## 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>
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.shwrote its own completion record showing it ran, and the harness itself saw at least three.bench/progressvalues 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
runningin 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 unlessRESTART_CHAOS_ALLOW_UNSANDBOXED_ORACLE=1is set inside a disposable VM. - R1 allows the workload budget plus outage time. When a Retry was needed R1 is
n/aand 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
todoorin_progresstask 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
runningwith no live evidence (no new run event,lastUsefulActionAtorexecution.lastConfirmedActivityAt, and no start) for more than 3 minutes after the server is ready. Arunningstatus alone is not proof of life. A quiet run is still live while a tool it started has not ended (for example a 4-minutebench.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/distat 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 runnerdistand the runnerd binary. Build before the wave, never during it. faults.jsonandtask-faults.json(each task's launch time and the faults that crossed it) are written after every fault, so--replayof 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.