Files
PaperClipAI/tests/restart-chaos
DottaandClaude Opus 5.5 644ee66f5d test(restart-chaos): R5 live tools and processes; fail a wave whose worktree changes mid-wave (#19697)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The restart chaos harness (`tests/restart-chaos/`) grades every task
on R1–R6; R5 catches silent stalls, including a run that stays `running`
with no live evidence
> - A B5 task runs `bench.sh` for about four minutes with no output, so
a healthy Retry run was graded `R5:silent_dead_run` while its runner
process was alive and its tool was still running
> - Separately, a runner `dist` rebuilt in the harness worktree during a
wave made later restarts run different code and produced a false
signature (RC-32's investigation)
> - This pull request makes R5 treat a run as live while a tool it
started has not ended or while its recorded local runner process still
runs, and fails a wave whose worktree changes mid-wave
> - The benefit is fewer false R5 failures and no silently mixed-code
waves

## Linked Issues or Issue Description

Refs #19629
Refs #19641

**What is the problem?**
R5 flags a quiet but live run (a long tool call, a live runner process)
as `silent_dead_run`. A build, install or branch switch in the harness
worktree during a wave goes unnoticed, though every restart re-runs the
control plane from that worktree.

**What is the expected behavior?**
A run with a tool in flight, or with its recorded local runner process
still alive (same PID and start time), is live for R5. A wave whose
checkout or runner build output changes during the wave fails as a
harness error.

**Why does it matter?**
False R5 failures send fixers after non-bugs, and mixed-code waves
produce signatures that are not product behavior.

## What Changed

- `observer.ts`: the run-event reader counts tool starts minus tool ends
(PRP item ids are not unique per tool call), and remembers the run's
latest local process identity until recovery reports it stopped. Samples
carry `toolInFlight` and `processAlive`. `localProcessAlive` checks `ps`
for the same PID with the same start time, so a recycled PID never
counts. Daytona runs are not checked (their process is remote).
- `grader.ts`: `deadRunningRun` skips a run with a tool in flight or a
live process.
- `types.ts`: `RunSample.toolInFlight` and `RunSample.processAlive`.
- `wave-guard.ts` (new) and `main.ts`: fingerprint `HEAD`, the tracked
diff contents (`git diff --binary HEAD`), untracked file contents, and
size/mtime of `packages/paperclip-runner/dist` and the runnerd binary.
The baseline is taken after the harness's own setup (preflight rebuilds
provider entrypoints). Re-check after each fault and at the end; fail
the wave (`worktree_changed_mid_wave`) if it changed.
- `main.ts`, `scheduler.ts`: `faults.json` and a new `task-faults.json`
(each task's launch time and crossing faults) are written after every
fault. `--replay` falls back to that log when a task has no grade file
(an interrupted or wedged wave), so a storm task replays the faults that
crossed it at the same offsets.
- `README.md`: both grading notes.

## Verification

- `pnpm exec vitest run --config tests/restart-chaos/vitest.config.ts`:
111 tests pass. New tests cover:
- a B5 run quiet for 4 minutes passes with a tool in flight or a live
process, and fails otherwise
- tool and process liveness come from run events and clear on tool end
and process stop
- `localProcessAlive` accepts this process's real PID and start time and
rejects a different start time
- the guard catches rebuilt dist, a re-edited dirty file, an edited
untracked file and a rebuilt runner binary, in a real temporary git repo
- a storm task with no grade file replays the faults that crossed it at
their offsets from its launch
- `node scripts/typecheck-test-projects.mjs tests/restart-chaos`:
passes.

## Risks

- Low risk, test harness only.
- The R5 exemption narrows R5. A run that is truly stuck while its
process lives (a hung provider) now passes R5 and falls to R1's time
budget instead.
- One `ps` call per running run per poll on local waves.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through 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>
2026-11-06 22:07:42 -06:00
..

Restart chaos harness (Phase 1 MVP)

Plan: doc/plans/2026-11-06-control-plane-restart-chaos.md.

A script, not an LLM. It starts an isolated Paperclip control plane (temporary PAPERCLIP_HOME, wrapper-owned embedded Postgres, its own port), seeds a "Chaos Lab" company, launches real agent tasks, kills or restarts the control plane during those tasks, and grades every task on R1–R6 plus a deterministic T-oracle.

Run

pnpm install --frozen-lockfile
pnpm --filter @paperclipai/paperclip-runner run build:runner-binaries   # native runner (debug)
set -a; source ~/.secrets; set +a                                   # provider keys, process env only
node cli/node_modules/tsx/dist/cli.mjs tests/restart-chaos/main.ts --env local \
  --adapters codex,claude,opencode --concurrency 4 --tasks 8 --faults K1,K2,K4 --seed 42
node cli/node_modules/tsx/dist/cli.mjs tests/restart-chaos/main.ts --replay w-20261106T101112-s42/t03
pnpm exec vitest run --config tests/restart-chaos/vitest.config.ts  # credential-free unit tests
node scripts/typecheck-test-projects.mjs tests/restart-chaos        # typecheck

Options: --triggers time,comment,retry,queued,tool,result (fault timing, below), --workloads A1,B1,B5,C1, --budget-cents (company hard cap, default 3000), --poll-ms (2000–5000), --keep (keep the temporary instance).

--rc06-masked keeps the company budget amount but disables its hard stop on the isolated Chaos Lab company, so one stuck accounting row (RC-06) cannot wedge every later task. Masked tasks are marked rc06-masked in the ledger and summary, and each wave still records its spend (wave_spend in the timeline). A replay inherits the masks saved in the source wave's plan.json; --replay <wave>/<task> --rc06-masked adds the mask to a replay of an unmasked wave. Each fault receipt records the host 1-minute load average (loadAvg1m); treat timeout failures above about 16 as load-suspect.

Restart storm (K13, --storm-minutes)

node cli/node_modules/tsx/dist/cli.mjs tests/restart-chaos/main.ts --env local \
  --adapters codex,claude,opencode --concurrency 6 --storm-minutes 60 --seed 7

A storm wave fires faults on its own seeded clock instead of one fault per task. Each fault is drawn from --faults (default K1, K2, K4, K6) and fires 2–4 minutes after the previous one settled (server ready), so a K4 hold never eats the next gap. Each fault hits every task in flight. While the storm lasts the harness launches a new task whenever one rests, keeping --concurrency in flight; --tasks (default 200) is only the pool. A pool that runs dry before the storm ends fails the wave as a harness error (storm_pool_exhausted). When the storm ends no new task or fault starts, the in-flight tasks drain to rest or their deadline, and only launched tasks are graded. Storm tasks show fault K13 in the ledger; storm_fault, storm_started and storm_ended are in the timeline and the receipts are in faults.json. A replay of a storm task fires the faults that crossed it, without a new storm. --triggers time,result may join a storm: a result task (C1) also fires its own K1 or K2 (from --faults) just after its run accepts a result, the next storm gap runs from its settle, and no triggered fault fires during the drain. Other triggers do not combine with a storm.

Daytona (--env daytona)

The control plane stays local; agent runs execute in Daytona sandboxes from an immutable runner image. No Docker is needed.

set -a; source ~/.secrets; set +a        # DAYTONA_API_KEY plus provider keys, process env only
node cli/node_modules/tsx/dist/cli.mjs tests/restart-chaos/main.ts --env daytona \
  --daytona-image ghcr.io/paperclipai/paperclip-daytona-runner@sha256:<digest> \
  --adapters codex,claude --tasks 3 --concurrency 2 --faults K1 --seed 11

PAPERCLIP_E2E_DAYTONA_IMAGE can replace --daytona-image. B5 is local-only (its oracle reads the live workspace, which is inside the sandbox).

vCPU budget. The Daytona org is shared with the live Cloud fleet. Chaos sandboxes use --daytona-cpu vCPU (default 4, with 4 GiB memory and 10 GiB disk), and --concurrency × --daytona-cpu must stay within 40 vCPU (RESTART_CHAOS_DAYTONA_VCPU_BUDGET). On a small org, set the budget below the org limit with room for verification probes: a 10 vCPU org fails creates with HTTP 400 "Total CPU limit exceeded", so use 8 there and --daytona-cpu 2.

Fleet safety. The harness never stops, archives or deletes a Daytona sandbox. Its Daytona client is a frozen wrapper that exposes only a label-filtered list. assertHarnessMayMutate refuses paperclip-create-* names (every plugin-created sandbox has one) and fleet-sbx-* snapshots, so a future mutating path cannot act on fleet sandboxes either. Cleanup goes only through Paperclip, by deleting the wave's own environment.

Image matching. The controller needs the image's own Linux amd64 /usr/local/bin/paperclip-runnerd (PAPERCLIP_RUNNER_REMOTE_BINARY_PATH) and /opt/paperclip-runner/provider-pack/ (PAPERCLIP_RUNNER_REMOTE_PROVIDER_PACK_PATH). daytona-image.ts gets them without a daemon: skopeo copy --override-os linux --override-arch amd64 docker://<image> dir:<cache>, then walks the layers from top to bottom (honouring .wh. and .wh..wh..opq whiteouts), extracts only those two paths, checks the ELF header, the pack manifest and the image labels, records their digests in receipt.json, and deletes the layer blobs. The result is cached in results/daytona-images/<digest>/, so it runs once per image. Run it alone with node cli/node_modules/tsx/dist/cli.mjs tests/restart-chaos/daytona-image.ts <image>.

Before starting, the harness compares the image's io.paperclip.runner.content-id label with the content ID of this checkout (pnpm test:e2e:runner:image-id, which hashes every runner input) and refuses to run on a mismatch. To get an image for the current master, dispatch a narrow image build and reject its paid gate:

gh workflow run runner-full-stack-e2e.yml --ref master -f cadence=manual -f all=false \
  -f id=core-compatibility.runner-codex.daytona.message-marker
# when the run waits on the paid environment:
gh api -X POST repos/paperclipai/paperclip/actions/runs/<run>/pending_deployments \
  -F "environment_ids[]=20786721735" -f state=rejected -f comment="Image build only"

The digest is in the "Publish verified Daytona image" job log (pushing manifest for …@sha256:…), or check out the image's org.opencontainers.image.revision.

Setup reuses runner-e2e: the bundled Daytona plugin (installFixtureDaytonaProvider, prepared outside the root workspace as CI does), the daytona environment fixture from catalog.ts, and the native Codex platform-qualification probe.

R6 sweep. After the wave, daytona-sweep.ts lists (read-only) the sandboxes whose paperclip-company-id and paperclip-environment-id labels both equal the UUIDs this wave's isolated instance minted, re-checks every row, and reconciles them with the environment's leases. It retries for the product's pending-cleanup backoff plus 90 seconds (6.5 minutes, capped at 8) before calling anything a leak. A sandbox archived after its lease was released is expected (the plugin archives on release and Daytona deletes it after 60 minutes). Any other live sandbox without a held lease, or an active/pending_cleanup lease, is a leak: it fails R6 for the task whose run owns it, or the wave when no task does. The harness then deletes the wave's environment through Paperclip and lists again: a wave sandbox that is still neither archived nor destroyed after 90 seconds fails the wave and is reported for a person to act on (the environment's 60-minute ttl also expires it). An environment DELETE that returns 409 because a sandbox cleanup is still pending is retried for the same settle window; if it is still blocked then, the wave fails (not as a harness error) and the instance is kept, because its database owns the cleanup work. The result is in <wave>/sandbox-sweep.json.

Fault timing (--triggers)

Each task samples one trigger with its cell. time (default) fires at the seeded offset. The others fire relative to a user action or run state seen by the observer, after a seeded delay:

Trigger Fires Plan
comment 0–5 s after the C1 follow-up was posted to a live run (C1 only) C1 + K1, B8
result 0–3 s after the run that received the C1 follow-up proposed or accepted its result, only while that run is still running (C1 only) C1 + K1, B8
retry 0–2 s after an accepted Retry click, as an extra K1 after the planned fault K8
queued on the first poll whose run is still queued with no start B1
tool 15–60 s after bench.sh progress first appears (B5 only) B6

A trigger whose condition can no longer hold (comment posted at rest, run already started, no Retry offered) is recorded as triggerMissed in the ledger; the task is still graded. --faults K6 is the crash loop: after the first kill, the replacement is killed again as soon as /api/ready reports recovering (or ready, if recovery was too quick to see), and once more just after ready. The receipt's crashLoop lists the phase each kill hit. A replay re-arms the task's own triggered faults instead of using their offsets.

Pieces

File Role
supervisor.ts Owns the server. Reuses tests/runner-e2e process code (config, ports, env isolation, wrapper-owned Postgres, process-tree stopper, replaceController). Faults: K1 SIGKILL + immediate restart, K2 SIGTERM + restart, K4 SIGKILL + 2–5 min hold, K6 crash loop. The controller runtime cache is kept (discarding it is K11).
seed.ts Chaos Lab company, encrypted provider secrets, native Codex / ACPX Claude / OpenCode agents from the runner-e2e catalog, and the chaos-sandbox project (git repo: python CLI, one failing test, bench.sh ≈ 4 min) with isolated git-worktree workspaces. It first turns on the instance enableIsolatedWorkspaces setting; without it the server ignores the project policy and every repo task shares the primary checkout.
scheduler.ts Seeded plan: workload × adapter × fault cells and a random fire time per task. Saved to results/<wave>/plan.json. --replay reruns one task alone with the same choices and fires the recorded sequence of faults that crossed it (other tasks' faults included) at the same offsets from launch.
observer.ts Polls each issue and its runs. When a task rests needing Retry it calls POST /api/issues/:id/retry once (once more only if a later fault started after that click), with the body useTaskRetry.ts sends. Collects T-oracle artifacts and the R6 sweep.
grader.ts Pure R1–R6 grading over the samples.
workloads.ts A1 brief document, B1 python CLI with tests, B5 long bench, C1 comment while running, with their T-oracles.
evidence.ts, ledger.ts Evidence bundle for each failure and the JSONL ledger plus SUMMARY.md.
daytona-image.ts Docker-free extraction of the image's runnerd and provider pack, cached per digest, and the controller/image content-ID check.
daytona-sweep.ts Daytona R6: read-only reconciliation of this wave's labelled sandboxes with leases; cleanup only through Paperclip.

Output (gitignored)

tests/restart-chaos/results/ (override with RESTART_CHAOS_RESULTS_DIR):

  • ledger.jsonl, SUMMARY.md — every graded task, per-cell pass rate, open signatures.
  • <wave>/plan.json, timeline.jsonl, server.log, faults.json, <task>.grade.json.
  • <wave>/evidence/<task>/ on failure — run ids and statuses, last 200 events per run, workspace operations, server log window around each fault, startup phase timings, fault timeline, seed, git SHA and the replay command. Known provider key values are redacted.

Grading notes

  • A task is restart-crossing when a run overlaps a fault window or the task was not yet at rest when the fault started. Non-crossing tasks are still graded.
  • R2 also checks that workspace files present before the first fault still exist at rest.
  • B5 passes only when bench.sh wrote its own completion record showing it ran, and the harness itself saw at least three .bench/progress values while polling. This is best-effort against a deliberately adversarial agent.
  • R4 fails when two runs of the issue executed at the same time: both running in one sample, or overlapping started→finished windows. A queued or scheduled wake behind a running run is not a duplicate unless it starts executing. A wake comment may be served again only after a run that did not succeed.
  • T-oracle commands (B1 tests and CLI) run agent-editable code. They run under a macOS Seatbelt sandbox with a scratch HOME, no network and no read access to the operator's home directory. On other platforms they are refused unless RESTART_CHAOS_ALLOW_UNSANDBOXED_ORACLE=1 is set inside a disposable VM.
  • R1 allows the workload budget plus outage time. When a Retry was needed R1 is n/a and R3 decides; a task that rests unfinished with no Retry fails both.
  • Faults are serialized; each one hits every task running at that moment.
  • A todo or in_progress task with no live run and no named wait is not a rest. The observer keeps watching it until it resumes or passes the R5 stall limit.
  • R5 also fails a run that stays running with no live evidence (no new run event, lastUsefulActionAt or execution.lastConfirmedActivityAt, and no start) for more than 3 minutes after the server is ready. A running status alone is not proof of life. A quiet run is still live while a tool it started has not ended (for example a 4-minute bench.sh) or while its recorded local runner process still runs with the same PID and start time.
  • The wave fingerprints the checkout and packages/paperclip-runner/dist at start and after every fault. A build, install or branch switch during a wave would make later restarts run different code, so it fails the wave as a harness error (worktree_changed_mid_wave). The baseline is taken after the harness's own setup (preflight rebuilds provider entrypoints) and covers the tracked diff, untracked file contents, the runner dist and the runnerd binary. Build before the wave, never during it.
  • faults.json and task-faults.json (each task's launch time and the faults that crossed it) are written after every fault, so --replay of a task in an interrupted or wedged wave, or a storm task, re-fires the faults that crossed it at the same offsets.
  • A fault that fails to complete fails the wave as a harness error (exit 2), even when recovery brings the server back.