4b85497f` started at 08:29:32 as a warm follow-up and requested
its process, then K1 killed the server.
- Recovery stopped the previous run's warm runner (pid 60249) and
claimed `resume_dead_runner`.
- The executor failed with `runner_state_identity_mismatch:
durable_identity_unreadable`.

The quarantined root held:
- `authority-epochs/epoch-c2842347…` with the previous owner `dc7d447b`:
runner `suspended`, every command completed;
- no `control-plane/` state and no `runner/runner-state.json`, only
provider state.

A Retry ran fresh. Phase 3 also saw the same signature on Daytona;
#20214 covers that remote shape.

**Expected behavior**
For a local runner proven dead (`resume_dead_runner`), a root that holds
only the archive of a suspended previous owner of this session restores
that epoch, and the follow-up continues from the previous turn. Without
a dead-runner claim it still fails closed.

**Steps to reproduce**
1. Start a warm follow-up and hard-kill the server after the rotation
archives the previous epoch, before it writes the new control plane.
2. Restart. Before this change, the follow-up fails with
`durable_identity_unreadable`.

**Paperclip version or commit**
09e24dd12c (wave). Branch rebased on current master.

## What Changed

- `native-session-executor.ts`:
- `undeliveredAttachRotationSource` becomes `interruptedRotationSource`,
and the new `latestSuspendedArchivedEpoch` shares the epoch checks:
named by its identity digest, a matching suspended runner state.
- Besides #20146's undelivered-attach shape, it accepts a root with no
`runner-state.json` and no active control plane (absent or empty). In
that case the epoch must belong to this session (`normalizedSessionId`)
and to a different run.
- The rollback moves an active control plane aside only when one exists.
- `native-recovered-owner-followup.test.ts`: #20146's rotation test adds
the "cut off before its new control plane" shape. With a dead-runner
claim it is admitted from the restored previous owner; without the claim
it still fails closed.

## Verification

- Red/green: on master, the new admitted case fails with exactly
`durable_identity_unreadable`. With the change it is admitted. The
fail-closed cases are unchanged.
- `vitest run` of the recovered-owner, restart-recovery and bootstrap
test files and `native-session-executor.test.ts`: 8 files, 1627 tests
passed (14 skipped).
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.

## Risks

- Low risk:
- The rollback still requires a `resume_dead_runner` claim on a local
runner, an absent runner state, and an archived epoch of this session
whose runner is suspended and whose name matches its identity.
- Restoring only moves files back within the root, and nothing is
deleted.

## 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

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 03:20:23 -06:00
DottaandClaude Opus 5.5 ad57d5cc12 fix(native): restart an unclaimed remote follow-up that carries only its inherited checkpoint (#20214)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A remote per-turn follow-up inherits the previous run's session
checkpoint at admission, rebound to its own identity. Its session root
still holds the previous owner's remote marker until the follow-up
rotates authority
> - If a restart lands before the follow-up's controller ever claims
execution, recovery should restart its bootstrap: nothing of this run
reached any runner
> - Recovery's unclaimed-bootstrap check required no checkpoint and no
provider evidence. The inherited checkpoint failed both, so recovery
claimed `reattach_remote_runner`
> - Even under a bootstrap claim, the executor skipped the per-turn
projection restore for every restart claim. It therefore never
rehydrated the previous owner's external marker, and failed with
`runner_state_identity_mismatch: durable_identity_unreadable`
> - This pull request does not count the inherited checkpoint as
evidence for an unclaimed remote run, and lets a bootstrap claim restore
the previous owner's projection, as a fresh follow-up start does
> - The benefit is that a follow-up drained in its first second on
Daytona restarts on its own

## Linked Issues or Issue Description

Refs #20153

**What happened?**
Daytona per-turn restart-chaos K13 storm w-20261109T074128-s9503
(revision 9046884811), t26 (codex C1): follow-up run `f1ddc43d` started
at 07:54:18 and was drained by SIGTERM at 07:54:19, during workspace
staging.
- It had not requested a runner process, and its coordinator was never
claimed (provider attempt 0).
- Recovery claimed `reattach_remote_runner` (`hasCheckpoint: true`,
`hasProviderEvidence: true`, both from the inherited checkpoint).
- The executor failed with `runner_state_identity_mismatch:
durable_identity_unreadable`, because the session root held the previous
run's external marker. A Retry succeeded.

**Expected behavior**
An unclaimed remote run whose only checkpoint is the admission-rebound
one, with no durable controller record and no provider events, restarts
its bootstrap (`remote_execution_never_claimed`). The executor
rehydrates the previous owner's projection and starts the follow-up from
it.

**Steps to reproduce**
1. Start a remote per-turn follow-up whose session root holds the
previous owner's external marker. Drain the control plane before the
follow-up's controller claims execution.
2. Restart. Before this change, recovery claims `reattach_remote_runner`
and the executor fails with `durable_identity_unreadable`.

**Paperclip version or commit**
9046884811 (wave). Branch rebased on current master.

## What Changed

- `native-restart-recovery.ts`:
- #20153's admission-rebound checkpoint test moves earlier. A new
`inheritedCheckpointOnly` holds for a remote sandbox run (not a plugin
task) with only that checkpoint, no durable controller record, no staged
attachment and no provider events.
- The unclaimed-bootstrap path and its classification then treat that
checkpoint as neither a checkpoint nor provider evidence.
- `native-inherited-runner-retry.ts` / `native-restart-recovery.ts`: a
warm continuation carries its settled predecessor's runner process
identity until it launches its own runner, and t26's row still held pid
596 at the restart.
- The new `carriesInheritedRunnerIdentity` reuses the same-run retry
path's proof (the exact pid, group and start time a settled predecessor
recorded).
- The restart classifier then ignores that inherited identity on the
unclaimed path, for a run that carries only its inherited checkpoint.
  - A process identity that is the run's own still holds the run.
- `native-session-executor.ts`: `restorePerTurnRunnerdController` now
also runs for a `bootstrap_incomplete` claim, but only when the root's
reference identity belongs to a previous run. A claim on the run's own
root returns early, as before.
- Tests:
- `native-runner-restart-recovery.integration.test.ts`: an unclaimed
remote follow-up with only its inherited checkpoint restarts, with no
process identity and with its predecessor's runner identity. It stays
held with its own runner identity, or when a provider event was
projected;
- `native-recovered-owner-followup.test.ts`: a bootstrap claim over the
previous owner's external marker is admitted, rehydrating the marker,
keeping the backup and quarantining nothing.

## Verification

- Red/green: both new tests fail on master. The classifier test claims
`reattach_remote_runner`, and the executor test fails with exactly
`durable_identity_unreadable`. Both pass with the change, and the held
case holds.
- `vitest run` over the restart-recovery, bootstrap, recovered-owner and
failed-workspace-recovery test files and
`native-session-executor.test.ts`: 9 files, 1715 tests passed (14
skipped). After the inherited-identity change, the restart-recovery,
bootstrap, recovered-owner, failed-workspace-recovery and
inherited-runner test files: 8 files, 407 tests passed (14 skipped).
Without the identity check, the inherited case is not restarted.
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.

## Risks

- Low risk:
- The inherited checkpoint stops counting only when the database shows
no controller record and no provider event for the run, and the existing
unclaimed-bootstrap conditions all still hold.
- The executor change runs the existing fresh-follow-up projection
restore, with all of its own checks, only for a root that still belongs
to the previous run.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 03:10:23 -06:00
DottaandClaude Opus 5.5 b1049b174e fix(native): retire a finished remote owner whose suspend never finished once its sandbox leases ended (#20211)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Before a per-turn follow-up starts a new runner, it retires the
previous turn's finished owner. Retirement requires the owner's
controller journal to be settled
> - A local runner that is proven stopped can no longer act on its own
lifecycle commands, so an unfinished `runner.suspend` from it does not
hold the follow-up
> - On a remote per-turn sandbox the same thing happens when a restart
or drain lands while the runner is suspending. But the remote path had
no equivalent rule, so the unfinished `runner.suspend` held the
follow-up even after the previous run's sandbox lease had ended
> - This pull request treats a remote owner's lifecycle commands as
settled once every sandbox lease of that run has been released or
expired, and none of them is the sandbox the follow-up now uses
> - The benefit is that a C1 follow-up after a restart on Daytona
continues on its own

## Linked Issues or Issue Description

Refs #20140

**What happened?**
Daytona per-turn restart-chaos K13 storm w-20261109T074128-s9503
(revision 9046884811, image 01246d43): 60 of 65 passed. Three C1
follow-ups failed with `runner_state_identity_mismatch:
prior_owner_terminal_state_indeterminate;
retirement_refused=journal_commands_unsettled(runner.suspend.pending)`:
- t04 codex, run `c7446d0c`;
- t16 claude, run `4b2c770f`;
- t39 claude, run `3ef7d934`.

For t04, the previous owner `fc585314` committed its `run.terminal`, and
its journal kept only `runner.suspend` pending. Its per-turn lease
(`5576f27d…`) expired at 07:43:52, and the follow-up ran on a new
sandbox. Each Retry succeeded.

**Expected behavior**
Once the previous run's sandbox leases have all ended, and the follow-up
runs on another sandbox, the previous runner cannot act on its suspend.
The finished owner is retired and the follow-up continues.

The owner stays held while any of these holds:
- a lease is active, retained or pending cleanup;
- the follow-up runs on the same sandbox;
- no lease is recorded.

**Steps to reproduce**
1. Finish a remote per-turn run whose controller journal keeps
`runner.suspend` pending after its committed run terminal, and let its
sandbox lease end.
2. Start a follow-up on a new sandbox. Before this change, retirement
refuses with `journal_commands_unsettled(runner.suspend.pending)`.

**Paperclip version or commit**
9046884811 (wave). Branch rebased on current master.

## What Changed

- `native-session-executor.ts`:
- the new `priorRemoteSandboxLeasesEnded` checks the previous run's
`environment_leases`: at least one lease, every one `released` or
`expired` with `releasedAt`, and none on the current target's provider
lease;
- `inspectFinishedPerTurnRunnerdOwner` passes the result as
`remoteRunnerGone` to `readSettledRunnerdProjection`, for the live root
and for quarantined copies. That function then ignores unfinished runner
lifecycle commands (`runner.suspend`, `runner.drain`,
`runner.shutdown`), exactly as it already does for a stopped local
runner.
- `native-recovered-owner-followup.test.ts`: a red/green test with lease
variants. A lease that ended or was released on another sandbox is
admitted. A retained lease, an ended lease on the same sandbox, or no
lease record stays held.

## Verification

- Red/green: on master, the two admitted cases fail with exactly the
production error; with the change they are admitted. The three held
cases hold on both.
- `vitest run` of the recovered-owner, remote-warm and restart-recovery
test files and `native-session-executor.test.ts`: 7 files, 1634 tests
passed (14 skipped).
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.

## Risks

- Low risk. Only runner lifecycle commands become settled, and only when
the database proves every sandbox of the previous run has ended and the
follow-up runs elsewhere. Unfinished turn, tool or result commands, a
missing run terminal and unanswered tool input still hold.

## 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

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 02:40:13 -06:00
DottaandClaude Opus 5.5 6fd46c0025 perf(budgets): judge Paperclip's share of restart recovery; report the provider's session load (#20183)
## Thinking Path

- Speed budgets protect the time to first visible agent activity, and
restart recovery is one of the judged metrics
(`native-speed-budgets.ts`, wave grader).
- In the B1 concurrency-6 chaos wave (`w-20261109T045320-s9807`), Codex
`restart_recovery` was p50 8.6 s and p95 11.2 s, against a budget of 6.5
s and 8.0 s. At concurrency 4 (K13) it was 3.8 s and 5.0 s.
- The preparation spans on a copy of the kept database break it down:
- Paperclip's share (ready → claim → prepare → runtime stage → runner
launch) is a steady 1.2–2.0 s.
- `provider.session.load`, the Codex app-server boot plus
`thread/resume` of long saved sessions, takes 3.0–6.3 s, 65–75% of each
recovery.
- Resumes run concurrently, and the worktree lock and the startup
reconciler are not on the path.
- Judging the full latency therefore mixes our code with provider and
session-size effects. Budget the part we control, so a regression in our
code shows up regardless of session size or concurrency, and report the
rest.

## Linked Issues or Issue Description

**What happened?**
`restart_recovery` breached its budget whenever many long provider
sessions resumed at once, although Paperclip's own recovery work stayed
within about 2 s. The breach did not point at anything Paperclip could
fix, and a real regression in our code could hide inside the
provider-load variance.

**Steps to reproduce**
1. Run a local chaos wave at concurrency 6 with long-running Codex tasks
and K1/K2/K4 faults (for example B1, seed 9807).
2. Compare `restart_recovery` in `speed.json` with
`provider.session.load` in the recovered runs' run logs.

**Expected behavior**
The budget judges Paperclip's share of a recovery. The provider's
session load and the full latency are reported but not judged.

## What Changed

- `server/src/services/native-runtime/native-speed-budgets.ts`:
- New budgeted metric `restart_recovery_control_plane`: from `ready` to
the start of `provider.session.load`, or to the next provider event when
nothing reloads (for example a reattached runner).
- Its budget is 2.5 s / 4.0 s for claude, codex and opencode. Measured:
1.2–2.0 s per run at concurrency 6.
  - The full `restart_recovery` stays in the table for reporting.
  - Breach payloads carry `restartTotalMs` and `providerLoadMs`.
- `server/src/services/native-runtime/native-run-trace.ts`:
- The per-run check records when `provider.session.load` starts, keeps
the recovery measurement, and judges it when the run finishes.
- It judges after the deferred diagnostics drain, so a provider span
committed after the provider event still counts.
  - It emits `restart_recovery_control_plane` breaches only.
- `tests/restart-chaos/ttft-baseline-stats.ts`: each recovery sample
gains `controlPlaneMs` and `providerLoadMs`. The provider-load start is
the span event's write time minus its duration.
- `tests/restart-chaos/wave-speed.ts`:
- Three restart rows per adapter: `restart_recovery` (report-only),
`restart_recovery_control_plane` (budgeted) and `restart_provider_load`
(report-only).
  - All three have outage time removed.
- `tests/restart-chaos/ttft-baseline.ts`: the recovery table adds a
"Paperclip share" column.
- Docs: `doc/run-log-events.md` (metric and payload) and the
speed-budget table in
`doc/plans/2026-11-07-durable-ownership-and-reconciliation.md`.

## Verification

- `server`: `npx vitest run
src/services/native-runtime/native-speed-budgets.test.ts`, 18 passed.
Two new tests:
  - a recovery dominated by provider load does not breach;
- a slow Paperclip share breaches with `restartTotalMs` and
`providerLoadMs`, even when the provider span is committed after the
provider event.

The existing recovery tests moved to the new metric. All six were red
before the trace change.
- `tests/restart-chaos`: `npx vitest run --config
tests/restart-chaos/vitest.config.ts wave-speed.test.ts
ttft-baseline-stats.test.ts`, 29 passed. New tests cover the sample
split and the grader rows (a judged share, a report-only provider load,
zero breaches).
- Server typecheck: no errors in the touched files.

## Risks

- **Lower sensitivity to provider-side slowdowns.** A provider
regression in session load no longer breaches. It stays visible in the
report-only rows and in breach payloads.
- **Runs with no `provider.session.load` span** (reattach, or an adapter
that doesn't emit it) are judged on the full latency against the
control-plane budget. That's conservative.
- **Run-log consumers that filter on `metric: "restart_recovery"`** see
`restart_recovery_control_plane` from now on. The doc notes the change
date.

## Model Used

Claude Opus 5.5 (`claude-opus-5-5`, Anthropic), 1M context window, tool
use and code execution, via Claude Code.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 01:22:28 -06:00
Nicky LeachandClaude Opus 5.5 9046884811 perf(native-runtime): claim a parked Runner while the follow-up run prepares (#20195)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Paperclip Runner executes native agent runs. A host can park an idle
Runner (release it and freeze it) between runs, and resume it for the
next run on the same task.
> - A follow-up run that reuses a parked Runner must claim it first. The
claim is a bootstrap ticket, a checkpoint flush, and the plugin resume
that thaws the Runner.
> - Core made the claim only inside `attachRun`, after all of its
per-run preparation. The claim does not depend on that preparation, so
the two ran in series.
> - This pull request starts the claim while Core still prepares the
run. `attachRun` then waits for the claim that is already in progress.
> - The benefit is a shorter start for every follow-up run on a parked
Runner. The model below gives about 285 ms per run at P50.

## Linked Issues or Issue Description

No public issue exists. The issue is described inline.

**What happened?**

A follow-up run that reuses a parked Runner claims the Runner only in
`attachRun`. Core calls `attachRun` after backend setup: runner
environment, assigned MCP tools, tool authority and the plugin task
owner. The claim waits for all of this, but it uses none of it.

**Expected behavior**

The claim runs at the same time as backend setup. Everything that needs
the new run's tool authority stays at attach.

**Steps to reproduce**

1. Run a Codex or Claude task on a host that parks Runners between runs.
2. Let the run finish and the Runner park.
3. Send a follow-up. Before this change, the plugin resume starts only
after backend setup ends.

**Paperclip version or commit**

`master` at 7086019d4b.

**Deployment mode**

Hosted, with parked Runner tasks.

## What Changed

- **Transport** (`runnerd-codex-transport.ts`):
- New `beginRunAttachment({ runId })`. It runs the attach admission
checks, then starts the existing `#claimReleasedRunner` as the held
attachment operation. It returns `false` and does nothing when the
Runner is not released and confirmed, a claim already exists, or
admission fails.
- The admission checks move into `#assertRunAttachmentAdmission`.
`beginRunAttachment` runs them first, and `attachRun` runs them again.
- The next `attachRun` for the same run waits for the early claim. An
`attachRun` for a different run, `release` and `turn/start` still fail
with `native_runner_run_attachment_in_progress` while the claim is held.
- After an early claim, `attachRun` fails with
`native_runner_resume_reconciliation_expired` before it registers if the
claim deadline has passed.
- **Pass-throughs:** `HarnessNativeSession`, `CodexHarnessSession` and
the session, harness and transport contracts get an optional
`beginRunAttachment`. Each layer does the same identity,
protocol-integrity and busy checks that its attach does.
- **Core** (`native-session-executor.ts`):
- The executor records when the in-memory warm entry it reuses was
parked (`released`).
- `createRunnerdBackend` gets `beginRetainedRunAttachment`. Core gives
it only for that parked in-memory warm entry.
- The plugin task owner preparation moves into `preparePluginTaskOwner`.
On the early path, Core prepares and rebinds the retained owner at the
same time as the runner environment and the assigned MCP tools, then
starts the claim.
- Cold, adopted, remote warm recovery and restart paths keep the old
order.

### What stays at attach, and why

- Registration, the quiescence probe, `run.attach` and the authority
rotation stay in `attachRun`. Checkpoint registration needs the new
run's tool authority epoch, and Core creates that epoch during backend
setup.
- The admission checks run again at attach, so a state change during
preparation still blocks the attachment.

## Verification

- `vitest run src/live/runnerd-codex-transport-release-resume.test.ts`
(runner): 21 passed. Five new modes:
- `early claim`: `attachRun` waits for the held claim and does not route
the new run before the claim ends;
- `early claim abandoned`: a close after the claim ends fails the
waiting `attachRun` with `closed`, and the new run is never routed;
- `early claim cancellation`: a close during the claim cancels it, and
the next `attachRun` fails with `closed`;
- `early claim expired`: the deadline passes during the claim, and
attach fails before it registers;
- `early claim stale ticket`: the deadline passes after the claim,
before attach.
- `vitest run plugin-runner-release-resume.integration.test.ts
plugin-runner-eviction.integration.test.ts` (server, with real Runner
processes from `cargo build --workspace --bins`): 2 files, 51 passed,
none skipped. New modes:
- `cached held claim` (Codex and Claude): the plugin resume is held, and
the test proves Core's tool preparation runs while the claim is in
progress;
- `cached cancellation` (Codex): a cancellation after an early claim
retires the Runner and the run stops cleanly.
- `pnpm run typecheck:typescript` (runner) and `pnpm typecheck`
(server): pass.
- Evidence (modeled, not measured live): traces of 8 resumed runs on
parked Runners in a hosted test deployment, on current `master`. The
claim takes about 300 ms, and it fits inside backend setup in 7 of 8
runs. The modeled saving is about 285 ms per follow-up on a parked
Runner at P50 (range 208–331 ms). I did not run this change on a hosted
deployment.
- Not run: the full server suite (CI runs it), smoke tests, and the
hosted park, claim and attach loop with this change.

## Risks

- **New failure mode:** Core now claims the parked Runner before backend
setup ends. If that run then fails preparation, or is cancelled before
attach, the existing retire path closes the claimed session. The Runner
is retired, so that agent's next follow-up starts cold. Before this
change, a preparation failure happened before the claim, while the
Runner was still parked.
- **Ordering:** the retained plugin task owner is rebound to the new run
earlier, before Core creates tool authority. Nothing in the owner
preparation reads that authority. A failure in tool authority setup now
happens after the rebind, and the retire path handles it.
- **Scope:** only an in-memory warm entry that was parked takes the
early path. Cold launches, adopted Runners, remote warm recovery and
restart recovery are unchanged.
- **Deadline:** the claim deadline now starts earlier. A very slow
backend setup can make the claim expire before attach. Attach then fails
with `native_runner_resume_reconciliation_expired` before it registers,
the same failure as a slow claim today.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with tool use
(shell, git, GitHub CLI) and subagents.

## 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
- [ ] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 22:56:08 -08:00
DottaandClaude Opus 5.5 3964ee1fca fix(native): a governance pause Stop with no turn result stays a cancellation (#20186)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A budget hard stop pauses the company; the pause's lifecycle Stop
cancels the agents' running native turns
> - When a Codex turn is interrupted this way, it ends without a
semantic result
> - The native executor treated that missing result as a retryable
interruption, so it rewrote the cancelled run to `failed` and scheduled
an exact resume
> - The pause held that recovery, and Raise budget and resume continues
only runs that are still cancelled, so the task stayed blocked with no
new run
> - This pull request makes the executor treat an acknowledged
governance pause Stop like a person's Stop: the run stays cancelled
> - The benefit is that Raise budget and resume continues the task
(#20144), with no manual Retry

## Linked Issues or Issue Description

Refs #20144 (resume continues budget-stopped work), #20143 (governance
pause stops are not failures), #20113

**What happened?**
Restart-chaos wave w-20261109T051242-s9802 (H1, seed 9802), task t03
(Codex, fault K2). The company budget crossed its hard limit at
05:19:39.9. The pause's lifecycle Stop ("Agent lifecycle stop
requested") cancelled run 59e976bc at 05:19:40.05, and Codex
acknowledged the interrupt. The turn ended without a semantic result,
and at 05:19:41.27 the executor rewrote the run to `failed` /
`native_session_interrupted`, with an agent-owned `active_run_watchdog`
recovery (exact checkpoint resume). The task went to `blocked`. After
`raise_budget_and_resume` at 05:20:20, no run started for 14 minutes.

**Expected behavior**
A pause's Stop is intentional. The run stays cancelled with its pause
record, and resuming continues the task once.

**Steps to reproduce**
Pause a company for budget while a Codex native turn runs, so the Stop
interrupts the turn before it records a result. Before this change, the
run becomes `failed` with a scheduled exact resume instead of staying
`cancelled`.

## What Changed

- `native-session-executor.ts`: the no-semantic-result branch now also
accepts an acknowledged governance pause Stop (`isGovernancePauseStop`
with an acknowledged native Stop receipt) as an intentional stop. It
settles the coordinator as `native_retry_cancelled` and raises
`NativeCancellationPendingRecoveryError`, as it already does for a
person's Stop and for a reassignment. The run is not rewritten to
`failed`, and no recovery action is created.
- The Stop's cancellation record is written by its fence before
dispatch, so the check does not depend on whether the terminal write has
landed.

## Verification

- `native-session-executor.test.ts`: new cases for "Agent lifecycle stop
requested" with a `pauseStop`, and for "Cancelled due to budget pause".
Each was red before the fix (it reached the retryable-failure write) and
is green now. A control case shows that a system lifecycle Stop without
`pauseStop` (termination) still takes the retry path.
- Full `native-session-executor.test.ts`: 1309 passed. Server typecheck
(`typecheck-layers`, low-memory): no errors.
- Not run: the H1 chaos rerun. Phase 3 runs it after merge.

## Risks

- A governance pause Stop that lands during a turn no longer schedules
an exact resume of that turn. The task continues on resume through a new
Retry (#20144) instead.
- Termination and cleanup use the same lifecycle Stop reason. They are
excluded because only the pausing path records `pauseStop`.

> 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`), Anthropic, via Claude Code with
tool use (shell, file edits, test execution). Extended reasoning
enabled.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-09 00:42:25 -06:00
Devin FoleyandPaperclip 9b71d03215 fix: recover interrupted native preparations and unblock upgrades (#20177)
## Thinking Path

> - Paperclip manages AI-agent companies and their work.
> - A native run prepares its workspace before a runner PID or
checkpoint exists.
> - A server crash can interrupt that stage and leave its controller on
another host.
> - Recovery needs a durable owner proof, a delivered recovery wake, and
the saved execution contract.
> - The old paths missed controller lease registration and boot proof,
skipped checkpoint-free preparations, and counted retained work as live
upgrade blockers.
> - This PR connects preparation to the existing controller lease and
recovery paths, and separates retained work from the upgrade census.
> - The result is bounded recovery without a second executor or loss of
saved work.

## Linked Issues or Issue Description

**What happened?**

A native preparation interrupted by a server crash could remain running
indefinitely with no runner PID or checkpoint. Native controller stamps
did not wake the shared instance lease. That lease was disabled on
volume-backed Railway services, and native takeover omitted the boot
binding needed for its cross-host proof. Scoped recovery selected
checkpoint-backed runs but skipped these preparations. The upgrade probe
then counted the retained row as current execution and could block every
later upgrade.

**Expected behavior**

Track the preparation's controller before a runner starts. Recover it
through the normal classifier after proving its owner stopped or fencing
that boot. Keep live or unprovable owners held. Deliver recovery wakes
to preparations without checkpoints. Preserve unresolved historical work
and report it separately from current execution during upgrade
observations.

**Steps to reproduce**

1. Save an observed native preparation with no runner process, result,
provider-start evidence or checkpoint.
2. Replace its controller with a process in another PID space. Let its
owner lease expire and send a scoped recovery wake.
3. Before this fix, recovery skips the checkpoint-free preparation or
cannot prove its foreign controller stopped. Upgrade readiness continues
to count that old row as a live blocker.

Related work: #18037, #19651, #19868, and #20168. The foreign-PID guard
from #19868 remains. The queued first-turn input fix from #20168 is
included through the current base.

## What Changed

- Register the existing instance lease when native execution and restart
claims are written. Keep passive identity reads free of ownership
effects. Keep that lease enabled on volume-backed Railway services
unless explicitly disabled.
- Preserve the existing PID/start-time proof within the same readable
PID space. Bind foreign or unknown-space takeover to its saved boot and
last write. A live lease or grace period keeps the run held with a
scheduled check. Repeated evidence waits preserve their timestamp.
- Include explicitly fenced, checkpoint-free preparations in the
existing finite recovery candidate inventory. Normal launch, checkpoint,
provider evidence and admission checks still decide whether work may
resume.
- Expose the existing board stop-confirmation operation for historical
foreign-host owners. Bind confirmation to the exact run, boot, PID,
process start and host. Reject changed ownership.
- Report narrowly defined old, unowned preparations as
`retainedBlockedRuns` outside the live upgrade census. Local executions,
pending admission, drain state, truncation and positive checkpoint proof
retain their barriers.
- Update the execution contract and add PostgreSQL, real-route, race and
preservation regressions.

## Verification

- Genuine red/green regressions cover the old upgrade census, missing
native lease registration, the volume-backed default, foreign-host
confirmation, and scoped recovery skipping checkpoint-free preparation.
Test bodies ran against real PostgreSQL before their corresponding
production changes.
- Combined verification before the final idle correction (head
`055be6c84d9`): **459 passed, 22 skipped, 11 files passed**. Covers
controller lease/identity, native restart classification and
integration, host confirmation, heartbeat recovery, instance route
authorization, upgrade readiness, and queued first-turn input. The
focused command used `pnpm exec vitest run` with those 11 suites and
`--maxWorkers=1 --no-file-parallelism`. The 22 skipped cases require the
Rust debug fake-Codex fixture, which was not built locally; the
real-process CI coverage must pass.
- `pnpm --filter @paperclipai/server typecheck`: passed on head
`055be6c84d9b058064daad0af71bb5d893ab9529`.
- Actual route proof uses the real heartbeat service and PostgreSQL.
Unauthorized access returns 403. The retained run and owner records
remain unchanged. Recovery integration admits one bootstrap claim across
two replacement controllers, keeps a live owner held, and preserves
local execution.
- `pnpm verify`: exit 2, requests broad CI because the execution
contract changed. Full local suite not run. Current-head CI must supply
broad coverage.
- Local source checkout on macOS ARM64, Node v25.6.1, pnpm 9.15.4. Tests
use isolated PostgreSQL. No live provider restart is claimed by those
fixtures.
- CI found an idle-query regression in the first version of the lease
wiring. Two focused PostgreSQL regressions reproduced the misplaced
identity-read notification and the missing claim notification. The fix
moves registration to actual ownership writes. `env -u npm_execpath pnpm
exec vitest run server/src/__tests__/maintenance-server-routes.test.ts
--maxWorkers=1 --no-file-parallelism`: **17 passed**, including 90 real
seconds and two qualified hourly windows with no extra idle queries. An
initial local setup attempt inherited npm metadata and did not run
tests; clearing that metadata selected the correct pnpm helper. Three
focused controller/native suites also passed **168 tests, 22
fixture-gated skips**. Server typecheck passed after the correction on
head `4a527326dcd5b3a9e286f0e4c3e761d3056af4d9`.
- The older CI server shard also exposed a same-space graceful-restart
regression. The new boot fallback had overridden local process-exit
proof. Seven suspension cases and a focused unit regression reproduced
it; the fix limits boot fallback to foreign or unknown PID spaces. Fresh
verification on `acf1065d98150210c1e227c7f3b05a1eb489730b`: **251
passed, 22 fixture-gated skips, 4 files passed**, including all **40**
graceful-restart suspension tests. Server typecheck passed. The local
regression failed before this correction, and the same-space and
foreign-space paths pass together after it.
- Current-head CI completed successfully on
`acf1065d98150210c1e227c7f3b05a1eb489730b` (run 42568109784). Greptile
reviewed that exact head at 5/5 with no unresolved review threads.
- Secret and private-data scans passed. No workflow, lockfile or
migration changes.

## Risks

- The instance lease now applies to volume-backed Railway services. Its
existing 30-second renewal, quiescence, grace and self-fence behavior
applies while work is held. Idle servers retain the existing no-query
behavior. An explicit `PAPERCLIP_CONTROLLER_INSTANCE_LEASE=off` remains
available.
- A controller lease proves only the server owner's state. It does not
prove an agent process stopped or authorize replay, resource release or
volume removal. The existing classifier and provider/runner checks
remain responsible for those decisions.
- Previous-release records keep their shape and saved state. A missing
boot lease stays unprovable and requires the scoped stop-confirmation
path. A changed confirmation target is rejected.
- The upgrade observation does not recover a held task by itself. Source
tests do not qualify a hosted replacement. Deployment and the affected
task's useful result must be verified separately.
- This repairs recovery after a crash; it does not claim to identify or
fix every source of heap exhaustion.

## Model Used

OpenAI `gpt-6.1-sol`, xhigh reasoning effort, through Codex in T3 Code,
with repository, shell, and GitHub tools. Context window size is not
exposed by the runtime.

## 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-08 21:53:13 -08:00
DottaandClaude Opus 5.5 b54317d3fb fix(native): give a preparing run's first turn the user's queued messages instead of interrupting it (#20168)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A Paperclip Runner (native) run prepares its workspace and
environment before it starts its first provider turn. This can take
about a minute.
> - A user's message that arrives during that time waits as a deferred
wake behind the run. The Interrupt control then cancelled the run before
any provider turn.
> - The cancel threw away the whole preparation. A new run had to
prepare again, so the user waited longer for the first token.
> - This pull request gives the run's first turn the queued messages.
The run seals its first-turn input immediately before `turn.start`, so
the messages are part of the prompt that the turn starts with.
> - The benefit is that the user sees the message handled in the same
run, with no cancel and no second preparation.

## Linked Issues or Issue Description

**What happened?**
A Paperclip Runner run took about 54 s to prepare (environment startup,
workspace, runtime selection). The user sent a second message 32 s into
that time and clicked Interrupt 21 s later. Interrupt cancelled the run
as `operator_interrupted` ("Interrupted to send queued messages") before
any provider turn. A new run then prepared again from the start. The
runtime-selection transaction that froze the run's input completed about
5 s before the click, and the coordinator claim came 4 s after it, so
the message could not be given to the first turn at any point in the old
code.

**Expected behavior**
When a user message arrives for a task whose current run has not started
its first provider turn, the run does not stop. The message goes into
that run's first turn. A run that is in a turn is interrupted as before.

**Steps to reproduce**
1. Assign a task to a Paperclip Runner agent with a sandbox environment,
so preparation takes a long time.
2. While the run prepares, post a second comment on the task.
3. Click Interrupt on the queued message before the run starts its
provider turn.
4. See that the run is cancelled and a new run prepares again.

**Paperclip version or commit**
Staging revision b43cccbb0.

## What Changed

- `server/src/services/native-runtime/first-turn-queued-input.ts` (new):
`claimFirstTurnQueuedInput` seals a run's first-turn input in one
transaction. It locks the task, the deferred wakes, and the run in the
same order as the queue routes. It takes the responsible user's plain
queued comments in queue order (not interaction answers, interrupt
intents, independent continuations, conversations, or other users'
messages). It renders them with source-trust sanitizing and secret
redaction, then writes a `firstTurnQueuedInput` receipt
(`paperclip.first-turn-queued-input.v1`) into the run context. A second
call for the same run returns the same messages.
`runAcceptsFirstTurnQueuedInput` is true for a running native (or
preparing native) run that has no receipt and no accepted provider turn.
- `packages/paperclip-runner/src/native-session-runtime.ts`: new
`getFirstTurnQueuedInput` option. The runner calls it immediately before
the first `session.startTurn` and appends the result to `task.prompt`
(or to `events` for a resumed-session continuation envelope). It is not
called for the disposition-only recovery turn.
- `native-session-executor.ts`: passes the claim to the runner. A failed
seal commits nothing, so the executor logs it and starts the turn
without the messages. The messages stay queued.
- `queued-comment-delivery.ts`: a message in a run's receipt counts as
delivered only after the provider accepted that run's turn
(`turn.accepted` or the provider's `turn.started`), and only if the
message was not edited after the seal. Release promotion, Send, and
later first turns use this rule. `explicit-native-continuation.ts` uses
the same rule for stopped native runs.
- `routes/issues.ts` Interrupt: when the target run has not sealed its
first turn and has no accepted turn, the route does not record interrupt
intent and does not cancel the run. The response has
`executionWait.reason = "first_turn_pending"`. Other runs are
interrupted as before.
- Queue views (`routes/issues.ts` and the wake-queue adapter) hide
messages that the active run took into its first turn. Queue edits keep
those ids on the wake, so a run that fails before acceptance still
leaves them queued.
- `run-state.ts`: the issue-control run projection includes the receipt,
so the queue poll can hide taken messages.
- `doc/execution-semantics.md`: new section "Queued messages before a
native run's first turn".

## Verification

- Red before the fix, green after:
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/issue-queued-comments-routes.test.ts -t "first
turn|already started"`: Interrupt on a preparing run and on a claimed
native run before `turn.start` does not stop the run, and the first turn
gets both messages in order. Before the fix, both cases cancelled the
run.
- `pnpm --filter @paperclipai/paperclip-runner exec vitest run
src/native-session-runtime.test.ts -t "first-turn queued input"`: the
claim runs immediately before `turn.start`, and the first turn's prompt
ends with the queued messages. Before the fix, the claim was never
called.
- `pnpm --filter @paperclipai/server exec vitest run
src/services/native-runtime/first-turn-queued-input.test.ts`: a run that
fails before `turn.start` leaves the message queued. The next run
delivers it, and after that no later run or copied retry context takes
it again. Before the delivery rule, the "exactly once" and "accepted
then failed" cases failed.
- Safety cases that pass before and after: Interrupt still cancels a run
whose provider accepted a turn (including a run saved by the previous
release with no receipt) and a run whose first-turn input is already
sealed. The existing "explicit interrupt fallback" cases for preparing
and native runs without a responsible user still pass.
- Speed: the seal is one short transaction before `turn.start`. In the
embedded-Postgres test it took 5.5 ms. It removes a full second
preparation (54 s on staging) from the message-to-first-token time.
- Related suites: `src/modules/wake-queue`,
`explicit-native-continuation`, `issue-queued-comment-queue`,
`issue-queued-comments-routes`, `queued-comment-consumption`,
`heartbeat/run-state` (888 tests), `native-session-executor.test.ts`
(1306 tests), and the full `native-session-runtime.test.ts` (238 tests)
pass. `pnpm --filter @paperclipai/server typecheck` passes.
- Not done: no live run against a real provider or sandbox. Staging was
read only.

## Risks

- Previous-release state: a deferred wake saved by the previous release
has the same shape and is taken normally. A run saved by the previous
release has no receipt. If it is resumed before its first turn, it seals
on the new release. If its provider already accepted a turn, Interrupt
stops it as before. A run saved by the previous release while it was in
`turn.start` but before acceptance counts as unsealed, so in that short
window an Interrupt does not stop it and the message is delivered at the
turn boundary.
- Rollback: if the server rolls back after a run sealed and its turn was
accepted, the old release does not read the receipt and can deliver
those messages a second time.
- A first turn that does not use the fresh-turn path (restart
continuation, disposition-only recovery) does not call the claim. Its
messages are delivered at the turn boundary as before.
- A message that arrives after the seal waits for the turn boundary.
Interrupt stops the run as before.
- No schema migration. The receipt is a key in the run context.

## Model Used

- Claude Opus 5.5 (Anthropic), model ID `claude-opus-5-5`, used through
Claude Code with tool use (shell, file edits, test execution, read-only
browser).

## 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 22:44:18 -06:00
DottaandClaude Opus 5.5 fa7950121d fix(native): move an interrupted bootstrap's session aside on the run's own created sandbox lease (#20154)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - When restart recovery proves a remote bootstrap reached no provider
work, it bootstraps the same run again in the same sandbox. Before
relaunching, it stops the interrupted runner (#20103)
> - The relaunch starts a fresh controller record, whose command ids
restart at `command_prp_00000001`. The sandbox still held the
interrupted runner's journal, which had already recorded that command id
with different data
> - The relaunched runnerd rejected it ("commandId was reused with
different command data") and exited while waiting for `run.prepare`.
Every same-run retry collided the same way until the retry budget ran
out and the task blocked
> - The proven interrupted-bootstrap session move (#20103) ran only for
a resumed lease. A same-run retry on a per-turn sandbox reuses the run's
own created lease, so nothing moved the interrupted session aside
> - This pull request applies that same proof-gated session move on the
run's own created lease
> - The benefit is that a same-run bootstrap retry starts its runner on
a clean journal, and the old journal is kept as evidence

## Linked Issues or Issue Description

Refs #20103

**What happened?**
Daytona per-turn restart-chaos M1 rerun w-20261109T013733-s9501 (master
8e3b64a257, image 34bc12bf):
- **t10 (codex M1):** the codex subtask's run `f8a8f483` went through
eleven same-run bootstrap retries between 01:56 and 02:07.
- Each relaunched runnerd logged `paperclip-runnerd: commandId was
reused with different command data` and exited about 12 s later while
waiting for `run.prepare`.
- The run then failed `native_session_retry_exhausted` ("Provider
startup failed on 3 attempts before any provider work began"). The
subtask blocked, and so did the parent.
- **t02:** the same "runnerd exited while waiting for run.prepare"
pattern appeared on retry run `2e13568f`.

**Expected behavior**
A same-run bootstrap retry moves the interrupted session aside, keeping
it as a `.bootstrap-restart-<time>-<uuid>` sibling, and claims a fresh
session root before relaunching. The relaunched runner then cannot see
the interrupted attempt's command ids. This already happened on a
resumed lease and now also happens on the run's own created lease.

**Steps to reproduce**
1. Let a remote bootstrap reach the runner (it journals
`command_prp_00000001`), then restart before any provider work.
2. Recovery bootstraps the same run again in the same sandbox. Before
this change, the relaunched runnerd sees the old journal, rejects the
reused command id and exits, and every retry repeats this.

**Paperclip version or commit**
8e3b64a257 (wave). Branch rebased on current master.

## What Changed

- `native-session-executor.ts`: the created-lease branch of remote
harness preparation now applies the resumed branch's proven restart. It
runs when all of these hold:
  - the session is `not_suspended` and belongs to this run;
  - there is no backup;
  - the claim is `bootstrap_incomplete`;
- the stale-runner stop proved the interrupted runner gone
(`hasRemoteBootstrapRestartProof`).

It then runs `moveInterruptedBootstrapSessionAside` and
`claimUntouchedRemoteSession`. If the move or the claim fails, it throws
`runner_harness_state_mismatch: created_not_suspended` and changes
nothing.
- An earlier revision of this PR archived only the `runner` directory.
Review showed that would leave a session the existing claim cannot
reopen on a resumed lease, so that revision was replaced.
- On a fresh command namespace: moving the session aside removes every
id the relaunched runner could see, so a separate namespace isn't
needed. It would also change the persisted command id format that saved
controller state depends on.
- `native-session-executor.test.ts`: the existing "bootstraps only an
untouched provider session" matrix runs the real move and claim scripts
against a temporary filesystem. It gains two created-lease cases:
- an interrupted bootstrap: the old session is kept as a sibling and a
fresh root is claimed;
  - a symlinked parent: refused, and nothing moves.

## Verification

- Red/green: both created-lease cases fail on master and pass with the
change. The resumed cases from #20103 are unchanged: 42 cases in the
matrix pass.
- `vitest run` over the restart-recovery and bootstrap test files and
`native-session-executor.test.ts`: 7 files, 1540 tests passed (14
skipped).
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.
- The collision itself happens in runnerd (the production log shows it
on every retry). The live check is a Daytona per-turn K2/K4 rerun.

## Risks

- Low risk. The move reuses the resumed path's proof gates, its symlink
checks and its whole-session move, which keeps the session and never
deletes it. The new branch acts only when every gate holds; otherwise
preparation continues exactly as before.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 21:06:26 -06:00
DottaandClaude Opus 5.5 510746c682 fix(native): restart a remote run whose controller never sent its runner a command (#20153)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A follow-up run on a remote sandbox inherits the previous run's
session checkpoint at admission, rebound to the new run's identity
> - A remote runner receives work only through the controller's Postgres
checkpoint, which the controller writes before every command. A run with
no checkpoint rows, no runner events and no recorded runner process
never sent its runner anything
> - Restart recovery still read the rebound admission checkpoint's
provider session id as provider evidence, and classified such a run
`reattach_remote_runner`. The executor then found the root still owned
by the previous run and failed with
`native_remote_recovery_lease_mismatch: stage=runner_verification
field=identity_run_id`
> - This pull request classifies that run as an incomplete bootstrap,
and lets the executor start it from the previous owner's settled root
> - The benefit is that a follow-up interrupted before its runner ever
got a command restarts on its own

## Linked Issues or Issue Description

Refs #20137

**What happened?**
Daytona per-turn restart-chaos M1 rerun w-20261109T013733-s9501 (master
8e3b64a257, image 34bc12bf), t02 (codex M1 parent):
1. Wake run `a867cb18` was admitted at 01:48:31 with a rebound
checkpoint inherited from run `dfeddafa`: identity of the new run,
`cursor: null`, no terminal turns, no active turn.
2. It recorded `native.process_start_requested` at 01:48:36, then a K4
hold froze the control plane.
3. At 01:53:11 recovery classified it `reattach_remote_runner`
(`hasCheckpoint: true`, `hasProviderEvidence: true`, from the rebound
checkpoint), although the run had no `native_runner_checkpoints` rows,
no runner-originated events and no recorded process identity.
4. The executor found the session root still owned by `dfeddafa` and
failed with `native_remote_recovery_lease_mismatch:
stage=runner_verification field=identity_run_id`. The task needed a
Retry.

**Expected behavior**
A remote run whose runner provably never received a command restarts its
bootstrap. The executor treats the previous owner's root as it would for
any follow-up start.

**Steps to reproduce**
1. Claim a remote sandbox follow-up that recorded
`native.process_start_requested` but has no controller checkpoint rows,
no runner events and no `native.process_identity_recorded`, with only
the admission-rebound session checkpoint.
2. Restart. Before this change, recovery claims
`reattach_remote_runner`, and the executor fails with `identity_run_id`.

**Paperclip version or commit**
8e3b64a257 (wave). Branch rebased on current master.

## What Changed

- `native-restart-recovery.ts`: the new
`remoteRunnerNeverReceivedCommands` condition.
- It applies to a remote sandbox run (not a plugin task) with a prepared
remote workspace when all of these hold:
    - no durable controller record, and no staged attachment;
- only the admission-rebound checkpoint (or none), and no provider
process events;
- no runner-originated events, and no
`native.process_identity_recorded`;
    - no run process fields;
- the same claimed and dead previous-controller conditions as
`remoteRunnerNeverLaunched`.
- It yields `bootstrap_incomplete` with the reason
`remote_runner_never_received_commands`, and does not count the rebound
checkpoint as this run's checkpoint.
- `native-session-executor.ts`:
- a `bootstrap_incomplete` claim requires the incomplete-bootstrap proof
only when the root carries this run's own identity;
- a root still owned by the previous run takes the normal previous-owner
path, and may retire a finished previous owner, as any follow-up start
does.
- Policy change, called out for review: a claimed remote run that
recorded only `native.process_start_requested` was held as
`ambiguous_remote_recovery_evidence`. Under the conditions above it now
bootstraps again.
- The controller writes every command to the Postgres checkpoint before
sending it, so with no checkpoint rows no command reached any runner,
and no provider work can exist.
- A runner process that was spawned but never commanded is stopped
before the new bootstrap by the existing stale-runner stop.
- A recorded process identity, an adapter invocation, a runner event,
process fields or a provider session still hold the run.
- Tests:
- `native-runner-restart-recovery.integration.test.ts`: the
classification for a follow-up with an inherited checkpoint and for a
first run without one, plus a held case when a runner process identity
was recorded. The old held expectation for "a runner process start was
requested" moved here;
- `native-recovered-owner-followup.test.ts`: the executor admitting a
`bootstrap_incomplete` follow-up from the previous owner's settled root.

## Verification

- Red/green:
- On master, the classification test claims `reattach_remote_runner`, as
in production. With the change it claims `bootstrap_incomplete` with
`remote_runner_never_received_commands`.
  - A recorded runner process identity keeps the run off this path.
  - The executor test is admitted with the change. On master it fails.
- `vitest run` over the restart-recovery, bootstrap, recovered-owner and
failed-workspace-recovery test files and
`native-session-executor.test.ts`: 9 files, all passing after the policy
test moved; `native-runner-restart-recovery.integration.test.ts` alone:
144 passed (14 skipped).
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.

## Risks

- Low risk:
- The new path requires positive proof that nothing reached a runner: no
controller record, no runner events and no recorded process. Any of
these keeps the existing classification.
- In the executor, a root that carries this run's identity still needs
the full bootstrap proof.
- A root that carries the previous run's identity goes through the same
previous-owner verification as any follow-up start.

## 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

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 21:06:21 -06:00
DottaandClaude Opus 5.5 3eea8b87bd fix(native): settle a finished owner whose journal holds a definitively answered command (#20148)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Before a per-turn follow-up starts a new runner, it retires the
previous turn's finished owner. Retirement requires that owner's
controller journal to be settled: every command answered, then a run
terminal
> - A restart can cut off a continuation turn. The recovered runner
answers that `turn.start` with `failed` and the nested code
`execution_indeterminate` ("it will not execute twice"), and the run
continues on a later turn to an accepted result
> - Retirement counted only `completed` commands as answered. A finished
run whose journal held that answered `turn.start` never counted as
settled, so the follow-up failed with
`retirement_refused=journal_commands_unsettled(turn.start.failed)` and
needed a Retry
> - This pull request counts definitive `failed` and `rejected` answers
as settled, except for runner lifecycle commands. An unknown-outcome
`turn.start` counts as settled only once a later `turn.start` completed,
which shows the run moved past it. Every other unknown or pending
command stays unsettled
> - The benefit is that a follow-up after a restart-interrupted, then
finished, run continues on its own

## Linked Issues or Issue Description

Refs #20140

**What happened?**
Local restart-chaos M1 K4/K6 rerun w-20261109T003126-s9701 (master
8e3b64a257), t07 (claude C1, K6):
- The previous run `9cb2c0b3` lost a continuation turn to a restart. The
runner answered that `turn.start` as `failed` with `result.result.code:
"execution_indeterminate"`.
- After the next restore it ran a new continuation to an accepted
result, and the run terminal was committed at 00:48:18.
- A hard kill then landed before the runner suspended, and recovery
finalized the result.
- Follow-up `372991c8` failed at 00:48:37 with
`runner_state_identity_mismatch:
prior_owner_terminal_state_indeterminate;
retirement_refused=journal_commands_unsettled(turn.start.failed)`.

**Expected behavior**
A command the runner definitively answered (`failed` or `rejected`)
leaves nothing outstanding, so it counts as settled. A `turn.start` with
an unknown outcome is never executed again by the runner, so once a
later `turn.start` completed, the run has moved past it and it also
counts as settled. The follow-up then retires the finished owner and
continues.

The following still count as unsettled:
- an unknown-outcome `turn.start` with no later completed turn;
- any other unknown-outcome command;
- a `pending` command;
- a failed runner lifecycle command, such as a failed `runner.suspend`
(the runner did not suspend).

**Steps to reproduce**
1. Finish a per-turn run whose controller journal holds a `turn.start`
answered `failed`, followed by a committed run terminal.
2. Start a follow-up. Before this change, retirement refuses with
`journal_commands_unsettled(turn.start.failed)`.

**Paperclip version or commit**
8e3b64a257 (wave). Branch rebased on current master.

## What Changed

- `remote-warm-session-recovery.ts`: the new
`unsettledControllerCommands` decides which commands are settled.
`isSettledRemoteWarmControlState` uses it.
  - `completed` is settled.
- An unknown outcome (raw `indeterminate`, or `failed` with
`execution_indeterminate` at `result.code` or `result.result.code`) is
settled only for a `turn.start` with a later completed `turn.start`.
- Other `failed` or `rejected` answers are settled, except for
`runner.suspend`, `runner.drain` and `runner.shutdown`.
- `native-session-executor.ts`: the retirement refusal message lists
unsettled commands with the same rule.
- `native-recovered-owner-followup.test.ts`: a red/green test whose
journals are in real lifecycle order.
- Admitted: a `turn.start` answered `failed` or `rejected`; a superseded
unknown-outcome `turn.start` in the runner's stored nested shape; a
superseded raw `indeterminate`.
- Held: the same unknown-outcome answer with no later completed turn; a
failed `runner.suspend`.

## Verification

- Red/green: on master, the admitted cases fail with exactly the t07
error. With the change they are admitted. The held cases stay held. If
only `result.code` is checked, the unsuperseded case fails.
- `vitest run` of `native-recovered-owner-followup.test.ts`,
`remote-warm-session-recovery.test.ts` and
`native-session-executor.test.ts`: 3 files, 1403 tests passed.
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.

## Risks

- Low risk. Definitive answers to non-lifecycle commands, and
unknown-outcome turn starts that a completed later turn superseded,
become settled.
- The run terminal requirement, post-terminal live-work checks, and
every lifecycle and process proof are unchanged.
- The same rule now also applies to remote warm recovery's settled
check, where a definitively answered command is equally finished.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 20:47:05 -06:00
DottaandClaude Opus 5.5 a0b9895bbd fix(native): roll back an undelivered warm attach rotation once its runner is proven dead (#20146)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A follow-up turn can attach to the previous turn's warm local
runner. The transport first rotates authority: it archives the previous
epoch (suspended runner state and settled controller) under
`authority-epochs/` and writes a new control plane that holds only the
`run.attach` command
> - A hard kill in that window, before the runner connects, leaves the
root with the new control plane and no `runner/runner-state.json`.
Restart recovery proves the warm runner dead and classifies the run
`resume_dead_runner`
> - The executor saw a root with the run's own identity and no runner
state, called its authority indeterminate, and quarantined it. The run
failed with `runner_state_identity_mismatch: authority_indeterminate`
and needed a Retry
> - The attach was never delivered, and the runner that would have
received it is proven dead, so it cannot have taken effect. The root's
real authority is still the archived previous epoch
> - This pull request rolls back such an undelivered rotation, so the
follow-up continues from the previous turn
> - The benefit is that a restart in the first second of a warm
follow-up no longer needs a Retry

## Linked Issues or Issue Description

Refs #20140

**What happened?**
Local restart-chaos K13 regression storm w-20261108T235957-s9401 (master
4420a5adcf), task t22 (codex C1):
1. Follow-up run `7b1b1650` started at 00:05:56 as a warm attach to the
previous run's runner (pid 11436).
2. The transport archived the previous epoch (`313ee831`: runner
`suspended`, every command completed) to `authority-epochs/epoch-2c2a…`.
It wrote a new control plane with `run.attach` pending,
`connectionCount` 0, no events, no delivery counts and
`bootstrapHistory.adopted` false.
3. A K1 at 00:05:57 killed the server before the runner connected.
Recovery stopped pid 11436 and claimed `resume_dead_runner`.
4. The executor found `runner/` non-empty (provider state) but without
`runner-state.json`, returned `authority_indeterminate`, and quarantined
the root. A Retry ran fresh.

**Expected behavior**
When a `resume_dead_runner` claim proves the local runner gone and the
run's own root holds only an undelivered `run.attach` over an archived
suspended epoch, recovery restores that epoch and continues. If delivery
is uncertain (any connection, event, delivery count or other command) or
there is no dead-runner claim, it still fails closed.

**Steps to reproduce**
1. Start a warm follow-up and hard-kill the control plane after the
authority rotation, before the runner connects.
2. Restart. Before this change, the follow-up fails with
`runner_state_identity_mismatch: authority_indeterminate`.

**Paperclip version or commit**
4420a5adcf (wave). Branch rebased on current master.

## What Changed

- `native-session-executor.ts`: the new
`rollBackUndeliveredAttachRotation` runs only for a `resume_dead_runner`
claim on this run with a local runner. It acts only when all of these
hold:
  - the active control plane is this run's own exact identity;
  - its only command is a pending `run.attach`;
- `connectionCount`, `ackedSourceSeq` and the delivery counts are 0,
there are no committed events, and it was never adopted and issued no
credentials;
  - it has no warm, staged or completed transition;
  - there is no `runner/runner-state.json`;
- the latest archived epoch is named by its identity's digest, shares
the runner instance, lease and session, and holds a `suspended` runner
state for that identity.

It moves the undelivered control plane to `continuity-breaks/` as
evidence, then puts the epoch's control plane and runner state back. The
executor then sees the previous owner and takes the normal
suspended-previous-owner path.
- `native-recovered-owner-followup.test.ts`: a red/green test of the
undelivered rotation. A possibly delivered attach (`connectionCount` 1)
and a missing dead-runner claim both still fail closed.

## Verification

- Red/green: on master, the undelivered case fails with exactly the t22
error. With the change, the follow-up is admitted: the previous control
plane is restored, `authority-epochs` is gone, and the undelivered
control plane is kept under `continuity-breaks`. The two fail-closed
cases fail on both.
- `vitest run` of `native-recovered-owner-followup.test.ts`,
`native-session-executor.test.ts`,
`native-runner-restart-recovery.integration.test.ts` and
`native-session-root-entries.test.ts`: 4 files, 1508 tests passed (14
skipped); after rebasing onto #20140,
`native-recovered-owner-followup.test.ts` again: 65 passed.
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.

## Risks

- Medium-low risk. The rollback changes durable state, but only for a
closed shape that proves the attach never reached any runner, after
recovery proved the runner process dead.
- A crash in the middle of the rollback leaves a root that still fails
closed, as before this change.
- The test exercises admission up to tool authority, not a full
real-runnerd turn. A chaos rerun of the K1 warm-follow-up window is the
remaining check.

## 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

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 19:36:44 -06:00
DottaandClaude Opus 5.5 bd97a3e6f7 fix(native): retire a finished per-turn owner past its own quarantined interrupted bootstrap (#20140)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A follow-up turn on a per-turn session must retire the previous
turn's runner state before it starts a new runner. Retirement proves the
previous owner finished, and it also proves that every quarantined copy
of that session root is settled
> - If restart recovery interrupts a run's own start (for example a hard
kill during `session.open`), recovery proves the half-started bootstrap
held no provider work, quarantines that root, and bootstraps the same
run again. The quarantined copy keeps the run's identity
> - After that run finished, retirement checked the old bootstrap copy
as if it were a finished owner. An unfinished `session.open` (or an
opened session without a turn) is never "settled", so the follow-up
failed with `runner_state_identity_mismatch:
prior_owner_terminal_state_indeterminate` and needed a Retry
> - This pull request skips a quarantined copy of the same owner when
the same bootstrap proof that let recovery quarantine it still holds
> - The benefit is that a follow-up after a restart-interrupted start
continues on its own

## Linked Issues or Issue Description

Refs #20137

**What happened?**
Local restart-chaos K13 regression storm w-20261108T235957-s9401 (master
4420a5adcf): 102 of 105 tasks passed. Two of the three failures share
this cause.

- **t58 (codex C1):**
- A K1 at 00:15:42 interrupted run `78dd97f1` during its first
`session.open`. Recovery quarantined that root (`run.prepare` completed,
`session.open` pending, no events) and bootstrapped again.
- The run then completed. A second K1 hit 190 ms after its result was
accepted, and recovery finalized the result.
- Follow-up `def668a6` failed with `runner_state_identity_mismatch:
prior_owner_terminal_state_indeterminate;
retirement_refused=quarantine_journal_commands_unsettled(session.open.pending)`.
- **t67 (claude C1):** the same pattern. The quarantined copy of run
`990936c0` holds a completed `session.open` with only session-open
events and no turn, so the refusal was
`quarantine_journal_terminal_unsettled`.

Both copies are in the kept instance's quarantine directory under the
previous run's own identity. Each Retry succeeded.

**Expected behavior**
A quarantined copy of the finished owner's own earlier bootstrap that
provably held no provider work does not hold the follow-up. Retirement
proceeds and the follow-up starts without a Retry.

**Steps to reproduce**
1. Let a per-turn run's first bootstrap be quarantined after a restart
(the run bootstraps again and finishes).
2. Start a follow-up turn.
3. Before this change, retirement refuses with
`quarantine_journal_commands_unsettled(session.open.pending)` or
`quarantine_journal_terminal_unsettled`.

This is not a code regression. The quarantine-copy check dates from
#19061. Today's recovery fixes let more interrupted starts bootstrap
again within the same run instead of blocking, and each such restart
leaves this kind of copy behind.

**Paperclip version or commit**
4420a5adcf (wave). Branch rebased on current master.

## What Changed

- `native-session-executor.ts`: the quarantine loop in
`inspectFinishedPerTurnRunnerdOwner` skips a copy when both of these
hold:
  - its durable identity matches the finished owner exactly;
- `runnerdStateProvesIncompleteBootstrap` holds for it. That is the
proof restart recovery uses before it quarantines an interrupted
bootstrap: no provider turn, and for a local runner, its journal and
processes proven gone.
  
  Every other copy still has to pass the settled-projection proof.
- `native-recovered-owner-followup.test.ts`: a red/green test covering
both cases:
  - an interrupted bootstrap copy is retired past;
  - a copy that had already issued a turn still holds the follow-up.

## Verification

- Red/green: on master, the new admitted case fails with exactly the t58
error. With the change it is admitted. The turn-issued copy is refused
on both.
- `vitest run` of `native-recovered-owner-followup.test.ts`,
`native-session-executor.test.ts` and
`native-runner-restart-recovery.integration.test.ts`: 3 files, 1504
tests passed (14 skipped).
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.

## Risks

- Low risk. The skip reuses the existing bootstrap-incomplete proof and
requires an exact identity match, so a foreign or work-holding copy
still blocks. Nothing is deleted; the copy stays in quarantine.
- Not covered: t22 in the same storm, a follow-up whose own unconnected
`run.attach` root was hit by a K1 (`authority_indeterminate`), has a
different shape and is tracked separately.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 19:21:32 -06:00
DottaandClaude Opus 5.5 6451d2bfbf fix(native): verify a staged attachment restart on the claimed sandbox lease (#20136)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A follow-up codex run on a per-turn Daytona sandbox gets a fresh
sandbox, with harness state restored from the previous turn's
checkpoint, and attaches the previous runner session to the new run
through a staged attachment
> - A graceful restart during that start suspends the run. The next
controller reattaches to the surviving remote runner, after proving it
is on the sandbox lease the restart claim names
> - The staged-attachment path required the lease to have been acquired
as `resumed`. A per-turn follow-up's lease is `created`, so every such
restart was refused with
`native_runner_staged_attachment_recovery_unproven`
> - The run then needed a Retry
> - This pull request binds the staged restart to the claimed lease the
same way the ordinary remote reattach does: same provider lease, same
remote directory, and not a replacement sandbox
> - The benefit is that a per-turn follow-up interrupted by a restart
continues on its own

## Linked Issues or Issue Description

Refs #20103

**What happened?**
Daytona per-turn restart-chaos wave w-20261108T225520-s9501 (master
15b987d9b8, image cbbe8224). Two codex C1 follow-up runs, created during
a K2 graceful drain at 23:11:45, were suspended mid-start:
- `4d1d3563` (t07);
- `71b43ea1` (t08).

Two to three seconds after the controller came back, both failed with
`native_runner_staged_attachment_recovery_unproven`, rested in
`native_continuation_requires_reconciliation`, and needed a Retry. The
stack shows the first guard in `verifyStagedAttachmentRestart`. Both
runs' environment leases were acquired with
`sandboxLeaseAcquisition.outcome: "created"`, because per-turn mode
creates a fresh sandbox for each turn. The guard accepted only
`"resumed"`.

**Expected behavior**
When the restart claim's provider lease and remote directory match the
run's own lease, the staged attachment's restart is verified as before,
and the run continues without a Retry. The rest of the staged proof is
unchanged. A replacement sandbox, or a different provider lease or
directory, is still refused.

**Steps to reproduce**
1. Run a codex follow-up on a per-turn Daytona environment, so the lease
is `created` and the start stages an attachment.
2. Gracefully restart the control plane during the start.
3. Before this change, the restarted run fails with
`native_runner_staged_attachment_recovery_unproven`.

**Paperclip version or commit**
15b987d9b8 (wave). Branch rebased on current master.

## What Changed

- `verifyStagedAttachmentRestart` (`native-session-executor.ts`) no
longer requires `sandboxLeaseAcquisition.outcome === "resumed"`. It
requires the same lease binding as `verifyRemoteRunnerReattachment`:
- the target's provider lease equals the claim's
`remote.providerLeaseId`;
  - the target's remote directory equals the claim's `remoteCwd`;
  - the lease is not a `replacement` sandbox.
- A new test case in `native-session-executor.test.ts` covers a created
sandbox (admitted), a replacement sandbox, another provider lease, and
another remote directory (all refused).

## Verification

- Red/green: on master, the created-sandbox case fails with
`native_runner_staged_attachment_recovery_unproven`. With the change it
reaches the staged recheck. The three refusal cases are refused on both.
- `vitest run` of `native-session-executor.test.ts` and
`native-restart-recovery-isolation.test.ts`: 2 files, 1305 tests passed.
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (`server`): passed.

## Risks

- Low risk. The check now matches the ordinary remote reattach, which
already admits created leases. Everything after it is unchanged: the
encrypted staged header, the source run and result, the template digest,
and the remote runner identity are all still proven before any RPC.

## 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

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 17:59:56 -06:00
DottaandClaude Opus 5.5 776f4cb602 fix(native): restart an interrupted remote bootstrap on a resumed reusable lease (t06) (#20103)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A native run on a remote sandbox must survive a control-plane
restart; a bootstrap interrupted before its first turn is restarted on
the same run
> - With a reusable (warm) sandbox lease, the restart always resumes the
same sandbox. The interrupted runner's state is still on disk there:
never suspended, and with no provider turn
> - The resumed check accepted only a suspended checkpoint or no state
at all, so it failed closed with `resumed_not_suspended`, and the task
needed a Retry (restart chaos t06)
> - The pre-phase had already proven no turn was sent and had stopped
the stale runner, but that proof never reached the resumed check
> - This pull request carries that proof forward, for this run only, and
starts the bootstrap again on the resumed sandbox
> - The benefit is that a warm task interrupted during startup continues
on its own after the restart

## Linked Issues or Issue Description

**What happened?**
In restart-chaos wave w-20261108T192459-s9501 (Daytona warm, claude C1),
run 9bf86b59's runner reached transport-ready at 19:37:42 UTC. The
control plane was then down (another task's K4, then this task's K1).
Restart recovery classified the run `bootstrap_incomplete` and restarted
it on the same run at 19:41:51. The reusable lease resumed the same
sandbox. `inspectRemoteHarnessState` found this run's runner state with
`lifecycle` other than `suspended`, and the run failed at 19:41:59 with
`runner_ingress_unavailable: runnerd process failed:
runner_harness_state_mismatch: resumed_not_suspended`. The task needed a
manual Retry. Per-turn and non-reusable leases do not resume, so they
take another branch and were unaffected.

**Expected behavior**
A same-run restart of a bootstrap that provably sent no turn starts the
bootstrap again on the resumed sandbox, with no Retry. It must never
take over a live provider session or another run's warm session.

**Steps to reproduce**
1. Run a task on a reusable (warm) Daytona lease.
2. Kill the control plane after the runner connected and before the
first turn, so the run is `bootstrap_incomplete`.
3. Before this change, the restart fails with `resumed_not_suspended` on
the resumed lease.

**Paperclip version or commit**
master at d007afbf86 (the wave ran on c5a172a183).

## What Changed

- `native-session-executor.ts`:
- **Pre-phase:** the `bootstrap_incomplete` remote-sandbox pre-phase
clears any earlier proof for the run, then records a per-run proof
(`recordRemoteBootstrapRestartProof`). It records one only for a
confirmed stop:
    - `absent_confirmed`: verification reported `process_not_running`;
    - `stopped` or `killed`: the exit was confirmed after the signal.

An uncertain probe or a runner that outlives SIGKILL records nothing
(`stopStaleRemoteRunnerBeforeBootstrap` now distinguishes these
outcomes).
- **Inspection:** `inspectRemoteHarnessState` also returns the `runId`
of a not-suspended runner state (`notSuspendedRunId`). Its other fields
are unchanged.
- **Resumed check:** on a `bootstrap_incomplete` restart, a
not-suspended state with no backup is restarted only when all of these
hold:
    - the on-disk state is this run's own;
    - the proof is present;
- the interrupted session folder moved aside by rename, kept as evidence
and never deleted. The runtime root, the sessions parent and the folder
must each be a real, non-symlink directory.

    The proof is consumed only after the move succeeds.

It then claims a fresh session through the existing
`claimUntouchedRemoteSession`, which still requires an unconnected
controller with matching identity.
- Every other case keeps `runner_harness_state_mismatch:
resumed_not_suspended`.

## Verification

- Red/green: a new resumed-lease scenario, `interrupted_bootstrap`, in
"bootstraps only an untouched provider session in a $outcome workspace
lease". It fails without the change and passes with it. It checks that
the old session folder is kept beside the new claim and that the claim
runs exactly once.
- Counter-cases that still fail closed, with nothing moved aside:
`interrupted_bootstrap_other_run` (a previous warm run's state on disk),
`interrupted_bootstrap_unproven` (no pre-phase proof) and
`interrupted_bootstrap_symlink_parent` (a symlinked sessions parent).
The existing warm "no-proof" case keeps `resumed_not_suspended`.
- Stale-runner stop: "does not confirm absence when the process probe is
uncertain", "reports a runner that outlives SIGKILL as not stopped", and
"records a bootstrap restart proof only for a confirmed stop" (one case
per outcome).
- `pnpm exec vitest run
src/services/native-runtime/native-session-executor.test.ts
src/services/native-runtime/native-runner-restart-recovery.integration.test.ts`
(server): 2 files, 1440 tests passed (14 skipped).
- `PAPERCLIP_TYPECHECK_LOW_MEMORY=1 pnpm typecheck` (server): passed.

## Risks

- **Taking over a live session:** this is the risk to watch. It is
bounded by every gate together: the `bootstrap_incomplete` claim, the
pre-phase proof from the restored controller record (no turn sent) with
the stale runner stopped, this run's own on-disk state, no backup, the
folder move, and the existing unconnected-controller claim. A failure at
any step keeps the current fail-closed error.
- **Upgrade safety:** the old runner's session folder is kept by rename,
never deleted. The change applies only to state a restart left behind,
so old-saved state takes the same gated path.

## Model Used

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

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 15:01:30 -06:00
DottaandClaude Opus 5.5 d007afbf86 fix(native): let a follow-up wait out the previous turn's warm release instead of failing busy (#20068)
## Thinking Path

- With a warm lifecycle, one session serves consecutive turns on a task.
A follow-up comment wakes the next run, which claims the warm session's
instruction copy and reuses the session.
- #20048 makes warm the default on remote sandboxes. Its merge condition
includes "no restart or follow-up ever leaves a task needing Retry".
- In the #20048 Daytona chaos wave, task t12's follow-up run was created
43 ms after the previous run settled. The previous run was still
releasing its warm session, so `claimWarmNativeInstructionCopy` saw it
busy and failed the run with `native_session_supervisor_busy`. The task
then needed a Retry.
- The release takes seconds and always finishes, so a follow-up should
wait for it rather than fail. A session busy because another run is
preparing or executing a turn is a genuine conflict and must still fail
at once, as existing tests require.

## Linked Issues or Issue Description

Refs #20048

**What happened?**
Wave w-20261108T142906-s9501, t12 (claude, warm): run 5b839da4 succeeded
at 14:46:36.224. The follow-up run f2bf2f05 was created at 36.267 and
failed immediately with `adapter_failed` /
`native_session_supervisor_busy`, from `claimWarmNativeInstructionCopy`
called by `instruction-working-copy.prepare`. Its automatic retry also
failed, and only a user Retry completed the task.

**Steps to reproduce**
1. Run a warm native session turn to completion.
2. While that run is still releasing its warm session (post-turn
instruction check, release, hand-back), admit the next run on the same
session.
3. The next run's instruction-copy claim throws
`native_session_supervisor_busy`.

**Expected behavior**
The follow-up waits for the previous run's release (bounded) and reuses
the session. A session held by a run that is still preparing or
executing fails admission at once, as before.

## What Changed

- `server/src/services/native-runtime/native-session-executor.ts`:
- When the provider turn ends, the executor records the session scope as
settling (`settlingNativeSessionScopes`). The outer `finally` clears the
mark once the run has handed every scope back.
- `claimWarmNativeInstructionCopy` waits, polling every 25 ms for at
most 30 s (`warmSessionReleaseWait`), while the warm entry is busy and
its scope is settling. It then re-reads the entry and runs the existing
checks. If the entry is still busy at the deadline, or busy for any
other reason, it throws `native_session_supervisor_busy` as before.
- No wait happens on the normal path (entry idle), so turn admission
adds no latency.
- `server/src/services/native-runtime/native-session-executor.test.ts`:
two cases.
- A follow-up claimed while the previous turn's post-turn check is held:
it waits, then succeeds once the release finishes. It fails on master
with the wave's error.
  - The release outlasts the bound: it fails busy.

**Previous-release state:** the change touches only in-memory admission
state, so no saved run or session state changes.

## Verification

- `cd server && npx vitest run
src/services/native-runtime/native-session-executor.test.ts
src/services/heartbeat/instruction-working-copy.test.ts`: 1301/1301
pass.
- With the wait removed (behaviour on master), the "release finishes"
case fails with `native_session_supervisor_busy`.
- The existing concurrency tests ("fences owned instruction preparation:
concurrent", and the settled-release ownership tests) still fail
admission at once.
- Not yet covered: the Daytona warm wave rerun for #20048.

## Risks

- **A wait that never ends.** The wait is bounded at 30 s and happens
only while the owner is past its turn, which always reaches the outer
`finally`. Every caller of the inner executor runs inside that `try`,
and attachment staging keeps the same session scope.
- **Hiding a real conflict.** Only a settling owner is waited for. A
preparing or executing owner fails at once, as the existing tests
assert.
- **Scope.** I tried a similar wait at execution admission, but it
conflicted with deliberate fences that reject a run during a settled
release (the existing "releases settled codex only under its current
owner" tests). It is not part of this PR.

## Model Used

Claude Opus 5.5 (`claude-opus-5-5`, Anthropic), 1M context window, tool
use and code execution, via Claude Code.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 13:57:32 -06:00
DottaandClaude Opus 5.5 b32ef9f111 perf(budgets): judge time to first visible agent activity; keep time to first text as a reported metric (#20077)
## Thinking Path

- The native speed budgets (plan invariant 8) judge how fast an agent
responds. They judged `task.time_to_first_token`: time to the first
deliverable **text**.
- In the clean local restart storm (w-20261108T153612-s9401), Claude
breached its TTFT budget (cold p50/p95 17.4/34.7 s against 16.5/30). The
per-run spans showed this was not a control-plane wait: in all 49 cold
runs (and 76% of warm), Claude started a tool call before writing any
text. Its first visible activity came at 7.4 s p50 from run creation;
first text came at 19.6 s. Codex never calls a tool first.
- So first text charges model tool work as latency for tool-first
adapters. What the user experiences as "the agent responded" is the
first visible activity: a text delta, a tool-call start, or a thinking
indicator.
- The coordinator decided: budgets judge time to first visible agent
activity from run creation, with the budget numbers unchanged; first
text stays a reported metric with no budget for tool-first adapters.

## Linked Issues or Issue Description

**What happened?**
Local storm s9401: the Claude TTFT budget breached on every aggregate,
while the control-plane steps (queue 0.05 s, prepare 0.3 s, runner
startup ~4 s, first provider event 1.3–1.8 s) were well within budget.
The rest of the first-text wait was Claude streaming tool input (about
5.5 s per call) and running tools before it wrote text.

**Steps to reproduce**
1. Run a Claude task whose first action is a tool call (most real
tasks).
2. Read the run log: `provider.time_to_first_agent_event` ends at the
tool call; `task.time_to_first_token` ends many seconds later at the
first text.
3. The speed budget judges the later one and reports a breach.

**Expected behavior**
The budget judges the first visible agent activity from run creation
(`task.time_to_first_agent_activity`). Time to first text is still
recorded and reported.

## What Changed

- `server/src/services/native-runtime/native-session-executor.ts`: when
the first meaningful agent event commits (the existing
`firstMeaningfulAgentEventKind`: text delta, tool-call start, or
reasoning), record `task.time_to_first_agent_activity`. It uses the same
detached anchor resolution as TTFT (accepted comment, answered question,
durable wake request, or run creation), so it adds nothing to the turn
path.
- `server/src/services/native-runtime/native-speed-budgets.ts`: the
metric is now named `time_to_first_activity` (was `ttft`), with
identical budget numbers. The type comment documents the definition and
why first text is unbudgeted.
- `server/src/services/native-runtime/native-run-trace.ts`: the budget
check judges `task.time_to_first_agent_activity` from run creation,
keeping the existing input-wait handling. `task.time_to_first_token` is
no longer budgeted.
- `tests/restart-chaos/ttft-baseline-stats.ts` and `ttft-baseline.ts`:
report first activity from run creation (the budgeted value) next to
TTFT.
- Docs: `doc/observability.md` (new span) and
`doc/plans/2026-11-07-ttft-baseline.md` (metric table).
- Tests:
- A tool-first turn records first activity at the tool call (5 s) while
TTFT records first text (16 s).
- A tool-first trace with slow first text but fast first activity is
within budget.
  - The existing budget tests now judge the activity span.

Observability path (AGENTS.md section 5.7): the new run-log span uses
only the existing `eventKind` and `anchor` attributes. Its name survives
run-log redaction intact; checked with `redactEventPayload`. The
operator OTLP gate is unchanged. It is not Telemetry.

## Verification

- `cd server && npx vitest run
src/services/native-runtime/native-speed-budgets.test.ts
src/services/native-runtime/native-run-trace.test.ts`: 44/44 pass.
- `cd server && npx vitest run
src/services/native-runtime/native-session-executor.test.ts -t "first
visible activity|first assistant text once|first-token timing"`: 7/7
pass.
- `npx vitest run --root tests/restart-chaos`: 159/159 pass; `tsc` on
`tests/restart-chaos` is clean.

## Risks

- **A metric rename.** Consumers of `run.performance.budget_exceeded`
see `metric: "time_to_first_activity"` instead of `"ttft"`. In-repo
there are none besides the tests; Phase 3's chaos speed grade switches
to the new span.
- **A looser budget for slow first text.** Intentional: first text is
reported, not judged. A regression in control-plane latency still shows
up in first activity.

## Model Used

Claude Opus 5.5 (`claude-opus-5-5`, Anthropic), 1M context window, tool
use and code execution, via Claude Code.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 12:32:42 -06:00
DottaandClaude Opus 5.5 c910651115 fix(native): start each rebound run with a fresh restart-continuation marker (#20053)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - When the control plane restarts during an agent turn, the runner
restores the same conversation. A Codex, Claude (ACPX) or OpenCode turn
lost in the restart is marked `provider_turn_lost_on_restore`, and the
run continues it once in the same conversation
> - That one continuation is guarded by a disposition-only recovery
marker in the session checkpoint. It is run state: it names a turn of
the run that used it
> - A follow-up run (a user comment on the same task) reuses the
provider session by re-binding the previous run's checkpoint to the new
run. Re-binding clears the run-scoped turn, result and request state,
but it kept the marker
> - The chaos K13 storm (wave w-20261108T134237-s9401) hit this three
times (t24 and t45 on Claude, t77 on Codex). The task's first run had
already used its restart continuation. The follow-up run inherited a
spent marker naming a turn it never had, so when a restart lost its own
turn, the driver kept the session closed. The run failed, and the user
had to click Retry
> - This pull request resets the marker at both re-bind sites, as for
every other run-scoped field
> - The benefit is that a restart during a follow-up turn continues on
its own instead of putting a Retry click on the user

## Linked Issues or Issue Description

Refs #19831 (durable ownership plan, restart continuation). Found by the
restart chaos campaign. In all three failed follow-up runs:

- After `resume_dead_runner`, the run emitted `turn.failed {code:
provider_turn_lost_on_restore, recoverable: true}` for its own active
turn.
- The checkpoint still carried `dispositionOnlyRecoveryConsumed: true`,
with `dispositionOnlyRecoveryTurnId` set to the previous run's
continuation turn.

## What Changed

- `native-session-resume.ts` (`rebindNativeSessionCheckpoint`) and
`native-session-executor.ts` (warm checkpoint rebind): a rebound run
starts with `dispositionOnlyRecoveryConsumed: false` and
`dispositionOnlyRecoveryTurnId: null`.
- Nothing changes inside a run: the driver's reopen rule
(`mapTerminalTurn`) and `nativeRestartInterruptedTurnId` are untouched.
The first commit changed the helper; review found the driver keeps its
own copy of the rule, and the second commit reverts the helper in favour
of this fix.

## Verification

- `native-session-resume.test.ts` "retains provider identity but clears
prior turn and event state" now seeds a spent marker on the previous
run. It fails on `master` and passes here.
- `native-session-executor.test.ts` "starts a new run's usage from the
prior run's total when a warm checkpoint resumes" (3 cases) seeds the
first run's checkpoint with a spent marker and asserts that the second
run starts with it reset. It fails on `master` and passes here.
- The other `native-session-resume.test.ts` tests pass. One test,
"archives a damaged prior epoch before completing guarded same-task
replacement with real runnerd", fails locally identically with and
without this change (ENOENT under `authority-epochs`, from the
real-runnerd environment). It's left to CI.
- Next: a targeted chaos rerun (Codex and Claude C1 under repeated K2)
on this branch. I'll add the result here.

## Risks

- **Previous-release story (upgrade-safe run state):** no persisted
shape changes. A run re-bound by this build gets a fresh marker. A run
re-bound before the deploy, still in flight with an inherited spent
marker, behaves as before: a lost turn falls back to Retry, once.
- Inside a run, nothing changes: the marker still bounds same-run
continuations, together with the provider-attempt restart budget.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, with tool use and code
execution in Claude Code.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 08:49:38 -06:00
Nicky Leach e7e870cfc4 fix(native): decide warm and adopted Runner process reuse from one key (#20005) 2026-11-08 01:02:50 -08:00
DottaandClaude Opus 5.5 a4dbde6181 refactor(recovery): judge native owner processes with the shared prover (#19997)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Native runs record the server and adapter processes that own them,
and recovery must prove an owner gone before it takes over or releases
its work
> - Phase 2 of the durable ownership plan gave the repository one
prover, `proveOwnerGone`. The native runtime still had four private
proofs of the same fact
> - The private proofs disagreed with the shared rules in edge cases:
some judged a PID from another PID space, and one accepted an
inconsistent start time as proof of reuse
> - This pull request moves those four proofs onto `proveOwnerGone` and
deletes the private liveness code
> - The benefit is one rule for "the owner is gone" across native
recovery, with the stricter shared behaviour where they differed

## Linked Issues or Issue Description

Refs #19933, #19950, #19953 (the shared ownership path and earlier Phase
2 kinds).

**What is the problem?**
Native recovery proved dead owners with four private checks instead of
the shared prover. The checks used different rules for PID spaces,
reused PIDs and unreadable start times.

**What should happen?**
Every native owner proof uses `proveOwnerGone`. Only a `gone` verdict
releases or takes over. The remote fence and the one-release legacy
fallback stay as they are.

**Why does it matter?**
Recovery decisions about the same process must agree. A dead PID in
another PID space must never be used as proof.

## What Changed

- `native-restart-recovery.ts` `evaluateNativeControllerTakeover`: the
local-process branch now calls `proveOwnerGone`. The remote fenced
branch (#19830), the `operator_attested` sentinel and the null-host
fallback (`processSpaceUnrecorded` with `legacyHostFallback`, recorded
by callers as `legacy_host_unknown_dead_pid_proof`) are kept. Reasons
are unchanged, plus a new `controller_pid_start_inconsistent`. Owners
built from receipts with no PID space are judged in this PID space:
their callers check the recorded host first.
- `native-failed-run-owner-release.ts`: `recordedProcessMayBeLive` is
deleted. `runProcessMayBeLive` and `controllerMayBeLive` release only on
a `gone` verdict. Each use of the legacy fallback is recorded as
`legacy_host_unknown_dead_pid_proof` when the release commits.
- `native-session-executor.ts`: `verifiedRecoveryProcessIsAlive` is
replaced by `recoveryProcessMayBeAlive`, which is false only when the
prover proves the runner gone. Signalling a recovered runner requires a
proven same process.
- `native-local-process-stop.ts` `recordedLocalExecutionStopped`: the
bound identity (launch event, host, PID, group, start time) is judged by
the prover. It uses `process_host_hash` when the row has one.
- New `native-runtime/native-owner-stamps.ts`: controller and
adapter-process stamp builders, shared with the ownership registry.

Not changed: `proveLocalWorkspaceOwnerStopped` (workspaces),
`evaluateNativeProviderProcesses`, the stop observation in
`recordNativeLocalProcessStop`, and `runProcessMayBeLive` in
`native-workspace-sync-retention.ts`.

## Verification

- `cd server && npx vitest run
src/services/native-runtime/native-restart-recovery.test.ts
src/services/controller-process-identity.test.ts`: 51 passed.
- `cd server && npx vitest run
src/services/native-runtime/native-failed-run-owner-release.test.ts`: 14
passed.
- `cd server && npx vitest run
src/services/native-runtime/native-controller-host-recovery.test.ts`: 2
passed.
- `cd server && npx vitest run
src/services/quarantined-task-retry.test.ts -t "keeps quarantine"`: 18
passed. `explicit-native-continuation.test.ts`: 414 passed.
`ownership-reconciliation-report.test.ts`: 23 passed.
- Red with the master versions of the two modules: 3 new tests fail
("accepts a reused PID only when the live process started definitely
later", "never releases on a dead PID recorded in another PID space",
"keeps the one-release fallback for a run process saved before its PID
space, and records it"). The tests were written after the code.
- Two fixtures changed to match the shared rules:
- `controller-process-identity.test.ts`: the "recycled" case recorded a
start after the live process, which is an inconsistent stamp. It now
records an earlier start (a real reuse), and the inconsistent case is
asserted as alive.
- `quarantined-task-retry.test.ts` `worker_alive`: the live worker now
records this process's real start time. The old fixture was a reused
PID, which the prover correctly proves gone.
- `cd server && npx vitest run
src/services/native-local-process-stop.test.ts`: 5 passed (review round
1). With the master module, 2 fail: the other-PID-space case and the
reused-PID case.
- Not run locally: typecheck (CI runs it) and the wide suites.

## Risks

Behaviour changes, all from the shared rules:
- A live PID observed to start before the recorded controller is no
longer accepted as recycled (`controller_pid_start_inconsistent`; the
run waits for evidence).
- A failed-run owner whose recorded adapter process or controller is in
another PID space, or is a remote sandbox PID, is no longer released by
a local probe. It keeps the lease path.
- An unreadable start time is no longer exit evidence for a recovered
local runner.
- A local execution whose PID was reused by a later process now counts
as stopped. Before, any live PID blocked the proof.
- A local execution whose row records another PID space is no longer
counted as stopped by a dead local PID.
- A PID space that cannot be read here makes a hostless receipt owner
unprovable.

No persisted state changes. Rows saved by the previous release keep the
one-release null-host fallback, as before.

## Model Used

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

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-08 02:35:15 -06:00
DottaandClaude Opus 5.5 f755361ffe fix(recovery): deliver a steered message the restart lost before the model read it (#19962)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A user can steer a running Codex or Pi turn: a comment goes into the
live turn instead of waiting for the next run
> - The provider acknowledges the steer at once, but the model reads it
only at its next step, after the in-flight tool call
> - A control-plane restart in that window kills the provider with the
message in memory. Restart recovery starts a continuation turn that does
not carry the message. The message is lost and no error shows
> - The restart chaos harness showed this in 6 of 6 steered runs (Codex,
K1, K2 and K6, 2 samples each): steer acknowledged, run succeeded, no
reply to the steered message
> - This pull request makes restart recovery deliver every acknowledged
steer that the model did not read, exactly once
> - The benefit is that manual Steer no longer loses messages on
restart, and the planned automatic steering can ship on top of it

## Linked Issues or Issue Description

**What happened?**
A comment steered into a running Codex turn got no reply when a
control-plane restart (SIGKILL, SIGTERM or crash loop) happened during
the agent's tool call. The run succeeded, and the steered comment had no
effect.

**Steps to reproduce**
1. Start a Codex task that runs a 40-second command.
2. During the command, post a comment and click Steer. The provider
acknowledges it.
3. Restart the control plane before the command ends.
4. Recovery resumes the turn with a continuation. The agent finishes the
task and ignores the comment.

**Expected behavior**
The agent reads and handles the steered comment once, after recovery.

**Root cause**
The provider keeps acknowledged steering input in memory until its next
model step. The restart continuation
(`paperclip.native-continuation.v1`) only told the model to continue the
current request, so the acknowledged input was gone.

## What Changed

- `unreadSteeredMessageIds` (runner package): derives
acknowledged-but-unread steers from run-log events in order. A
`steering_acknowledgement` item adds the message id (once per id). A
`userMessage` item in the same turn reads the oldest unread steer. Codex
records each steered input as one `userMessage` item when it enters the
conversation. A `userMessage` item in a later turn reads all earlier
steers, because the continuation carries them. `turn.completed` reads
all steers.
- `readUnreadSteeredMessages` (server): reads those facts from
`heartbeat_run_events` (only transport-validated events with a
`sourceEventId`). It also reads the comment or interaction text for the
same company and issue. The run log is the durable record of both
"acknowledged" and "read", so no new column is needed.
- The restart continuation now includes `steeredMessages` and one
instruction to handle them, oldest first. The runtime reads them through
a lazy `getUnreadSteeredMessages` option, only when a restart
continuation starts. Native recovery wires it for every run.
- `queuedInteractionSteeringBody` is extracted, so recovery rebuilds a
steered interaction response with the same text the steer sent.
- Fake Codex gets `--consume-steer`, which emits the `userMessage` item
for an accepted steer, like real Codex.

## Verification

- Red/green live test with real runnerd and fake Codex
(`runnerd-restart-continuation.test.ts`, "delivers a steered message the
restart lost exactly once"): start a held turn, steer it, SIGKILL runner
and provider, restore and recover.
- "unread": the continuation carries the message exactly once. Without
the runtime change this test fails.
- "read" (`--consume-steer`): the continuation does not carry it again.
- Both: after the continuation completes, a later restart has nothing to
deliver.
- `steering-delivery.test.ts`: ordering, dedupe, initial-input,
later-turn and completed-turn rules.
- `unread-steered-messages.test.ts` (embedded Postgres): ignores events
without a source id and messages from other issues. It reads interaction
text, ignores model-output items as read evidence, and returns nothing
after the continuation input.
- `pnpm vitest run src/steering-delivery.test.ts
src/live/runnerd-restart-continuation.test.ts` (runner) and `pnpm vitest
run src/services/native-runtime/unread-steered-messages.test.ts`
(server): pass on the rebased revision.
- `issue-queued-comments-routes.test.ts` and
`native-session-runtime.test.ts -t restart`: pass.
`native-session-resume.test.ts` "archives a damaged prior epoch…" fails
locally on plain `origin/master` too (local runnerd binary); CI runs it
with a fresh build.
- Restart chaos (Codex steer mode, K1/K2/K6) runs after this lands in
the harness slot. Before: 0 of 6 steered messages answered.

## Risks

- Duplicate delivery: a provider that records steered input without a
`userMessage` item, or a `userMessage` event lost in the crash window
before persistence, makes recovery send the message again. The model
then sees it twice. That is safer than losing it, and the instruction
asks the model to handle each one once.
- Pi (ACPX) steering has no `userMessage` read evidence today, so a Pi
steer that the model already read before a restart may arrive again in
the continuation.
- Only the restart continuation carries the messages. Other recovery
paths start after a completed turn, which already read every steer.
- No schema or migration change. A session saved by an earlier release
resumes normally; its run log already holds the acknowledgement events.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, via Claude Code with
tool use (shell, file editing, 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 22:22:52 -06:00
DottaandClaude Opus 5.5 bf3a067076 feat(recovery): settle the finalizer and cleanup leases on the shared ownership path (#19950)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Native runs keep their ownership in `native_run_finalizations`, and
the shared ownership reconciler now settles proven-gone owners (Phase 2
of the durable ownership plan)
> - The finalizer lease (`native-finalizer:*`, 5 min) and the
retained-session cleanup lease (`native-cleanup:*`, 60 s) recorded only
a random token. They named no holder process
> - A server killed while it finalized or cleaned up kept the run
waiting for the whole lease. The lease was released by age alone. A
graceful shutdown also keeps an in-progress finalizer lease for the next
boot to wait out
> - This pull request records the holder process with each claim and
moves both kinds onto the shared prover and a compare-and-swap settle
> - The benefit is that a dead holder's run continues in the first pass
after boot, and a live or unprovable holder is never released

## Linked Issues or Issue Description

Refs #19933 (the settle hook and the first moved kind, merged).

**What happened?**
A finalizer or cleanup lease whose server process died stayed held until
the lease expired (5 min or 60 s). The run stayed `running` and its
follow-up work waited.

**What did you expect?**
The next boot proves the dead holder gone and frees the lease at once. A
live holder, or one that cannot be proven gone, keeps its lease.

**Steps to reproduce**
1. Accept a native result and let the finalizer claim it.
2. Kill the server (SIGKILL) before the finalizer commits.
3. Start the server. The run stays `running` for up to 5 minutes.

## What Changed

- `native_run_finalizations.lease_holder` (jsonb, migration 0446):
`{token, bootId, pid, hostHash, processStartedAt}` of the process that
took a token-only lease. It names the holder only while `token` equals
`lease_owner`, so renewals keep it and a later lease never inherits it.
The executor's `controller_*` columns are not changed.
- The finalizer claim (`native-run-finalizer.ts`) and the cleanup claim
(`native-session-executor.ts`) write it in the same UPDATE as the lease,
from `currentControllerProcessStamp()` (no I/O).
- New `native-token-lease-settlement.ts`: compare-and-swap settle that
expires exactly the proven-gone holder's outstanding lease, after it
notifies the finalization or cleanup work that the expiry frees.
- Both claims also wake the ownership worker queue in their transaction,
so a quiet worker watches the new holder (Greptile round 1).
- `ownership-registry.ts`: `native_finalizer_lease` and
`native_cleanup_lease` register `settle`. Their owner is the holder
process; rows without a holder keep the token fence. Listings cover
outstanding leases only.
- `heartbeat/recovery.ts`: restart recovery settles both kinds before it
finalizes and schedules cleanup. A failure is logged and the reconciler
pass retries it.
- Two sparse partial indexes on `lease_expires_at` for the two listings,
so the settle watch re-check stays indexed.

Bespoke code deleted: none. These kinds had no liveness check; their
only release was lease age (the takeover in the claim), which stays as
the fence for unprovable holders.

## Verification

- `cd server && npx vitest run
src/__tests__/heartbeat-native-restart-suspension.test.ts -t
"finalizer|cleanup|holder|exact lease"`: 12 passed (rerun after the
rebase on master). The crash-point test also asserts the ownership wake
for its run; it fails without the signal.
- `cd server && npx vitest run
src/__tests__/ownership-reconciliation-report.test.ts`: 17 passed.
- Red on the base branch (server code at `bea3bfb20b`, tests and schema
from this branch): 7 new tests fail, 5 pass (the 5 are existing tests).
Red: the crash-point restart test, the two reconciler settle tests, the
three live/unprovable counter-cases (owner was a token fence), and the
exact-lease CAS test. The tests were written after the code.
- New tests:
- crash point: a finalizer claim was written and its holder killed
before commit; the next restart finalizes the run, and this boot's claim
stamps itself as holder;
- a dead finalizer or cleanup holder is settled by a recording pass,
never by a read-only pass (`record: false`); the accepted result and
phase are untouched;
- live counter-cases: a live earlier-boot PID (`pid_alive`), the current
boot (`current_process`), a dead PID in another PID space
(`different_process_space`, unprovable) keep the lease through a pass
and a restart;
- a holder written for another token, and a holderless row of the
previous release, stay token fences, also with
`PAPERCLIP_EPHEMERAL_SERVER=true`;
- settle refuses a lease taken over after the proof
(`owner_changed_since_proof`).
- Not run locally: typecheck (CI runs it) and the wide suites.

## Risks

- Previous-release story (rules/upgrade-safe-run-state.mdc): rows saved
by the previous release have no `lease_holder`. They stay token fences
and the existing claim takes them over at expiry. Neither lease outlives
5 min, so this covers at most 5 min after the upgrade. A rollback
ignores the new column.
- Unprovable holders (other host or PID space, unknown space): no
operator action. The lease is short and self-expiring; at expiry the
next claim takes it over and the old holder's next token
compare-and-swap fails. That fence is the handoff. A different host is
never proof.
- The settle only expires a lease. Finalization and cleanup still run
under their own checks (cleanup keeps its maintenance-history proofs).
Settling ownership does not settle the accepted result, workspace
preservation, or accounting.
- Migration adds a nullable column and two partial indexes on a sparse
predicate. Low risk.

## Model Used

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

## 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

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Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 22:16:34 -06:00
DottaandClaude Opus 5.5 a4a3e342ec fix(recovery): charge a restart attempt only when the provider accepted a turn and made no progress (#19948)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A run has an execution recovery budget: three provider attempts for
native runs, and two failure retries for legacy runs
> - In the restart chaos campaign, control-plane restarts used up that
budget for runs that were healthy (RC-22, 22b, 22c, 40 and 60)
> - #19720 and #19747 fixed two variants with watermark heuristics, and
legacy interrupted preparation still spent the failure budget
> - The durable-ownership plan (section F, invariant 5) asks for one
rule: charge an attempt only when a recorded outcome proves that
provider work started and no progress followed
> - This pull request adds that rule and moves the native restart charge
and the legacy preparation retry onto it
> - The benefit is that a restart never spends budget for work the
provider never started, while real failure loops and crash loops stay
bounded

## Linked Issues or Issue Description

Refs #19720, #19747, #19856

**What happened?**
A control-plane restart charges a provider attempt by heuristics. The
first crash restart always charges. A later restart charges unless the
previous resume had no start evidence (#19747) or completed work
(#19720). A runner that spawned but whose provider never accepted a turn
counted as started, so a K6 crash loop could still spend the budget.
Legacy runs whose preparation a restart interrupted
(`providerWorkStarted: false`) spent `failureRetries`, the same counter
as real failures (`execution-recovery-attempt.ts`).

**Expected behavior**
An attempt is charged only when the provider accepted a turn
(`turn.accepted` or `turn.started`) and no accepted turn then completed
work. A startup before spawn, a runner that spawned but was never
admitted, and a `turn.start` the provider did not accept are not
charged. The generation-12 cap still bounds uncharged restarts.

**Steps to reproduce**
Start a native run at its last attempt. Kill the controller after the
runner spawns but before the provider accepts a turn. Before this
change, the next restart claim blocks the run with
`execution_recovery_budget_exhausted`.

## What Changed

- New `server/src/services/native-runtime/provider-attempt-outcome.ts`:
the one rule. `readProviderAttemptOutcome()` returns
`provider_not_started`, `provider_started_without_progress` or
`provider_progressed` from run events. `providerAttemptChargesBudget()`
charges only the second. `providerAttemptWindowStart()` starts the
attempt window at the latest `native.process_start_requested`, so
earlier work never counts for a later attempt.
`PROVIDER_ATTEMPT_CREDIT_GENERATION_LIMIT` (12) is the shared cap.
- `restartResumeKeepsAttempt()` (`native-restart-recovery.ts`) now
applies that rule to the attempt the restart interrupted, including the
first restart. It keeps the unstarted-resume carry from #19747, the
reattachment rule (an adopted provider counts as started), the drain
exemption from #19625, and the generation-12 cap. A history entry from
an older release without a recorded position still charges.
- Legacy runs: `interrupted_preparation` is now an uncharged retry lane
(`execution-recovery-attempt.ts`). It keeps its own counter, bounded at
the same cap (12), and never changes `failureRetries`. `retries.ts` uses
the longest transient delay after the second lane attempt.
- `doc/execution-semantics.md` states the rule.
- Accounting has its own "provider work started" readers (inventory
Summary finding 5). Phase 3 owns those; this PR exposes the rule for
them to adopt and does not change them.

## Verification

- `native-runner-restart-recovery.integration.test.ts` (embedded
Postgres, real `claimNativeRestartRecoveries`): 129 passed. New cases,
red on master:
- not charged at the last attempt for a claimed remote bootstrap, a
remote bootstrap retry, and a claimed unlaunched remote run;
- not charged when the runner spawned but was never admitted, and when
the provider did not accept `turn.start`;
- not charged on the first restart when the original attempt already
made progress;
- a normal retry that spawned but was never admitted is not charged, and
earlier work still does not count for it.
- Counter-cases, green on master and with the change: an accepted
`turn.accepted` or `turn.started` with no progress is charged; the
generation cap blocks at the last attempt; crash loops with and without
progress stay bounded; the #19720 and #19747 cases still pass.
- `execution-recovery-attempt.test.ts`: new lane tests (red on master).
- `workspace-recovery-preparation-dispatch.test.ts` (25 passed),
`heartbeat-process-recovery.test.ts` (interrupted-run cases),
`run-dispatch/adapters/postgres.test.ts` (interrupted cases).
- `server` typecheck (`scripts/typecheck-layers.mjs`, low-memory mode):
no errors.
- Not run: chaos waves (the coordinator schedules them on this host),
and the full server suite (CI covers it).

## Risks

- Behavior change: the first crash restart no longer charges when no
accepted turn is recorded. If a crash lands before the controller
projects the provider's `turn.accepted`, that attempt is not charged.
This fails toward more retries, and the generation-12 cap bounds it.
- A legacy preparation crash loop now gets up to 12 retries instead of
2. Each retry still passes the normal issue gates and keeps the
transient delay.
- The new queries use the `(run_id, seq)` index, once per restart claim.
Nothing new runs before `turn.start`.

> 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`), Anthropic, via Claude Code with
tool use (shell, file edits, test execution). Extended reasoning
enabled.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 21:20:05 -06:00
DottaandClaude Opus 5.5 18644a3263 feat(recovery): instrument 20 durable write boundaries with crash points (#19938)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A control-plane restart between two durable writes leaves an
in-progress record owned by a dead process
> - #19937 added `crashPoint(name)` and a registry of 20 named
boundaries from the Phase 0 inventory
> - A name without a call site cannot fire, so the crash-point suite
cannot test it
> - This pull request puts one call at each registered boundary and adds
a test that keeps the registry and the call sites in step
> - The benefit is that the on-demand suite (next pull request) can kill
the control plane at every known write-ahead gap

## Linked Issues or Issue Description

Refs #19831 (plan, Phase 5). Refs #19846 (inventory, "Write-ahead
coverage"). Stacked on #19937 (helper and registry). Refs #19861
(ownable kind ids).

**Problem**
The registered crash points have no call sites.

**Expected behavior**
Each registered point is called at its gap: after the first durable
write or outside effect returns, before the next one starts. Disarmed
(always in production) each call is one comparison.

**Scope**
Call sites and a coverage test only. The suite runner and CI workflow
follow.

## What Changed

- Server call sites (`@paperclipai/shared/crash-points`):
- `sandbox-creation-operations.ts`: around the provider `create` call
(intent → provider → lease).
- `native-session-executor.ts`: after `native.process_start_requested`,
before spawn.
- `paperclip-control-plane-port.ts`: after the result-accept
transaction, before finalization starts (only when a result was
inserted).
- `native-run-finalizer.ts`: after `commitNativeStatusDecision`, before
the run projection.
- `workspace-operations.ts`: `workspace_finalize` only — after the
running row, and after `settle()` before the done row.
- `environment-runtime.ts`: provider release → lease row; teardown claim
→ destroy; reusable destroy → lease release; stop-and-retain claim →
stop.
- `heartbeat.ts`: lease release → runtime services; budget reservation
hold → dispatch.
- `heartbeat/queue.ts`: run claimed `running` → wake request `claimed`.
- `run-cost-accounting.ts`, `usage-receipts.ts`: accounting commit →
spool unlink; receipt spool → DB row → unlink.
- `packages/paperclip-runner/src/crash-point.ts`: a small copy of the
helper for controller code in this package, which does not depend on
`@paperclipai/shared` (adding that dependency would change the runner
content ID). It arms only `runner.*` names. runnerd never sees the
variable: its environment is an allowlist.
- Runner call sites: after the runnerd spawn, before its identity is
published (both spawn paths); `turn.start` result received → controller
journal saved → next send.
- `server/src/__tests__/crash-point-call-sites.test.ts`: every
registered point has a call site, every call names a registered point,
and every `kinds` entry is an ownable kind id of the Phase 1 registry.

## Verification

- `cd server && npx vitest run
src/__tests__/crash-point-call-sites.test.ts` → 3 passed.
- `pnpm --filter @paperclipai/server typecheck` → clean. `pnpm --filter
@paperclipai/paperclip-runner exec tsc --noEmit -p .` → clean.
- Behavior with nothing armed is unchanged: each call returns at its
first comparison (measured in #19937: about 3.7 ns).

## Risks

- Low risk. No call changes control flow unless `PAPERCLIP_CRASH_POINT`
names it and `NODE_ENV` is not `production`.
- Points on the path before `turn.start` (process start, runner spawn)
cost nanoseconds, within plan invariant 8.
- `usage-receipts.ts`: the persist-then-unlink one-liner became a block
with the same statements in the same order.
- The runner package change gives the runner a new content ID, as any
runner source change does. No persisted run state changes
(rules/upgrade-safe-run-state.mdc).

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, via Claude Code with
tool use (shell, file edits) and a read-only exploration subagent that
mapped the boundaries.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 20:56:33 -06:00
Nicky Leach 94718ce168 fix(native): continue on a replacement when a retained Runner retires before claim (#19897) 2026-11-07 14:51:32 -08:00
DottaandClaude Opus 5.5 99529f9d71 feat(observability): local speed budgets and a run-log budget check (#19863)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - When someone messages an agent, the reply must start as fast as
possible, and restart-safety work must not slow it
> - The durable ownership plan makes this invariant 8 ("fast turns") and
asks Phase 1 to turn the Phase 0 baseline into p50/p95 budgets per
adapter
> - Without budgets, a regression in time to first token, agent boot or
restart recovery shows up only when someone reruns the baseline by hand
> - This pull request records the budgets and adds a per-run check that
writes a run-log row when a run exceeds its p95 budget
> - The benefit is that every later phase can show "no regression
against the budgets" from the run log, without new waits on the turn
path

## Linked Issues or Issue Description

Refs #19831 (plan, "Performance constraint", rule 4, and invariant 8).
Refs #19846 (the Phase 0 baseline these budgets come from). Stacked on
#19861.

**Problem**
The plan requires p50/p95 budgets per adapter for TTFT, agent boot and
restart recovery latency, and a check against them. Neither exists.

**Expected behavior**
Budgets are recorded in the plan and in code. A run that exceeds a p95
budget gets one run-log row that names the metric, the measurement and
the budget.

**Impact**
Phase 2–5 exit criteria can cite budget breaches from chaos waves and
staging. The check adds no wait before `turn.start`.

## What Changed

- New `server/src/services/native-runtime/native-speed-budgets.ts`: the
local budget table (codex, claude, opencode) for TTFT and agent boot
(cold and warm) and restart recovery latency. Each budget is 1.2× the
baseline, rounded up to 0.5 s. `evaluateSpeedBudget` judges one run
against p95. An unknown start kind uses the looser budget. Remote runs
and adapters without a baseline are not judged.
- `native-run-trace.ts`: the trace takes an optional `budget` subject.
It checks `task.time_to_first_token`, agent boot (end of
`heartbeat.queue` to the end of the first `runner.turn.submit` or
`runner.session.resume`) and restart recovery once each. It writes
`run.performance.budget_exceeded` through `defer`, so the write is
detached from the event path. `finish` now drains diagnostics that defer
more work.
- `native-session-executor.ts`: passes the adapter and environment to
the trace, labels cold or warm at the existing `provider_session` reuse
receipts, and checks restart recovery at a recovered run's first
provider event, measured from the startup recovery `ready` time.
- Docs: budget tables in
`doc/plans/2026-11-07-durable-ownership-and-reconciliation.md` ("Speed
budgets (Phase 1)"), and the new event in `doc/run-log-events.md`.

## Verification

- `npx vitest run
src/services/native-runtime/native-speed-budgets.test.ts
src/services/native-runtime/native-run-trace.test.ts` (in `server/`): 34
tests pass. They cover:
  - every budget has p50 ≤ p95;
  - the provider-to-adapter mapping;
  - p95 judgement, and the looser budget when the start kind is unknown;
- one breach for a slow boot, and none for a second submit or a fast
TTFT;
  - a deferred TTFT breach is written before the trace closes;
  - restart recovery is checked once;
  - remote runs and runs with no budget subject write nothing.
- `npx tsc --noEmit -p server`: no errors.

## Risks

- Low risk. This is a run-log change only (AGENTS.md §5.7, no extra
review). The OTLP and Telemetry paths are unchanged.
- The baseline samples are small (2–12 per cell) on a shared host.
Budgets carry 20% headroom, and the codex restart budget (8.0 s p95) is
tight. Expect some breach rows on a loaded machine. They are diagnostics
and change no behavior.
- Restart-recovery budgets use run 4 of the baseline, as merged in
#19846.
- Restart recovery is measured from the startup recovery `ready` time to
the first provider event, which matches the baseline definition.
- Previous-release story: no persisted run state changes. The new event
is additive.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, in Claude Code with
tool use and code 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 15:27:42 -06:00
DottaandClaude Opus 5.5 76994c5027 fix(native): bound failover backup restores by inactivity, not total time (#19906)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - A native per-turn session that continues an earlier conversation
first restores its failover backup from durable storage. This happens
before the coordinator claim, so no provider has started.
> - That restore ran under a fixed 300 s total deadline
(`AbortSignal.timeout(300_000)`). The deadline covers the download and
the local decrypt, digest, extraction and provider-artifact steps.
> - On staging, restore time for resumed sessions grew during the day.
It reached 300 s, and then every resumed run of one review agent failed
with the generic "The operation was aborted". Fresh sessions were not
affected.
> - A failure at this point also enters the saved-work reconciliation
path, so the user request stopped.
> - This pull request bounds each durable read by inactivity instead of
total time. A slow transfer continues while bytes arrive. A read that
stops sending bytes fails with a named code.
> - The benefit is that resumed sessions no longer fail only because
their backup is large or the store is slow.

## Linked Issues or Issue Description

Refs #19894 (adds the same idle-deadline rule for workspace snapshot
reads; this PR covers the separate native failover-backup reads).

**What happened?**

On staging, a PR-review agent had 17 runs fail in about 80 minutes. Each
failure had the message "The operation was aborted" and the code
`native_continuation_requires_reconciliation`. Every failing run resumed
an existing session (`sessionIdBefore` set, per-turn lifecycle). Every
fresh-session run in the same window succeeded. In each failing run, the
error came 304–309 s after the `environment.startup` span, and no
`native.coordinator.claim` span was recorded. The run result had
`executionRecovery: { kind: "bootstrap", providerWorkStarted: false }`.
Earlier resumed runs of the same agent show the time from
`environment.startup` to `native.coordinator.claim` growing from about
30 s to about 200 s before the failures started. The only fixed 300 s
deadline on that path is the failover-backup restore in
`restoreDurableHarnessForExecution`.

**Expected behavior**

A resumed session restores its backup when the store keeps sending
bytes, even when the total time is more than five minutes. A read that
stalls fails with a named, diagnosable code. A failed restore publishes
no partial backup and keeps the saved backup.

**Steps to reproduce**

1. Persist a native failover backup with provider artifacts.
2. Restore it through a storage reader that sends bytes slowly, so the
full restore takes longer than the deadline.
3. Before this change, the restore fails with "The operation was
aborted". A reader that stops sending bytes, with no caller deadline,
waits indefinitely.

## What Changed

- `native-harness-backup-storage.ts`: add `downloadIdleTimeoutMs` to
`restoreDurableNativeHarnessBackup` and
`verifyDurableNativeHarnessBackup`. When set, each durable `getObject`
(the backup object and the provider artifacts) runs under an idle timer.
Each received chunk renews the timer. The timer is active only while a
read is in flight, so local decrypt, digest, extraction and copy are
never timed. On expiry the whole restore aborts and throws
`native_harness_storage_download_stalled`. Caller cancellation keeps its
own error.
- `verifyRecoverableNativeHarnessBackup` and the executor's
`restoreDurableHarnessForExecution` use the five-minute idle limit
(`NATIVE_HARNESS_DOWNLOAD_IDLE_TIMEOUT_MS`) instead of
`AbortSignal.timeout(300_000)`.
- The whole restore or verification keeps a 30-minute outer limit. It
fails with `native_harness_storage_restore_deadline_exceeded`, so a hung
local step stays bounded and named.
- The executor passes the startup Stop signal
(`providerPackSourceAbort`) into the restore, so Stop (also a Stop that
came before the restore began) ends it. Only a startup that already
completed does not reuse its signal. The restore checks the signal after
the local copy and before it publishes `current`.
- The wrapped storage is a `Proxy` that replaces only `getObject` and
forwards every other member to the real service.
- `doc/DEVELOPING.md`: document the idle limit and the named code.

Previous-release story (`rules/upgrade-safe-run-state.mdc`): no
persisted shape changes. Backups, artifact rows, receipts and
checkpoints saved by the previous release restore unchanged. A deploy
that lands during a restore stops the process. The new process starts
the restore again from the saved durable backup under the new limit. The
existing hash, size, encryption and atomic publication checks are
unchanged.

## Verification

Run from `server/`:

- `pnpm exec vitest run
src/services/native-runtime/native-harness-backup-download-deadline.integration.test.ts`
— 4 tests passed (embedded PostgreSQL, local-disk storage, an OpenCode
backup with provider artifacts). The tests are in a focused suite, so
the existing 990-line storage suite does not grow.
- `pnpm exec vitest run
src/services/native-runtime/native-harness-backup-storage.integration.test.ts`
— 68 existing tests passed.
- New: "keeps restoring a backup whose download outlasts the idle window
while bytes keep arriving". With the former total-deadline policy, the
same slow transfer fails with "The operation was aborted" and publishes
nothing (the staging message). With the idle limit, the restore
completes after more than twice the window, restores the session and the
OpenCode launch artifacts, and verification also completes.
- New: "names a download that stops sending bytes and publishes no
partial backup". It checks restore and verify, checks that no `current`
backup is published, and then restores the same saved backup
successfully.
- New: "stops at the outer bound during local copy and publishes
nothing".
- New: "lets Stop end a progressing download with its own reason,
including a Stop before it starts".
- RED: with the production files reverted to `origin/master`, the stall
test does not finish and times out after 10 s, because no stall is
detected. The other two tests pass on the old code, because the total
deadline was the executor's caller policy. The first test reproduces
that policy directly.
- `pnpm exec vitest run` on `native-harness-online-preservation`,
`native-harness-filesystem-independence` and
`native-controller-migration` integration suites passed.
`native-warm-checkpoint-ownership.integration.test.ts` fails locally on
master as well, because the local Rust `paperclip-runnerd` binary is not
built.
- `node scripts/typecheck-layers.mjs` passed for all layers.

Not verified: a live resumed run on staging with this build. The staging
evidence shows where the time goes (before the coordinator claim, on
resumed sessions only) but does not show which restore step was slowest.
The fix removes the total deadline for every step on that path.

## Risks

- A restore that progresses very slowly can now take longer than five
minutes. Before, it failed. The run still stops on caller cancellation.
- A local step that hangs (for example a stalled disk) is now cut off by
the 30-minute outer limit instead of 5 minutes. A stalled local writer
also pauses the read through backpressure, so it can be reported as
`native_harness_storage_download_stalled`.
- A failure before the coordinator claim still enters the existing
saved-work reconciliation path. This PR does not change that
classification. It removes the cause of these failures.

## Model Used

- Provider: Anthropic. Model: Claude Opus 5.5 (`claude-opus-5-5`), with
tool use (shell, file edits, read-only browser for API inspection) in
Claude Code.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 14:34:57 -06:00
DottaandClaude Opus 5.5 f439150cb3 fix(recovery): limit the null-host owner fallback to single-host servers and record each use (#19883)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - #19868 and #19871 made restart recovery judge a recorded pid only in
the PID space that recorded it
> - Rows saved before those host columns existed have no recorded host.
They kept the previous local dead-pid proof, so in-flight native runs
would not be stranded at upgrade
> - On an ephemeral (multi-host) server that fallback is unsafe: the row
may have been written on another host
> - This pull request limits the fallback to single-host servers,
records every use, and gives ephemeral servers a working board action
> - The benefit is that single-host upgrades still recover on their own,
multi-host servers never accept a cross-host proof, and the next release
can remove the fallback with evidence

## Linked Issues or Issue Description

**Bug description**
After #19868 and #19871, a `native_run_finalizations` row with
`controller_host_hash = null`, or a run with `process_host_hash = null`,
still accepted "the pid is dead here" as proof on every server. That
includes an ephemeral server, where the row may come from another host.
Nothing recorded how often the fallback was used, so it had no safe
removal path.

**Expected behavior**
- Single-host server: the fallback applies for one release, and each use
writes a `legacy_host_unknown_dead_pid_proof` activity-log entry.
- Ephemeral server (`PAPERCLIP_EPHEMERAL_SERVER=true`): the row is
unprovable, and the board has an action to confirm the previous server
stopped.
- A mismatched host is always unprovable.

Refs #19868, #19871, #19846

## What Changed

- `native-restart-recovery.ts` `evaluateNativeControllerTakeover`:
- A coordinator row with `controllerHostHash: null` returns
`controller_host_unrecorded` when `ephemeralServerEnabled()` is true.
- Otherwise a pid proof from that row carries `legacyHostFallback:
true`.
- `operator_attested` is accepted as proof
(`operator_attested_controller_stopped`).
  - Receipt-built owners, which have no host key, are unchanged.
- New `recordLegacyHostFallbackProof` writes the activity-log entry. It
is not a run-log event: run events are progress evidence for restart
recovery's crash-loop credit, and the record must not change any
recovery decision. It is called from restart recovery, the
dead-controller result-lease release, native retirement, and remote
warm-session recovery.
- New `native-controller-host-recovery.ts`:
- `requestNativeControllerStopConfirmation` (board-owned
`native_controller_host_unverified` recovery action, idempotent, never
displaces another active action).
- `confirmNativeControllerStopped`. It verifies the exact recorded
controller and stamps `operator_attested` with compare-and-set. It then
resolves the action, wakes live-run recovery, and logs
`issue.native_controller_stop_confirmed`.
- Route `POST /issues/:id/recovery-actions/confirm-controller-stopped`.
It is board-only and requires `runtime:confirm_owner_stop`. Generic
`restored`/`false_positive` resolution of this cause is refused. A
shared `confirmNativeControllerStoppedSchema` validates the body.
- UI: `WorkspaceExportRecovery` reuses the "Confirm the previous server
stopped" control for this cause, and the generic recovery card hides it.
Adds the `issuesApi.confirmControllerStopped` client call.
- `recovery/service.ts` orphan reaper: a null `process_host_hash` is
judged only when not ephemeral. A successful use records the entry
best-effort, after the terminal write. On an ephemeral server the run is
left to its existing Stop control.
- `ephemeralServerEnabled` moves to a leaf `ephemeral-server-mode.ts`
(re-exported by `ephemeral-server-contract.ts`). Importing the contract
module from recovery code created an import cycle in the runner child
process.
- The new route is registered in OpenAPI.
- `doc/execution-semantics.md`: documents the host rule and the
one-release sunset.

## Verification

- `native-restart-recovery.test.ts`: null host on a single-host server
is released with the flag. Null host on an ephemeral server is
unprovable. A mismatched host is unprovable in both modes. An attested
controller is accepted. Receipt owners are unchanged.
- New `native-controller-host-recovery.test.ts` (embedded Postgres):
  - The fallback writes the activity-log entry and no run event.
  - Ephemeral mode creates exactly one board action.
  - A wrong run id is refused.
- Confirmation stamps the attestation, after which takeover is allowed.
The action resolves and the activity is logged. A second confirmation is
refused.
- `recovery-stale-issue-lock-sweep.test.ts`: on a single-host server a
null host is terminalized and records one event. On an ephemeral server
it is left alone with no event. The existing audit-failure case still
clears the lock.
- `WorkspaceExportRecovery.control.test.tsx`: the controller
confirmation posts to `confirmControllerStopped` and never to the
copyback endpoint.
- Locally: these suites plus `remote-warm-session-recovery`,
`native-controller-recovery.integration` and
`native-startup-cleanup-recovery` (136 passed), and after the CI fixes
`native-runner-restart-preparation` and `native-runner-restart-recovery`
integration, `openapi-routes` and the suites above (256 passed); the UI
recovery suites (52 passed); `node scripts/typecheck-layers.mjs` with no
errors in the touched files; `pnpm check:token-gates` clean.

## Risks

- Previous-release story: no schema change. Null-host rows saved by
earlier releases recover as before on single-host servers, now with an
event, and wait for the board on ephemeral servers. The next release
removes the fallback; the event count shows whether any rows remain.
- On an ephemeral server, a null-host orphaned run process is not reaped
automatically. The operator uses Stop. That is the intended "unprovable"
outcome.
- A board confirmation is an attestation. It applies only to the exact
recorded controller (boot id + pid) and only while the host is still
unrecorded.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used with tool use and
code execution in Claude Code.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 13:25:47 -06:00
DottaandClaude Opus 5.5 0189fedffc fix(native): bound an idle warm local runner whose controller died (#19879)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - A warm runner (`lifecycleMode: warm`) keeps runnerd alive between
runs so a follow-up turn starts fast. The follow-up default flip (next
PR) makes warm the default for local Codex and OpenCode agents.
> - The controller owns a warm runner's idle window. Runnerd ignores the
idle timeout itself.
> - A graceful controller shutdown suspends idle warm sessions. A
controller that dies (SIGKILL, crash) does not. Local runners launch
with no process reconnect grace, so the idle runner kept running until
its 1-hour connection lease ran out, owned by nobody.
> - This pull request gives warm local runners the 7-minute reconnect
grace that remote runners already use.
> - The benefit: idle runners are reaped by proof within a bounded time,
never left orphaned, before warm becomes the default.

## Linked Issues or Issue Description

Refs #19874 (warm completion contract), #19846 (TTFT baseline), #19852.

**What existing behavior does this improve?**
Ownership of an idle warm local runner after its controller dies.

**Current behavior**
`runnerProcessReconnectGraceMs` is `undefined` for local targets, so
runnerd launches without `--reconnect-grace-ms`. An idle warm runner
whose controller was killed stays alive until its connection lease (one
hour) expires. The restart-chaos harness cannot show this: its K1 kills
the controller's whole process tree, runner included.

**Proposed behavior**
`localRunnerProcessReconnectGraceMs(policy)` returns the remote grace (7
minutes) for a warm policy and `undefined` for per-turn. After the
grace, runnerd records `transport_reconnect_grace_exceeded`, stops its
provider, keeps durable state and exits. The next run resumes cold.

**Reason and benefit**
The restart plan requires idle runners to be reaped by proof, never
orphaned. Seven minutes is far longer than a controller restart (13–20 s
locally) and the long-outage fault holds (3–5 minutes), so a live turn
still reattaches.

## What Changed

- `native-runner-recovery-contract.ts`:
`localRunnerProcessReconnectGraceMs`.
- `native-session-executor.ts`: the local runnerd transport passes it as
`runnerProcessReconnectGraceMs`. Remote targets keep `null`
(lease-owned).
- `runnerd-warm-idle-orphan.test.ts` (new): real runnerd and fake Codex.
An idle warm runner, after its turn completed, whose controller
detaches.
- `doc/DEVELOPING.md`: the grace and its bound.

## Verification

- `pnpm --filter @paperclipai/paperclip-runner exec vitest run
src/live/runnerd-warm-idle-orphan.test.ts`: with a process grace, the
idle runner exits with `transport_reconnect_grace_exceeded` and the next
transport resumes the same provider session cold. With no grace (`null`,
today's local launch), the runner is still alive after the controller
left.
- `cd server && npx vitest run
src/services/native-runtime/native-runner-recovery-contract.test.ts`:
warm gets the remote grace; per-turn keeps none; the grace outlasts a
controller restart and a long outage.
- `tsc --noEmit` passes for `server` and `packages/paperclip-runner`.
- Local restart measurement with warm runners (K1/K2, codex, claude,
opencode, n = 3 each): every interrupted run recovered, with recovery
latency equal or lower than per-turn. The chaos waves with this change
are in the default-flip PR.

## Risks

- A warm local runner whose controller stays down for more than 7
minutes exits. A turn in progress then resumes through
`resume_dead_runner`, the same path as a controller crash that kills the
runner. Remote runners already behave this way.
- Previous-release story (`rules/upgrade-safe-run-state.mdc`): no
persisted state changes. A warm runner launched by the previous release
keeps the launch arguments it started with (no grace) until it exits.

> 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

- Anthropic Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with
tool use (shell, file edit, 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 13:11:18 -06:00
DottaandClaude Opus 5.5 68db7ed9e3 fix(recovery): never accept a dead local pid as proof for an owner on another host (#19868)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - After a restart, recovery decides that an in-progress record's owner
is gone and takes it over
> - Two of those proofs use `kill(pid, 0)` on the local host. A pid that
is dead here says nothing about a process on another host or in another
PID namespace
> - So a controller or runtime-control owner that is still alive
elsewhere can be taken over while it still runs
> - This pull request records the owner's PID space (the existing
`controller-process-identity` host hash) and judges a pid only in that
same space
> - The benefit is that a different host is never proof. Those records
follow their existing lease or TTL instead

## Linked Issues or Issue Description

**Bug description**
The Phase 0 ownership inventory (finding 2) found three proofs that
accept "the pid is dead here" as proof for an owner on another host:
`evaluateNativeControllerTakeover` (`native_run_finalizations` has no
host column), the runtime-control sweep (`workspace-operations.ts`), and
the orphan reaper `terminalizeOrphanedRunningRun`. Only
`controllerProcessExited` checked the host.

**Steps to reproduce**
1. Run two control-plane processes on different hosts, or in different
PID namespaces, against one database.
2. Let host A own a native finalization lease or a runtime-control
operation.
3. On host B, run restart recovery. If A's pid number is not alive on B,
B takes over the live owner.

**Expected behavior**
An owner whose PID space differs from this process's, or cannot be read,
is unprovable. Its record waits for its lease, fence, or TTL.

Refs #19846

## What Changed

- Migration `0441`: add nullable
`native_run_finalizations.controller_host_hash`.
- `controller-process-identity.ts`: export `currentProcessSpaceHash()`
and `sameProcessSpace()`. An unreadable space is stored as `"unknown"`,
which never matches.
- `native-restart-recovery.ts`: `currentNativeControllerIdentity`
carries `hostHash`, which both coordinator claim writes
(`native-restart-recovery.ts`, `native-session-executor.ts`) store.
`evaluateNativeControllerTakeover` returns `controller_host_unprovable`
before any pid probe when the recorded space is not this one.
`native-dead-controller-result-lease.ts` selects the column.
- `workspace-operations.ts`: runtime-control owner stamps record
`hostHash`. `ownerProcessProvenGone` requires the same PID space (EPERM
= alive), otherwise the existing staleness TTL applies.
- Not in this PR: the orphan reaper `terminalizeOrphanedRunningRun`.
`heartbeat_runs` has no host for `process_pid`, and its writers are
spread across legacy and native paths. It follows as a separate PR with
its own column.

## Verification

- `npx vitest run
src/services/native-runtime/native-restart-recovery.test.ts
src/__tests__/workspace-runtime-control-recovery.test.ts`: 55 passed.
New cases cover another host and an unreadable space (dead and recycled
pid) for takeover, plus another host, unreadable space, and legacy stamp
for the sweep. The sweep cases also confirm that the TTL still reclaims
after the heartbeat lapses.
- Red before the fix: the 5 new cases fail on the old code. Green after.
- `native-controller-recovery.integration.test.ts`,
`native-failed-run-owner-release.test.ts`,
`native-startup-cleanup-recovery.test.ts`: 71 passed.
- `pnpm db:generate` produced `0441_lucky_chameleon.sql` (one `ADD
COLUMN`) and pruned to five snapshots. `pnpm --filter @paperclipai/db
check:migrations` passed. Server `tsc --noEmit` shows no errors in the
changed files.

## Risks

- Previous-release story: `native_run_finalizations` rows saved before
this column have `controller_host_hash = null`. They keep the previous
local dead-pid proof for this release. Making them unprovable would
leave every native run in flight at the upgrade in `awaiting_evidence`
with no TTL, because local takeovers have no lease fallback. Rows
written by this release onward are strict. Runtime-control stamps
without `hostHash` are strict now, because that path has a staleness
TTL.
- Owners built from other receipts (workspace finalization owner,
workspace stop proof) pass no host and keep the previous behavior. Track
2's shared `OwnerStamp` should absorb them.
- A new row on a host that really moved (redeploy onto a new machine)
waits for its lease or an operator instead of being taken over by pid.
That is the intended "different host is never proof" rule.
- No new I/O before `turn.start`. The hash is computed once at module
load.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used with tool use and
code execution in Claude Code.

## 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

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 11:14:48 -06:00
DottaandClaude Opus 5.5 a9ac2e2039 feat(native): split local runner startup into stage, launch and session-load spans (#19852)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - When a person messages an agent, the agent must start its turn fast.
Time to first token (TTFT) and agent boot are first-class metrics.
> - The Phase 0 baseline (#19846) found that local runner startup costs
1.6–17 s at p50 and up to 50 s at p95. It is the largest part of TTFT.
> - The run log records that startup as one span
(`runner.session.bootstrap` or `runner.session.resume`). We cannot see
if the time goes to staging, to the `paperclip-runnerd` process launch,
or to the provider session load.
> - This pull request splits local runner startup into three sub-spans
in the run log.
> - The benefit: the follow-up work to cut follow-up-turn TTFT can
measure each step before and after.

## Linked Issues or Issue Description

Refs #19846 (TTFT baseline, finding 1 and gap "No sub-spans exist inside
local runner startup"). Refs #19838.

**What existing behavior does this improve?**
The run-log performance spans for local native runner startup.

**Current behavior**
The local path records one `runner.session.bootstrap` or
`runner.session.resume` span that covers runtime staging, the runner
process launch and the provider handshake together. The remote path
already records `runner.runtime.stage` and `runner.process.launch`; the
local path does not.

**Proposed behavior**
The local path records three sequential child spans of
`runner.session.startup`: `runner.runtime.stage`,
`runner.process.launch` and `provider.session.load`.

**Reason and benefit**
The TTFT work needs to know which step dominates before it changes the
runner lifecycle. Without these spans, a change to warm runner reuse
cannot show which cost it removes.

## What Changed

- `RunnerdCodexTransport` has a new optional `onStartupStep` callback.
`#start` and `#resume` time three milestones and call it synchronously.
A failing callback never changes startup. A nested startup (exact
adoption from `thread/start`) keeps the outer clock.
- `runner.runtime.stage`: launch preparation before the runner process
exists.
- `runner.process.launch`: spawn until runnerd accepts the run
(`run.prepare`, or the recovery attachment on resume). An adopted live
runner records no launch. This keeps the existing meaning in
`summarizeStartupReuse`: a launch span means a fresh runner.
- `provider.session.load`: `session.open` (or the recovery probe) until
the provider identity is confirmed.
- `recordNativeRunnerStartupStep` (`native-run-trace.ts`) records each
step as a `run.performance.span` row with `mode` and `target: "local"`.
It uses `trace.defer`, so the run-log write never delays `turn.start`.
- The native executor passes the callback only for a local target.
Remote launchers keep their own spans, so there are no duplicates.
- `redaction.ts`: allowlist `runner.process.launch` and
`provider.session.load` as native span names.
- `doc/run-log-events.md`: new section "Local runner startup sub-steps".

Data path (AGENTS.md §5.7): run log only, plus Observability spans when
an operator sets an OTLP endpoint. The attributes (`mode`, `target`,
`outcome`) are already in the closed span-attribute allowlist. No
Telemetry change.

## Verification

- `pnpm --filter @paperclipai/paperclip-runner exec vitest run
src/live/runnerd-codex-transport-startup-steps.test.ts`: a real runnerd
and the fake Codex fixture. Bootstrap and a cold resume each report
stage, launch and session load in order, with `ok` outcomes and no
overlap. A throwing sink does not change startup.
- `cd server && npx vitest run
src/services/native-runtime/native-run-trace.test.ts
src/__tests__/redaction.test.ts`: the rows have the correct parent,
offsets, durations and failed level. A stalled run-log sink does not
block the caller. The rows settle before
`task.provider_session.measured`. The names survive redaction.
- The existing `runnerd-codex-transport*` suites pass (412 tests). Under
host load (load average 16–27), the first full run had 7 timing failures
in suites that do not set the callback. Each failing file passed when I
ran it again alone. `runnerd-codex-transport-settlement` passed 3/3 for
the failing case alone.
- `tsc --noEmit` passes for `packages/paperclip-runner` and `server`.

## Risks

- Low risk. Without `onStartupStep`, the transport behaves as before:
the clock is not created and each milestone call is an optional-chain
no-op.
- More run-log rows: three per local runner startup.
- The step boundaries are controller-side observations.
`runner.process.launch` includes the runnerd authentication and the
`run.prepare` acknowledgement, not only the OS spawn.

> 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

- Anthropic Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with
tool use (shell, file edit, 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 10:57:31 -06:00
DottaandClaude Opus 5.5 824b25654c fix(ui): keep a Retry for retained-file holds whose source cannot be verified (#19840)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - When a native run finishes but its files cannot be saved, the task
stays blocked behind a retained-file recovery hold.
> - The server records that hold as blocked and retryable, and the task
notice tells the user to "Retry to try again".
> - The task page hides its own Retry for these holds and relies on the
retained-file recovery panel instead.
> - That panel only binds the recovery record when a read-only source
inspection returns `verified`.
> - Inspection can return `blocked` for normal reasons: a sandbox that
predates ownership receipts (state saved by an older release), or a
workspace that moved on after its files were recovered.
> - Then neither surface offers an action, and "Check file recovery
status" always answers "File recovery changed. Refresh the task", also
after a reload.
> - This pull request binds the record by its own identity, uses
inspection only to gate the physical file-recovery request, and keeps
the task Retry visible whenever the panel has no control of its own.

## Linked Issues or Issue Description

Refs #18848 (the change that added the retained-file recovery panel and
hid the generic Retry for these holds).

**What happened?**

A blocked task with an active
`native_workspace_sync_out_retry_exhausted` hold showed "The saved files
need recovery before work can continue", "The recorded source is
unavailable or has changed", and "Saving the agent's files failed after
automatic retries. Retry to try again". It showed no Retry and no
recover button. "Check file recovery status" always answered "File
recovery changed. Refresh the task to inspect the current recovery", and
a reload did not change it. The hold was saved by an earlier release:
`systemRecovery` exhausted with `allocation_ownership_ambiguous` /
`service_required`, and `workspaceRecovery` blocked with `retryable:
true`. The source inspection endpoint returned `status: "blocked"` for
it. A second task whose files were already recovered showed the same
"need recovery" and "has changed" text, because its inspection reported
a reference mismatch after recovery.

**Expected behavior**

A retryable hold always shows a working Retry or recover control. A
notice that says "Retry" has a Retry button. Status checks never loop on
"changed, refresh". Recovered files show as recovered. When the source
cannot be verified, the page names the reason and who must inspect it.

**Steps to reproduce**

1. Use an active retained-export hold whose `workspaceRecovery` is
blocked and retryable, and whose `systemRecovery` is exhausted.
2. Make the source inspection (`GET
/api/issues/:id/recovery-actions?inspectSourceRunId=…&inspectSourceActionId=…`)
return `status: "blocked"`.
3. Open the task as a board operator.
4. Before this change, the page shows no Retry and no recover button.
"Check file recovery status" reports "File recovery changed. Refresh the
task".

**Paperclip version or commit**

Observed on build `8812c19`. The regressions fail on master `0f5ce5050e`
before the production edits.

## What Changed

- `WorkspaceExportRecovery`: bind the recovery record by action, run and
schema identity, not by inspection status. Inspection status now gates
only the physical "Recover saved files" request (and the request
re-checks it before POST).
- `WorkspaceExportRecovery`: report through `onRecoveryControlChange`
whether the panel offers its own control. It reports `true` only while
the source is loading or verified and the files are not yet recovered,
or while it shows the previous-server stop confirmation.
- `IssueDetail`: hide the task Retry for retained-export holds only
while the panel reports that it owns the control. Otherwise the existing
task Retry (`POST /issues/:id/retry`) shows. The server renews a bounded
recovery generation and re-verifies the source.
- Show recovered files as recovered even when inspection no longer
matches after recovery.
- Name an unverifiable source in plain words (with the code for other
reasons). State that Paperclip does not apply files it can't verify.
- Recovery text never asks a person to inspect a sandbox or environment,
and never names an owner or administrator as the one who must act. This
covers the retained-file panel, the run source inspector, the copyback
wait, and the native cleanup quarantine message. The execution blocker
and the recovery action read model describe a spent recovery budget from
its current state, so text saved by older releases ("If Retry keeps
failing, inspect the run and its environment") is not shown.
- Task Retry uses the existing `createUuid()` helper, so it works on
plain-HTTP previews without `crypto.randomUUID`. An accepted Retry also
refreshes the inspected file-recovery state. After a failed accepted
request, the unverified-source reason stays visible; it hides only while
recovery runs.
- When the recovery record was replaced, "Check file recovery status"
reloads the task detail instead of telling the user to refresh.
- Tests: component regressions for an old-release hold, a recovered hold
with a mismatched source, verified ownership, and a replaced record. A
page regression proves Retry is shown and calls `retryTask` for
unverified and stale sources. A server safety test proves that Retry for
the old-release hold shape is accepted, opens one new bounded
generation, queues file recovery again, keeps the hold active, and is
idempotent.

## Verification

- RED (master `0f5ce5050e` production files, new tests): 5 component
tests fail. The failure output shows the exact staging text: "Check file
recovery status", "File recovery changed. Refresh the task to inspect
the current recovery.", "The recorded source is unavailable or has
changed." 2 page tests (unverified and stale) fail with `expected [
'Check file recovery status', … ] to include 'Retry'`.
- GREEN: `cd ui && npx vitest run
src/components/WorkspaceExportRecovery.control.test.tsx
src/components/WorkspaceExportRecovery.test.tsx
src/components/RunWorkspaceRecoverySurface.test.tsx
src/components/ExecutionBlockerNotice.test.tsx
src/pages/IssueDetail.test.tsx` passes 320 tests.
- Server: `cd server && npx vitest run src/services/task-retry.test.ts`
passes 81 tests, including the new old-release safety case. This is
safety evidence, not a red: the server path was already correct, and the
defect was in the UI.
- Full UI suite: 11564 pass. 4 tests in `IssuesList.test.tsx` and
`CompanyEnvironments.test.tsx` failed under full-suite load and pass in
isolation (106/106). They are unrelated to this change.
- `pnpm check:token-gates` is clean. `node scripts/run-tsc.mjs -p
ui/tsconfig.json --noEmit` reports no errors in the touched files. The
remaining errors are local artifacts that were not built (plugin SDK UI
entry, generated Storybook catalog).
- Staging was read only (GET requests). The inspect request did not loop
in a fresh tab: two calls in 30 seconds. Most of the tab's request
volume is periodic company issue-list refetches, which this change does
not touch.

## Risks

- Low risk. This is a UI-only behavior change. Server authorization,
source verification, stop receipts, and the bounded recovery policy are
unchanged and remain authoritative.
- The task Retry is now visible for retained-export holds whose source
does not verify. Retry renews one recovery generation. The worker
re-runs the same source-identity checks, so Retry cannot bypass an
ownership refusal. If the refusal is permanent (for example an ambiguous
sandbox allocation), the hold returns to exhausted and the page names
the reason. An automatic fallback for such sources is follow-up work.
- Wording: a parametrized UI test renders every recovery state and
asserts that no administrator, owner, or "inspect the environment" copy
appears. A server test proves that a stored old-release message is
replaced by state-derived text. Both failed before the change.
- Previous-release story: the old-release hold shape (board-owned,
`systemRecovery` revision 5 exhausted with `service_required`,
`workspaceRecovery` blocked and retryable) is covered by component,
page, and server tests. No persisted state shape changes.

> 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 (Anthropic), model ID `claude-opus-5-5`, used through
Claude Code with tool use (repository search, file edits, shell, test
execution, and a read-only browser).

## 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 10:24:03 -06:00
DottaandClaude Opus 5.5 630411af53 fix(recovery): require a 1 s start-time gap and treat EPERM as alive in owner proofs (#19848)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - After a restart, recovery code decides whether the process that owns
an in-progress run is gone
> - Two proofs compare process start times to the millisecond, but `ps
-o lstart` on macOS and BSD reports whole seconds
> - So a live owner can look like a reused PID, and recovery can release
it while it still runs
> - Signal-0 handling also disagrees: one check treats EPERM as dead,
while all others treat it as alive
> - This pull request puts one start-time rule and one EPERM rule in
`controller-process-identity.ts` and uses them at every site the Phase 0
ownership inventory named
> - The benefit is that no proof releases a live owner because of clock
precision or a permission error

## Linked Issues or Issue Description

**Bug description**
The Phase 0 ownership inventory (finding 1) found inconsistent "owner
gone" proofs. `native-failed-run-owner-release.ts`
(`recordedProcessMayBeLive`, `runProcessMayBeLive`) and
`native-session-executor.ts` (`verifiedRecoveryProcessIsAlive`) treat
any start-time difference of 1 ms or more as a reused PID.
`native-restart-recovery.ts` and `controllerProcessExited` require a gap
of at least 1 s. `local-service-supervisor.ts` (`isPidAlive`,
`isProcessGroupAlive`) treats EPERM as dead.

**Steps to reproduce**
1. On macOS, record a live process start time with millisecond
precision.
2. Run the abandoned-owner release pass, or the recovered-runner
liveness check, against that live PID.
3. The pass releases the owner, or the check reports the runner as gone.

**Expected behavior**
A sub-second start-time gap is ambiguous and keeps the owner. EPERM
means the process exists.

Refs #19846

## What Changed

- `controller-process-identity.ts`: export `processExists` (EPERM =
alive) and `processStartsDefinitelyDiffer` (gap >= 1 s; a missing time
proves nothing). `controllerProcessExited` uses the new helper.
- `native-failed-run-owner-release.ts`: the controller and run-process
checks use the shared helpers instead of exact millisecond equality.
- `native-session-executor.ts`: `verifiedRecoveryProcessIsAlive` accepts
a start time within 1 s as the same runner. Its signal path uses the
same check.
- `native-restart-recovery.ts`: `definitivelyDifferentProcessStart`
delegates to the shared helper. No behavior change.
- `local-service-supervisor.ts`: `isPidAlive` and `isProcessGroupAlive`
treat EPERM as alive.

## Verification

- New `controller-process-identity.test.ts`: the 1 s boundary, EPERM and
ESRCH for every signal-0 check, and a live spawned runner whose recorded
start is 500 ms off.
- `native-failed-run-owner-release.test.ts`: two new cases (controller
and run process) with a live child and a recorded start 500 ms off. The
owner stays `observed`.
- Red before the fix: with the old call sites, all 4 new cases fail
(`releaseAbandonedNativeOwners` returns 1 and releases the live owner;
EPERM returns false; the live runner reads as gone). Green after the
fix.
- `npx vitest run src/services/controller-process-identity.test.ts
src/services/native-runtime/native-failed-run-owner-release.test.ts
src/services/native-runtime/native-restart-recovery.test.ts
src/__tests__/local-service-supervisor.test.ts`: 59 passed.

## Risks

- Low risk. The change only makes proofs stricter: a sub-second gap or
EPERM now keeps an owner that the old code released. Such a row waits
for the existing lease, TTL, or real process exit.
- A recycled PID whose new process started within 1 s of the recorded
one now stays held until it exits. That is the same rule the takeover
path already used.
- Previous-release story: no persisted shape changes. Rows saved by the
previous release are evaluated with the stricter rule.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used with tool use and
code execution in Claude Code.

## 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

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

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 10:06:35 -06:00
DottaandClaude Opus 5.5 e2d490c61b feat(observability): anchor native time to first token at the accepted wake (#19838)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - When someone messages an agent, the reply must start fast. The
durable ownership plan (#19831) makes time to first token (TTFT) a hard
invariant.
> - Phase 0 of that plan records a TTFT baseline per adapter and
environment, measured from the moment the message or wake is accepted.
> - Today `task.time_to_first_token` starts at the wake comment, the
answered question, or the run row's creation. A wake request that was
accepted earlier (deferred, coalesced or retried) is not part of the
measurement, and the span does not say which start it used.
> - This pull request moves the start back to the earliest accepted
input and names it on the span.
> - The benefit is that the baseline and later budgets measure what the
user waits for, with no new work before `turn.start`.

## Linked Issues or Issue Description

Refs #19831

**What is the problem?**
`task.time_to_first_token` does not include the time between an accepted
wake request and the creation of its run row. It also does not record
which input it started from.

**What is the expected outcome?**
The span starts at the earliest accepted input and carries an `anchor`
attribute: `comment`, `question_response`, `wake_request` or
`run_created`.

**Why does it matter?**
Phase 0 of the durable ownership plan sets TTFT budgets from this
baseline. A start that skips queue time hides the latency that deferred
wakes add.

## What Changed

- `resolveNativeTimeToFirstTokenStart` (pure) in `native-run-trace.ts`
picks the start and the anchor. `anchor` joins the closed span-attribute
allowlist.
- `readNativeRunWakeRequestedAtMs` reads
`agent_wakeup_requests.requested_at` for the run. It never throws.
- `native-session-executor.ts` calls it only after the first deliverable
text, so it adds no wait before `turn.start`. The span now ends at the
text commit time, not after the trace write.
- Updated `doc/run-log-events.md` and `doc/observability.md`.

## Verification

- `cd server && npx vitest run
src/services/native-runtime/native-run-trace.test.ts
src/services/native-runtime/native-run-wake-anchor.test.ts` (26 pass).
- `cd server && npx vitest run
src/services/native-runtime/native-session-executor.test.ts -t first`
(41 pass). The existing TTFT test now asserts the anchor for each
ingress.

## Risks

- Low risk. This changes only the run-log and OTLP span. It is not
Telemetry (AGENTS.md §5.7), and it does not change runtime behavior.
- One indexed primary-key read per native dispatch, after the first
text. A read failure drops the anchor and keeps the old start.
- TTFT values can grow for deferred wakes. That is the intended
correction. `startOffsetMs` can be negative when the wake request comes
before the trace start.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), via Claude Code with tool use and
code 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
- [ ] I will address all Greptile and reviewer comments before
requesting merge

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 09:57:30 -06:00
DottaandClaude Opus 5.5 84908d176b fix(recovery): name the failed check in native_remote_recovery_lease_mismatch (#19839)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Remote native runs execute in a sandbox, and recovery can reattach a
run to its original sandbox runner
> - Reattachment checks the saved lease, workspace, and runner identity
in five places. Each failed check throws the same bare
`native_remote_recovery_lease_mismatch`
> - On staging, 34 OpenCode runs on 31 tasks failed with this bare error
in one evening. The run records could not show which check failed, so
the cause could not be confirmed from the run alone
> - This pull request makes every producer name the failed step and
field with closed values
> - The benefit is that an operator and the next investigation can see
which reattachment check failed, without new logging or identifiers in
the error

## Linked Issues or Issue Description

Refs #19399, Refs #19733, Refs #19755, Refs #19779

**What happened?**
Remote same-run retries failed with
`native_remote_recovery_lease_mismatch` and the task was blocked for
reconciliation. The error is thrown by environment acquire, environment
resume, workspace preparation, workspace sync, and remote runner
verification. All of them used the same bare string. The run's `error`
field and its run events did not show which check failed.

**Steps to reproduce**
1. Start reattachment for a remote native run whose saved lease,
workspace reference, or runner identity no longer matches.
2. Read the run's `error`.
3. It shows only `native_remote_recovery_lease_mismatch`.

**Expected behavior**
The error names the step and the field that differed, with no
identifiers, and existing consumers of the code keep working.

## What Changed

- New
`server/src/services/native-runtime/remote-recovery-lease-mismatch.ts`:
the code constant, a closed `stage` and `field` vocabulary, and
`remoteRecoveryLeaseMismatch(stage, field)`. It builds
`native_remote_recovery_lease_mismatch: stage=<stage> field=<field>`.
- `environment-run-orchestrator.ts` (stages `environment_acquire` and
`environment_resume`), `heartbeat/workspace-preparation.ts`
(`workspace_preparation`), `native-workspace-sync.ts`
(`workspace_sync`), and `verifyRemoteRunnerReattachment` in
`native-session-executor.ts` (`runner_verification`) now throw the
detailed form. Each check keeps the same condition and order. Only the
message changes.
- `restart-interrupted-turn.ts` uses the shared constant. It already
matches the code exactly or as the `code: ` prefix, so automatic
continuation after a reattachment loss is unchanged. No other consumer
matches the code.
- `doc/execution-semantics.md` documents the detail format.

## Previous-release state

This change adds no persisted state and changes no saved identity. Runs
that a previous release failed keep the bare
`native_remote_recovery_lease_mismatch` in `error`. Runs failed by this
release store the detailed form. The only consumer (`isReattachmentLoss`
in `restart-interrupted-turn.ts`) accepts both forms, and
`workspace-recovery-retry-copyback.test.ts` covers both.

## Verification

- Exact-detail assertions in the producer tests:
- `server/src/__tests__/environment-run-orchestrator.test.ts`: every
scope, status, expiry, provider, lease-ID, cwd, plugin-task, and resume
case asserts its stage and field. Against the previous producer, 21 of
these cases fail (the message was the bare code). With this change, all
57 tests pass.
- `native-session-executor.test.ts`: a replaced sandbox reports
`runner_verification`/`provider_lease_id`. A missing durable runner
identity reports `identity_run_id` before any sandbox read.
- `native-workspace-sync.test.ts`,
`heartbeat/workspace-preparation.test.ts`,
`native-controller-recovery.integration.test.ts` assert their exact
detail.
- End to end on embedded PostgreSQL:
`heartbeat-native-remote-failure-retention.test.ts` records
`native_remote_recovery_lease_mismatch: stage=environment_resume
field=lease` on the run when the provider no longer resumes the lease,
and it still requests the user's Retry once.
`workspace-recovery-retry-copyback.test.ts` adds a detailed-form row
that still continues once.
- The affected server test files pass locally. `pnpm --filter
@paperclipai/server typecheck` passes.

## Risks

- Low risk. Only the error text changes. Conditions, ordering, and
fail-closed behavior are unchanged.
- Logs and run errors show a longer message. The detail has closed
values only, so it adds no identifiers or secrets.
- A first version of this PR also changed remote retry selection. Review
showed that a plain resume in a new sandbox hits the remote workspace's
unsaved-work hold, and that a `destroy` disposition does not prove the
old sandbox is gone. That change is removed. It needs a separate design.

## Model Used

- Claude Opus 5.5 (Anthropic), model ID `claude-opus-5-5`, run in Claude
Code with tool use (shell, file editing, read-only browser access to
staging).

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 09:27:14 -06:00
DottaandClaude Opus 5.5 a94881d1a7 fix(heartbeat): save a comment refused by a temporary hold and route post-quarantine input to its own gate (#19829)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A user's follow-up comment or Retry must be delivered once,
eventually, even when a temporary company admission hold (accounting
still settling) is active
> - #19741 kept claimed runs queued through such a hold and woke held
work when it cleared
> - A restart-chaos wave still lost a comment, because its wake was
refused before admission and written as a terminal skip
> - The same wave left a Retry waiting forever for a stop record of a
process that never existed
> - This pull request saves the refused comment as a deferred receipt,
and routes input after a pre-launch quarantine failure to the
quarantine's own gate
> - The benefit is that the comment is delivered after the hold, and the
task asks for the action that actually unblocks it instead of offering a
Retry that can never start

## Linked Issues or Issue Description

Refs #19741 and #19702.

**What happened?**
In a restart-chaos wave, a failed run's accounting held the company for
600 s.
1. A user commented while the task's run was live. The enqueue budget
gate refused the comment's wake before it reached the deferral behind
the live run. Because it was a user request with no saved receipt, it
was written as `skipped` (`budget.blocked`). The live run finished
without it and the task ended `done`, so the comment was lost.
2. A Retry created a run that the native cleanup-quarantine fence
refused before it requested any runner launch
(`native_session_cleanup_quarantined`, no process events). A second
Retry then waited with `process_identity_missing` ("The previous run has
no verified stop record") for a process that never existed. The task
kept offering Retry, and that Retry could never start.

**Expected behavior**
A comment refused by a temporary hold stays saved and is delivered once
later. Input after a run that was refused before launch is handled by
the quarantine gate: Retry is not offered (send a new message), and a
new message gets the verified-stop check of the previous provider
session.

## What Changed

- `heartbeat/queue.ts`: when the enqueue budget gate refuses a user's
comment wake and the block is temporary (not a reached hard stop, per
`isBoardOwnedBudgetBlock`), the wake is saved as a
`deferred_issue_execution` receipt. The receipt carries the comment ids
and an `executionWait` of `budget.blocked`, and the gate notifies the
deferred-receipt worker and throws `PersistedExecutionWaitRefusal`. It
is not written as `skipped`. Normal promotion (when the live run ends)
and #19741's hold-release wakeups deliver it.
- `native-local-process-stop.ts`: new `nativeRunRefusedBeforeLaunch`. It
returns true for a failed native run with
`native_session_cleanup_quarantined`, no recorded process, and no
launch-request or identity event.
- `explicit-native-continuation.ts`: such a run passes the
process-identity check, so the existing quarantine branch decides. A
Retry gets `cleanup_quarantined` (shown with `canRetry: false` and "send
a new message"). A new message gets
`verifyStoppedNativeSessionForContinuation`. Any launch request or
identity record keeps the original stop proofs.

- `native-session-executor.ts`
(`verifyStoppedNativeSessionForContinuation`): when the source has no
process record and no launch event, the verifier relies on the previous
owner's stop evidence. Before this change it required the source to
share the owner's process identity, so a new message stayed held even
after the owner stopped. A source that carries a process identity must
still match the owner exactly.

## Verification

Each new test fails on `master` and passes with this change, on embedded
Postgres:
- `server/src/__tests__/heartbeat-held-comment-wake.test.ts`: a comment
whose wake the hold refuses at enqueue is saved with a `budget.blocked`
wait and is not skipped. It is delivered exactly once after accounting
settles.
- `server/src/services/explicit-native-continuation.test.ts`:
- A run refused by the quarantine before launch routes a new message to
the quarantine's stop verification and a Retry to `cleanup_quarantined`.
These failed on `master` with `process_identity_missing`.
- Guards (green on both): a quarantined run that requested a launch, and
another failure without a process record, still require
`process_identity_missing`.
- `server/src/services/quarantined-task-retry.test.ts`: a never-launched
quarantined source is certified once the previous owner has stopped (red
on `master`). It stays held if the source requested a launch or the
owner is still running. All 31 tests pass, and the `stopped native
conversation physical cleanup` suite passes (46).
- Related suites pass locally (6 files, 620 tests): explicit native
continuation, held comment wake, queued comments routes, comment wake
batching, refused assignment wake, deferred receipt work. Two
`deferred-execution-receipt-work` tests failed once under parallel load
and passed when run alone.

## Risks

- The saved-comment path applies only to user comment wakes refused by a
temporary budget hold. Hard stops, system wakes, case handoffs, durable
chat requests, and existing saved receipts are unchanged.
- The pre-launch rule is limited to the quarantine failure code with no
launch evidence. Every other missing process identity still requires the
existing stop proof.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, run as an agent in
Claude Code with tool use (shell, file editing, local test execution,
kept restart-chaos instance inspection).

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 08:54:14 -06:00
DottaandClaude Opus 5.5 b2af45f0f1 fix(runner): let OpenAI API-key Codex agents generate images with their existing key (#19654)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - New users often connect a Codex agent with an OpenAI API key during
onboarding.
> - A user asked such an agent for a logo. The agent said that the
built-in image generator was not available and that its fallback needed
a separate API key. It then drew an SVG by hand.
> - #19516 removed `--disable image_generation`. That change is correct,
but it does not reach this path. The pinned Codex 0.160.0 shows its
`image_gen` tool only when Codex signs in with ChatGPT. The check is
`image_generation_available` in `codex-rs/core/src/tools/spec_plan.rs`.
An API key never gets the tool.
> - The runner keeps the provider key out of the agent's shell on
purpose, so the skill's `scripts/image_gen.py` fallback cannot run.
> - This pull request adds a Paperclip `generate_image` tool. The server
makes the image with the agent's existing OpenAI key. The key never goes
to the agent process or the shell.
> - The benefit is that API-key Codex agents can make images with no
second key. The spend goes to the agent's budget and the budget can stop
it.

## Linked Issues or Issue Description

Refs #19516

**What happened?**
An agent connected through onboarding with an OpenAI API key (Codex
harness, `gpt-5.6-sol`) could not generate images. The agent said: "The
image skill's built-in generator isn't available in this run, and its
fallback would require a separate API key." It then drew an SVG instead.

**Steps to reproduce**
1. Create a company with a Codex agent that uses an OpenAI API key.
2. Ask the agent for a raster image, for example a logo PNG.
3. The agent reports that image generation is not available. It does not
make the image.

**Expected behavior**
The agent makes the image with the OpenAI key that already powers it.

**Root cause**
The agent ran on the native runner's Codex app-server path, with
`auth.json = {"OPENAI_API_KEY": ...}`. Codex 0.160.0 removes
`image_gen.imagegen` from the model's tools unless
`current_auth_uses_codex_backend()` is true. That function is true only
for a ChatGPT sign-in.

I proved this with the real pinned binary. I gave it the runner's
isolated launch arguments and the API-key auth file, and pointed it at a
local Responses endpoint. The first model request offers only `exec`,
`wait`, `request_user_input` and the collaboration tools. #19516's test
checked only `codex features list`, so it could not see this gate.

## What Changed

- **New `server/src/services/native-runtime/generate-image-tool.ts`:**
  - The tool schema and definition.
- `imageGenerationBindingForRun`. It applies only to native Codex runs
on a direct OpenAI `api_key` connection with no router selection.
- The OpenAI Images API call (`gpt-image-2`, `b64_json`, PNG check, 180
s timeout). The reply is read as a stream with a byte cap before it is
parsed. A decoded image larger than 20 MiB is refused.
- A reviewed rate card for `gpt-image-2`: text input $5, image input $8
and image output $30 per 1M tokens, from
developers.openai.com/api/docs/pricing, retrieved 2026-11-06.
  - A create-only, symlink-confined local write.
- **`paperclip-runner-tool-authority.ts`:**
  - Adds the `imageGeneration` binding.
- Advertises the tool only for standard mode with a workspace. A remote
target must also have an installer. Dot, Muse, Grok and native review do
not get the tool.
- Adds the `#generateImage` handler. Before any spend, it checks again:
the run and task, budget authority, `issue:mutate`, case handoff, and
the connection.
- Stores a claim-before-spend per-call receipt in
`resultJson.imageToolReceipts`. A retry or recovery replays the receipt
and does not pay again.
- Saves a `charged` receipt (usage, price, request ID and charge time)
as soon as OpenAI returns. A failed save, failed accounting write or
crash can then still settle the spend. A retry or recovery records the
cost once and never buys again.
- Records one `cost_events` row through `createCostEventInTransaction`.
The row is `metered_api` with `costStatus: "estimated"`, and the budget
is evaluated. The row is recorded even if saving fails.
- Checks the task's project budget, as well as the company and agent
budgets, before spending.
- Writes content-free `runner.image_generate` activity entries: started,
completed, failed and unconfirmed.
- **`ai-connections.ts`:** adds `selectImageGeneration`. It checks again
that the connection is an active, healthy OpenAI `api_key` connection
with no custom routing. It also checks the responsible user's
membership, the grant audience and the agent or company installation.
These are the same rules that runtime selection uses.
- **`native-session-executor.ts`:** gets the binding from the run's
admitted `contextSnapshot.aiConnection`. The value comes only from the
server, never from tool input.
- **`native-session-resume.ts`:** the native tool contract changes from
`v18` to `v19` and now lists `generate_image`. A persisted provider
thread cannot add tools when it resumes, so older threads must rotate.
- **`doc/runner-api-tools.md`:** a new section about image generation
for OpenAI API-key Codex agents.
- **#19516: kept, not reverted.** Its changes have no effect on the
API-key path. They are still correct for Codex agents that sign in with
ChatGPT, because `image_gen` works there and saves to
`CODEX_HOME/generated_images`. Those agents need the read grant that
#19516 added. On the API-key path, the new tool replaces the built-in
tool. The tool's description tells the agent to use it instead of
`image_gen` or `scripts/image_gen.py`.

## Verification

**Red on `master` (e482f0f632).** Behavioural red with the first version
of the new test:

```
 FAIL  src/services/native-runtime/generate-image-tool.test.ts > generate_image for OpenAI API-key Codex agents (N-12) > lets an API-key Codex agent make an image with its existing OpenAI key, saved in its workspace and billed
AssertionError: expected [ 'connections_search', …(51) ] to include 'generate_image'
 ❯ src/services/native-runtime/generate-image-tool.test.ts:78:60
      Tests  1 failed | 3 passed (4)
```

The final test file on master's source also fails. The reason is that
the module does not exist: `Cannot find module
'./generate-image-tool.js'`.

**Real pinned Codex binary.** The new test is
`packages/paperclip-runner/src/drivers/codex/codex-api-key-image-tools.test.ts`.
It uses the runner's isolated launch, the API-key `auth.json` and a
local Responses endpoint. It shows that the model gets no `image_gen`,
`imagegen` or `image_generation` tool, and that a server-advertised
`generate_image` tool does reach the model:

```
 Test Files  1 passed (1)
      Tests  1 passed (1)
```

**Green after the fix:**
`server/src/services/native-runtime/generate-image-tool.test.ts` uses
embedded PostgreSQL and a stubbed OpenAI fetch.

```
 Test Files  1 passed (1)
      Tests  11 passed (11)
```

The 11 tests cover these behaviours:

- **Main path.** The tool is advertised. The request goes to
`api.openai.com/v1/images/generations` with the existing key. The PNG is
written to the workspace. The key does not appear in the result or in
activity. One `cost_events` row is written: 50 text tokens and 1000
output tokens, which is $0.03025, estimated, from the rate card. A retry
and `recover()` replay the receipt with no second fetch and no second
cost row.
- **No binding:** the tool is not offered and `execute` refuses.
- **Budget hard-stop.** The stop pauses the agent, so the call is
refused before any fetch and no file is written.
- **Bad grant:** the call is refused before any fetch.
- **Project budget stop.** The task's project is paused by its budget,
so the call is refused before any fetch.
- **Charge settlement.** A crash left a `charged` receipt. The retry and
`recover()` record the cost once, report the image path and do not buy
another image.
- **Oversized reply.** The read stops before the body is parsed.
- **Save failure.** The spend is still recorded. A same-call retry does
not pay again and reports the failure.
- **Binding gate.** Only Codex on a direct OpenAI API key gets the
binding. A subscription, ACPX, OpenRouter or a routed connection does
not.
- **Rate card math.**
- **Provider errors.** The error text does not contain the key, and
non-PNG data is rejected.

**Neighbouring suites:**

- `src/drivers/codex` in the runner package: 24 files, 350 tests passed.
- Server: `paperclip-runner-tool-authority.test.ts`,
`native-session-resume.test.ts`, `fast-responses.test.ts`,
`ai-connection-session.test.ts` and the new suite. 157 of 158 passed.
- The one failure is `native-session-resume.test.ts › archives a damaged
prior epoch … with real runnerd` (ENOENT on `authority-epochs`). It
fails the same way on unmodified `master` in this local environment, so
this change did not cause it.
- `tsc --noEmit -p server/tsconfig.json`: clean.
- `pnpm verify` exits 2 (broad). Required CI supplies the broad
coverage.

## Risks

- **New security surface: this needs maintainer sign-off.** The server
now sends the agent's OpenAI API key to `api.openai.com` on the agent's
request. The tool is limited in these ways:
  - The key stays in the server.
- Each call checks run, task, budget, mutation and connection authority
again.
- The destination name comes from the server and must match
`^[a-z0-9-]+-[0-9a-f]{8}\.png$`. The write is create-only and confined
to the workspace root. On macOS it uses `O_NOFOLLOW_ANY`. On Linux it
uses a `/proc` descriptor walk.
- **Spend.** Each call costs money. The tool description tells the agent
to make only what the task needs. The cost is an estimate from a rate
card (`costStatus: "estimated"`), not an invoice. The rate card applies
the image-output rate to all output tokens, so the estimate errs on the
high side.
- **Checkpoint rotation.** The tool-contract bump from v18 to v19 makes
existing native provider threads start fresh once at their next turn.
This is what the contract requires when the tool surface changes.
- **Pricing drift.** If OpenAI changes `gpt-image-2` prices, the rate
card must be updated.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude
Code with tool use (shell, file edits, sub-agents) and extended
reasoning.

## 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

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 07:48:39 -06:00
DottaandPaperclip 909f4d1a33 fix(native): recover exact historical provider pack code (#19779)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Native sessions retain the provider pack that admitted their saved
state.
> - An image update can replace that pack's executable, proxy, or
contract.
> - Older sessions can predate the durable three-file launch artifact
receipt.
> - The current image's archive cannot satisfy a different pinned
manifest.
> - This pull request obtains the exact public code from its recorded
release image.
> - Full source, archive, and installed-file checks still control
provider admission.

## Linked Issues or Issue Description

Refs #19558, #19622, #19755.

A saved OpenCode session can fail with
`runner_remote_provider_archive_invalid` after an image update. Its
original provider state and checkpoint remain valid, but its pinned pack
differs from the controller's pack. The old manifest can name a release
that still has the exact code in GHCR. Matching the OpenCode version
does not prove matching proxy or contract bytes.

## What Changed

- Resolve a pinned historical pack from the recorded source-SHA image in
the public Paperclip GHCR repository. Verify the platform manifest, raw
config, source identity, dedicated code layer, selected pack manifest,
archive contents, paths, and hashes.
- Keep a private temporary cache of verified public code. Rebuild it on
an empty host. Bound each source to 4 GiB and three minutes, with two
active imports or cache verifications, 32 distinct queued sources, and
disk-headroom checks. Share warm-cache verification by manifest while
each caller keeps its own cancellation.
- Select this verified archive through the existing uploader. Preserve
installed-pack and preinstalled-pack checks. Refuse unavailable
historical transport before clearing the target. Keep the current-source
identity guard from #19755. Refuse an oversized layer argument before
any target effect.
- Attach the source wait to the actual per-turn startup. Stop, lease
loss, and startup completion cancel it. Keep existing Runner admission
and turn limits.
- Document the registry retention requirement and the distinction
between public code recovery and encrypted provider-state backup.

## Verification

- Genuine baseline RED: the real uploader rejects the selected old pack
before any remote effect. Treatment installs the exact old code through
that uploader.
- Current head: all 19 source/integrity/cache/deadline controls, all 45
archive controls, and 29 actual-caller and manifest/startup controls
pass (93 total). Four review regressions fail against the prior head and
pass with the fixes. The server and colocated test TypeScript graph
passes. Module-boundary and whitespace checks pass.
- Actual public GHCR cold reconstruction: 1,054,587,008 compressed code
bytes, 115.4 s, about 248 MiB maximum owner RSS. All 114 file layers and
the overlay passed source validation.
- Linux Node 24.22.2 fixture: the real historical pack passes the normal
uploader, full installed-file verifier, and pinned OpenCode version
check. It used one transfer, no application startup, no network, and no
provider calls. Revision12b0d2ba passed in 220.2 s with about 282 MiB
owner RSS. The earlier prototype passed in 108.5 s; both measurements
are retained. The three-minute source limit and the fixture's
four-minute limit were unchanged. The later review fixes add shared
cache verification, hash cancellation, and an early size guard. They do
not change extraction or the accepted Linux fixture input.
- Earlier fixture failures are retained: unsafe hardlink classification
was corrected with confined-link controls; a cached image lacked the
required zstd CLI; Docker Desktop bind storage caused GNU tar
directory-identity errors. The passing fixture uses the official Debian
zstd binary and an owned Linux tmpfs target. Production extraction code
is unchanged.
- Fresh Greptile review is 5/5 on
7b1a249478 with no open findings. All
required CI gates passed on the reviewed head. [CI
run](https://github.com/paperclipai/paperclip/actions/runs/42353011485),
[fresh
review](https://github.com/paperclipai/paperclip/pull/19779#issuecomment-6704065994).
No hosted session was retried by this change.

## Risks

- Cold historical recovery reads about 1 GiB of public code for the
measured release. Registry latency or missing images can block it. The
source deadline remains three minutes.
- GHCR administrators can delete release images. Source-SHA tags and
this temporary cache are not a permanent code-retention guarantee. A
provider-state S3 backup does not replace legacy executable bytes.
- Targets must support the existing qualified archive transport and
selected platform. Failed checks preserve the saved state and prevent
provider dispatch.
- The Linux fixture proves code installation and verification. Hosted
conversation continuation still needs acceptance after normal delivery.

## Model Used

OpenAI Codex, GPT-6 family, with reasoning, repository tools, and local
code execution. The host does not expose the exact deployment ID or
context-window size.

## 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 references)
- [x] My branch name describes the change 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-07 02:06:02 -06:00
Nicky LeachandPaperclip beb3e55072 Continue a released Runner after confirmed graceful eviction (#19760)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Core can release a completed Runner while its host retains the
session.
> - A host can later retire that Runner under its retention policy.
> - Graceful retirement saves a suspended session before physical
shutdown.
> - A cached Core owner still expects the old physical task and rejects
a new allocation.
> - This pull request retires that dead local controller after verified
stop.
> - The benefit is ordinary session continuation for Codex and qualified
Claude.

## Linked Issues or Issue Description

Refs #19611, #19683, #19196, #19733 and #19157.

After a host gracefully evicts a released task, the next run can receive
a new allocation. A cached controller rejects it with
`native_session_released_owner_scope_mismatch`. The detached-controller
path can already recover the suspended session.

## What Changed

- Require the exact source, old task and current account/workspace scope
before releasing a cached controller.
- Use the existing physical-stop receipt checks. Detach only the local
controller, then use the same suspended-state admission as the detached
path.
- Preserve the current run's instruction reservation. Retain a failed
detach for cleanup.
- Add actual Core, PostgreSQL and native Runner tests for Codex and
qualified Claude through ACPX. Route them once through the native CI
lane.

## Verification

- The original real-entry Codex case failed at the cached-task scope
check after native retirement, confirmed process exit and a recorded
stop receipt.
- The current head's native CI lane passed all 16 eviction cases for
Codex and qualified Claude. These check cached and detached owners,
current instruction preparation, reused-allocation inspection, missing
stop/state, foreign identity and non-suspended state. They verify the
same provider session, two ordinary turns, one accepted source result
and no replacement submit on refusal.
- Local checks passed the composition matrix, 12 targeted executor
controls, 43 CI lane-selection checks and server TypeScript. All eight
refusal cases now assert the expected error and whether the checkpoint
request or host read was reached. This addresses the first standard
review's test finding.
- Commands: `pnpm exec vitest run
src/services/native-runtime/plugin-runner-eviction.integration.test.ts`,
focused `native-session-executor.test.ts` controls, `node
../node_modules/typescript/bin/tsc --noEmit -p tsconfig.json`, and `node
--test scripts/__tests__/run-vitest-stable-shard.test.mjs`.
- [Full
CI](https://github.com/paperclipai/paperclip/actions/runs/42349579107)
passed on head `9a25709ef43365b1f1849413b935785838eca19b`. [Standard
review](https://github.com/paperclipai/paperclip/pull/19760#issuecomment-6703629255)
is 5/5 on this head, with no unresolved findings. Whitespace and
added-line secret/PII checks passed.

## Risks

- Controlled provider processes and an authenticated local host fixture
model the Launcher edge. This does not qualify live vendor transcript
storage, mounts or a deployment.
- This covers graceful eviction before allocation or before stopped-task
inspection during `describe`. Loss after that inspection or an ambiguous
claim remains held for reconciliation. No unavailable reply proves
physical stop.
- Missing or invalid suspended state still refuses continuation. The
deterministic refusal rule from #19733 remains unchanged. Abrupt death
without a suspended checkpoint stays with the separate #19157 work.
- No new capability, mode, schema, dependency, deployment or activation
is added. The existing draft #19157 and dependent branches remain
unchanged.

## Model Used

OpenAI GPT-6.1 Sol (`gpt-6.1-sol`), high reasoning, through Codex with
repository tools and code execution. The runtime does not expose a
context-window size.

## 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-06 23:21:45 -08:00
DottaandClaude Opus 5.5 3895195f4b fix(native): report a retained provider pack the controller does not ship as incompatible (#19755)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Remote OpenCode runs stage a controller-owned provider pack into the
sandbox before the provider starts
> - Since #19558, an ordinary OpenCode continuation retains the pack
that an earlier release admitted for its saved provider session
> - After a controller release changes the pack, the controller no
longer ships those bytes, and the continuation must stay blocked
> - The configured-pack upload path did not detect that case: it read
the build-time archive receipt for the old digest and failed with
`runner_remote_provider_archive_invalid`, a generic, retryable error
that suggests corrupt image files
> - This pull request compares the configured pack's identity with the
selected identity before any upload and fails as
`runner_remote_provider_artifact_incompatible`
> - It also puts a fixed reason in each real archive integrity error
> - The benefit is a correct, permanent classification that matches the
bundled-image path, no wasted retries, and a diagnosable message for
real archive corruption

## Linked Issues or Issue Description

Refs #19558, #19743

**What happened?**

On a hosted deployment, two remote OpenCode runs of a review agent
failed before the provider process started. The error was
`runner_remote_provider_archive_invalid` (classified as a generic
`native_session_interrupted`). Both runs continued an issue whose
provider session was admitted by an earlier release. In both runs, the
run log shows `provider_pack.compatibility`, `provider_pack.verify`, and
`provider_pack.verify_preinstalled` fail, then
`provider_pack.archive.verify` fails after 4–6 ms. Fresh runs of the
same agent on the same controller passed pack preparation with the
current pack.

The cause is not a cache race. The archives are created at image build
time (`Dockerfile` `runner-provider-pack` stage) and the server never
rewrites them. The retained authority selects the old pack digest.
`readProviderPackLayers` then compares the receipt's
`providerPackDigest` (current release) with that old digest and throws
`runner_remote_provider_archive_invalid`. Directory staging (no archive)
instead clears the staged remote pack, uploads the different pack, and
fails only at the final verification.

**Expected behavior**

A continuation pinned to a pack that the controller does not ship fails
as `runner_remote_provider_artifact_incompatible`, as the bundled-image
path already does ("the image provider pack did not match the bundled
release identity"). It does not clear or upload anything. Real archive
corruption keeps `runner_remote_provider_archive_invalid` with a fixed
reason that the run report shows.

**Steps to reproduce**

1. Build a provider pack and its archives for digest A.
2. Call `uploadVerifiedProviderPack` with that pack and a selected
(retained) digest B.
3. Before this change: the call fails with
`runner_remote_provider_archive_invalid` (v1 and v2 archives), or
resolves after it clears and re-uploads the remote pack (directory
source).

## What Changed

- `uploadVerifiedProviderPack` takes the configured pack's
`sourceDigest`. If it is not the selected `expectedDigest`, the call
fails with `runner_remote_provider_artifact_incompatible: selected
provider pack <12 hex> is not the controller's pack <12 hex>; ...`. The
check runs before the remote clear, the archive read, the directory hash
and any upload.
- The executor passes the configured pack's identity
(`readRemoteProviderPackIdentity(root, false)`, the same reader that
selects the current pack).
- Archive integrity errors keep the
`runner_remote_provider_archive_invalid` prefix and add a fixed reason:
`receipt_unreadable`, `receipt_identity_mismatch`, `receipt_invalid`,
`layer_invalid`, `layers_unreadable`, `archive_unreadable`,
`archive_not_file`, `size_mismatch` or `sha256_mismatch`. The run report
keeps only the outer message, so the reason must be in the message.
Filesystem causes stay on `cause` and do not put private paths in the
message.
- The v1 reader now uses the shared `verifyArchive` helper.
- `doc/execution-semantics.md` documents the rule.

## Verification

- Red before the fix (production files unchanged, new tests only): `npx
vitest run src/services/native-runtime/provider-pack-archive.test.ts`
gave 5 failed / 38 passed. The v1 and v2 cases failed with exactly
`runner_remote_provider_archive_invalid`, which is the hosted error. The
directory case resolved after it cleared and uploaded the remote pack.
The reason tests got a bare `runner_remote_provider_archive_invalid`.
- Green after the fix: the same file gave 43 passed.
- `npx vitest run
src/services/native-runtime/native-session-executor.test.ts`: 1245
passed. This includes the #19558 continuation cases.
- `remote-provider-pack`, `remote-provider-pack-authority` and
`remote-provider-pack-verification` tests: 69 passed.
- `pnpm --filter @paperclipai/server typecheck`: all layers passed.
- Review follow-up (`c8156841a9`): an unreadable numbered layer now
reports `archive_unreadable`. The layered-corruption test deletes
`0.tar.zst` and checks for that reason before any transfer. The archive
file gave 43 passed.
- Hosted evidence came from read-only run, event and issue-run reads
only. No hosted retries, recovery or deploys.

## Risks

- This change does not unblock an affected session. It makes the failure
honest and permanent: `runner_remote_provider_artifact_incompatible` is
already a permanent, pre-session failure code, so the run is not retried
with the same result. To recover, the session needs its original
artifacts (the captured provider-artifact path, which #19743 repairs for
new admissions) or an authorized continuity break.
- Low risk for other paths. Fresh launches select the configured pack's
own identity, so the digests are equal. Restored provider artifacts and
compatible installed packs return before this upload path.
- Callers that match `runner_remote_provider_archive_invalid` with a
substring still match. No code compares the exact message.
- Not tested end to end against a hosted sandbox. The executor-level
wiring of `sourceDigest` has typecheck coverage but no dedicated
executor test.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic. Agentic tool use with
shell, code editing, test execution and read-only authenticated browser
diagnostics.

## 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
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

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

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-07 01:10:29 -06:00
Nicky Leach 167e39c4ef fix(runner): keep warm run.attach events on ordinary accounting (#19707) 2026-11-06 23:09:57 -08:00