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PaperClipAI/doc/native-workspace-finalization-recovery.md
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Devin FoleyandPaperclip 79c34058cd fix(native): retain unexported workspaces after execution failure (#16397)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Native agents can edit files in a remote sandbox before they submit
a result.
> - A process identity or startup failure can end the run before file
export.
> - Cleanup can then delete the sandbox and its unpublished files.
> - This pull request retains the exact source and records a file repair
action before cleanup.
> - Operators can recover the files without replaying the failed turn or
changing the task owner.

## Linked Issues or Issue Description

**What happened?**
A native remote process had completed local edits when process identity
recovery failed. The run still had a prepared workspace reference and no
accepted result. Cleanup deleted the source sandbox. No file recovery
card appeared. A restarted run can hit the same path during setup,
before the native executor starts.

**Expected behavior**
Retain the exact unexported source. Show the existing file recovery
card. Require source stop and file recovery evidence. Keep task
ownership, status, and external action reconciliation separate from file
repair.

**Steps to reproduce**
1. Run a native agent in a remote ephemeral workspace and make
unpublished edits.
2. Fail process identity recovery before result acceptance or file
export.
3. Allow failure handling and lease cleanup to run.
4. Before this change, cleanup can destroy the source without a file
repair action.

Refs: #16341 for related process identity diagnostics. Refs: #16349 for
startup ownership fencing. This change addresses file retention after
failure.

## What Changed

- Record source retention and a file recovery action in the terminal
native failure transaction.
- Cover restarted preparation failures before the terminal setup writer
and cleanup run.
- Require the exact company, run, lease, provider allocation, and
workspace binding. Require the exact live recovery claim to settle an
owned preparation failure. Refuse stale or competing claims.
- Reuse the existing stop-only cleanup and file-only reconciliation
path. Leave accepted results and scheduled same-run recovery on their
existing paths.
- Document the retention rule and add database and runtime boundary
regressions.

## Verification

- All 1,242 tests passed across the full heartbeat recovery suite,
native executor, native source retention, runtime teardown, run
completion, and legacy file recovery.
- The integrated missing-descriptor regression fails before the
inner-handler fix and passes after it. The runtime retention and owned
restart regressions also reproduce their prior failures.
- The tests cover exact source identity, current and stale claims,
atomic rollback, cancellation, idempotence, and file-only repair on a
completed task.
- `pnpm -r typecheck` passed on the final code.
- `pnpm build` passed on the final code.
- Full repository CI passed on
`3945eb2ba5c228c5d4992da02b765dcf2e634cb8`: 54 successful checks and two
skipped Storybook checks.
- Apex scored 5/5 on that exact commit. Both earlier findings are fixed
and all review threads are resolved.
- The unsharded local `pnpm test:run` is still in progress. It is not
counted as a local full-suite pass; complete suite coverage is verified
in CI.

## Risks

- Failed runs can retain a sandbox that needs operator cleanup after
file recovery. This uses the existing retention policy and recovery
controls.
- This does not recover files from allocations that were already
deleted.
- No schema migration, UI change, or telemetry change is required.

## Model Used

- OpenAI GPT-6 through Codex. Tool use, code execution, and reasoning
assisted this change. The environment identifies the model as GPT-6; it
does not expose a more specific serving snapshot 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 `#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>
2026-10-14 23:07:15 -07:00

24 KiB

Native workspace finalization ownership and recovery

A native provider can fail before it submits a result while its workspace still contains unpublished edits. A prepared workspace reference is not an export receipt. Terminal provider failure pins the exact bound sandbox and records a file-recovery obligation in the same transaction as the failed run. Both setup failure handlers record that obligation before their terminal writer and provider cleanup run. This includes descriptor reads that fail inside runtime selection. Only its exact live recovery claim can settle an owned preparation failure; another owner or a stale claim prevents cleanup. Settling that claim and recording file retention share a transaction.

The recovery card names the original run and requires evidence that its exact allocation stopped and its files were recovered. Recording that evidence does not retry the old turn, certify unknown external actions, change the current task owner or status, or require an accepted native result. Accepted-result export recovery and same-run provider recovery keep their existing paths. An export that has already finalized does not create this file obligation.

Native workspace export and merge acquire a PostgreSQL advisory lock scoped to company and run before the first physical copyback. The live heartbeat and the reconciler share that lock. Recovery skips a busy owner without recording another workspace operation or spending a retry. Recovery also rechecks the coordinator's terminal state and retry time under ownership: an earlier sweep snapshot cannot start another export after live finalization publishes a permanent repair or delay. A completed workspace barrier is reread under ownership before export, and a committed coordinator cannot be overwritten by a late failure receipt.

An unverified workspace owner keeps one board recovery action for its exact run and owner fingerprint. Repeated recovery checks do not consume attempts or rewrite that action. Task completion or cancellation does not prove the old physical writer stopped, so reads and recovery sweeps retain this action while the matching run still carries that owner receipt. After the receipt is cleared or replaced, ordinary stale-action cleanup applies. Cleanup is attributed to the system; historical cleanup from page reads does not add tasks to a person's inbox or refresh issue activity timestamps.

The lock transaction holds no row locks. Ordinary progress and finalization receipts remain visible through the normal database pool. A dedicated connection outside the application pool is reserved for the duration of copyback and closed when it settles; even a one-connection application pool remains available for progress writes. Its run profile carries nativeWorkspaceFinalizationOwner, an exact token, host, PID, and process-start receipt. Losing the lock connection does not prove physical copyback stopped: a contender still refuses a receipt whose controller is alive. The original callback joins before its token is released, and publication checks the lock connection and token. Graceful completion clears the receipt. If that cleanup write fails after the callback joins, only the same exact controller boot retains positive in-process join evidence and may resume after reconnecting; an unknown token or a new boot does not inherit that authority. A controller that has exited on the same host can be recovered automatically only when a durable successful workspace barrier proves its copyback finished. A dead parent can leave tar/Git children alive, so incomplete copyback requires operator stop verification even on the same host. PID reuse is checked against its recorded start time rather than trusted by PID alone.

When PostgreSQL configures an idle-transaction timeout, the owner probes its dedicated lock transaction at one third of that interval, capped at 30 seconds. The probe stops and joins before the transaction is released. This keeps a live copyback from losing its lock only because filesystem work has no database statements. It does not disable the database timeout or reconnect a failed lock session. Publication still requires the physical connection and the exact durable owner token. A disabled timeout adds no periodic probe.

Automatic cloud recovery

New Railway copyback receipts record the exact project, environment, service and deployment ID. On takeover, the existing finalization reconciler asks the cloud harness to inspect that deployment. The harness resolves the stack's owned resources independently and issues a short-lived Ed25519 receipt only when the exact deployment is REMOVED with deploymentStopped: true. This covers all processes in the deployment, including orphaned copyback children. Missing, truncated, live or unavailable provider evidence leaves the physical fence intact.

The tenant verifies the configured harness key, disjoint receipt audience, stack, run, owner token, deployment identity and expiry. It records proof and an activity entry when replacing only the exact owner under the existing advisory lock. The normal reconciler resumes the accepted result; it does not create a provider turn or change approval/monitor waits. A changed owner during verification fails closed.

Stop proof alone does not authorize old work to overwrite a current task. After the provider read, automatic recovery uses the operator path's shared binding checks under short coordinator, issue and run row locks, atomically with the owner claim. The task must still be open, assigned to the run or its authoritative review participant, and bound to that running native execution and accepted result. A different checkout, newer execution or queued/running legacy execution prevents takeover. Publication checks repeat this validation; row locks are never held across physical copyback I/O.

The harness endpoint is POST /v1/tenant/workspace-worker-stop. The fleet-wide server token authorizes a read request, never stop evidence: responses must be signed by the harness. This endpoint requires the companion cloud harness change. Deploying only the application keeps unknown owners fenced. No cloud provider credentials are delivered to tenant applications.

The task view shows only “Restoring saved work…” after the server confirms recovery or an operator queues it, then removes the notice when commitment resolves recovery. It exposes no process identifiers, shutdown form or manual resume control. Legacy receipts without platform identity and unsupported platforms say operator assistance is needed; operators use the documented exact-owner API below after independent stop proof. The three diagnosed historical receipts do not gain a deployment identity merely by upgrading. Never infer one from elapsed time or a hostname.

Unverified copyback after controller replacement

Generic orphan recovery does not turn a missing provider PID into process_lost while the native coordinator is workspace_finalizing with an accepted result bound to the same company, issue, and run. The finalizer owns that unfinished suffix, including the interval before it acquires its physical owner receipt. The heartbeat's phase or profile alone does not establish this authority. The conditional orphan write rechecks the durable result and the heartbeat's PostgreSQL tuple version, so a result published while the write waits on its row lock cannot be overwritten using an older statement snapshot. Result publishers lock and update that heartbeat in the same transaction as acceptance.

The running run keeps its source lease while the existing finalizer either completes, records its bounded failure policy, or requires operator stop verification. A new queued run or a healthy child task cannot clear an unverified copyback hold. Verified finalization clears the matching run's hold after commitment. Existing terminal-task dispositions and explicit cancellation remain unchanged; this does not recover a source already destroyed by an older controller or claim that an unfinished export succeeded.

The controller cannot verify a process on a foreign or unknown host, or orphaned copyback children after an abrupt parent death before the success barrier. It surfaces native_workspace_finalization_owner_unverified as board-owned recovery, with no automatic provider wake. This is an intentional limit: elapsed time or a missing database connection never proves the old copyback process stopped.

An instance operator must first verify through the deployment platform that the exact prior controller and its copyback subprocesses have stopped. Retain the sandbox, accepted native result, and workspace descriptor. Do not run a new provider turn, delete workspace contents, or relax archive confinement.

For legacy receipts, an authorized company owner, company administrator or instance administrator records independently verified platform evidence through the operator API. The task has no shutdown form or resume control. The API is POST /api/issues/:id/recovery-actions/resume-workspace-finalization with:

{
  "actionId": "<recovery-action-id>",
  "runId": "<run-id>",
  "ownerToken": "<owner-token-from-recovery-evidence>",
  "controllerAndCopybackStopped": true,
  "stopEvidence": "<deployment-platform evidence for this controller and its children>"
}

This is an operator attestation, not an automatic deployment-platform probe. The separate runtime:confirm_owner_stop authorization action limits this attestation to active company owners or administrators, the trusted local board, or an instance administrator. Ordinary runtime managers and agents cannot release the physical owner receipt. Missing role data keeps the client notice read-only. A missing advisory connection alone is insufficient. Admission rejects an active copyback lock, an observably live local controller, a changed owner, a newer run, or an unbound result. It records the exact owner and operator evidence atomically with releasing the receipt. The accepted result, workspace descriptor, source lease, task status, monitors, and approval waits are unchanged. The ordinary reconciler performs copyback and applies the saved result through the status arbiter. No provider wake is enqueued. The recovery action remains visible until finalization commits. Admission supports saved-result copyback from result_accepted, workspace_finalizing, and retryable_failure; an abandoned retry does not need a replacement run. The existing retry schedule remains unchanged. Repeating the same confirmation before reconciliation is idempotent; it cannot release a newer owner. Generic recovery resolution, including false-positive dispositions, cannot dismiss this hold or bypass saved-result finalization.

Repeated sweeps preserve these copyback-specific instructions, including for older actions whose recovery budget was already exhausted. They must never recommend starting a replacement provider run for this hold.

For older servers without this action, the maintenance fallback follows.

After that platform verification, use a database maintenance transaction to release only the exact receipt shown by the recovery action. Replace the four placeholders with the action's company, run, token, and source issue. The advisory lock prevents concurrent acquisition during this change; the token comparison prevents clearing a newer owner. A zero-row update means ownership changed and requires fresh inspection. This maintenance operation is for a full-control instance operator, not an agent tool.

BEGIN;
SELECT pg_advisory_xact_lock(hashtextextended(
  'native-workspace-finalization:<company-id>:<run-id>', 0));
UPDATE heartbeat_runs
SET runner_profile_json = runner_profile_json - 'nativeWorkspaceFinalizationOwner'
WHERE company_id = '<company-id>'::uuid
  AND id = '<run-id>'::uuid
  AND native_issue_id = '<issue-id>'::uuid
  AND runtime_mode = 'native'
  AND runner_profile_json->'nativeWorkspaceFinalizationOwner'->>'token' = '<owner-token>'
RETURNING id;
COMMIT;

Resolve the existing board recovery action with a note containing the platform stop evidence. The ordinary reconciliation sweep then resumes workspace finalization from the accepted result. Confirm the run's native phase and resultJson.finalizationPhase are committed, there is no nextAttemptAt, and no workspace operation is still running. The accepted provider result is reused.

Automatic unsafe archive recovery

An unsafe link in a native workspace must not fail a completed task or require an operator to repair a sandbox. The accepted agent result remains authoritative.

Daytona validates every exported archive before extraction. If validation rejects an archive, export once more using files, directories, and relative symlinks whose resolved targets stay inside the workspace. The fallback does not follow or delete symlinks. It omits unsafe or unresolvable links, stores hard-linked files as ordinary bytes, and preserves directory exclusions and empty directories. The second archive passes the same confinement checks. A fixed informational message records the fallback in the provider log.

If native copyback still rejects the archive or its source confinement check, Paperclip discards that export, records workspace_export_omitted at info level in the local run log, and completes finalization using the original accepted result. It does not create a task warning, recovery card, repair request, or new provider turn. The normal completion policy still enforces ownership and explicit workflow constraints. Lost remote files are an accepted tradeoff.

The live path and restart finalizer use the same policy under workspace finalization ownership. Ownership loss, transport failures, missing sandboxes, and other unrelated errors retain their existing handling. No unsafe archive is extracted. No host path or link target is copied into the informational run event.

Repairing a failed workspace export without rerunning the agent

Transient export failures retry three times, then produce native_workspace_sync_out_retry_exhausted. The accepted result stays saved, and the exact sandbox is stopped and retained for export-only recovery. The reason identifies a transport/copyback failure, not an inferred disk-space cause. New unsafe archives use the automatic policy above and do not create this hold. Historical unsafe-archive holds recover automatically as described below; they do not use this operator flow.

A board member with runtime management access can complete the saved result:

  1. Read the recovery action, run, and environment lease. Verify the company, run, provider sandbox ID, and stopped-provider receipt. Preserve that exact sandbox; do not acquire a replacement or seed the host workspace over it.
  2. Through the provider console or official SDK, resume that sandbox and inspect the export failure while preserving all user files. Restore transport access or other provider prerequisites before retrying. Extending the sandbox retention window can be necessary during this repair.
  3. Use the operator API to record the repair and request export-only retry. The task shows operator assistance is needed, without an infrastructure form. The board API is POST /api/issues/:id/recovery-actions/retry-workspace-export with { "actionId": "<recovery-action-id>", "runId": "<run-id>", "repairNote": "<repair and preservation evidence>" }.
  4. Confirm the same run commits, the saved result determines the task outcome, and the recovery action resolves. No new provider turn or wake is created. A reusable repair sandbox is stopped and retained again. An ephemeral sandbox follows its original destroy-after-turn policy only after the exact result commits and the workspace reference contains a finalized host-copy receipt.

Admission requires the same accepted result, task owner, descriptor, and lease; confirmed prior provider stop; an available repaired sandbox; and no newer task execution or competing current lease. It shares finalization ownership and resumes only the recorded provider lease through its verified lifecycle method. That method drains old activity and verifies the saved workspace identity before reopening the provider's controller admission gate; an external console restart alone does not reopen that gate. Admission rejects a missing or replacement sandbox and revalidates after probing the exact workspace. A changed binding or unavailable sandbox returns 409 without reopening work. A duplicate queued request is idempotent. Unsafe archives use automatic salvage or omission during retry. Generic ordinary recovery resolution cannot retry, mark done, or send the task for review in place of export-only retry. Explicit board false-positive/cancellation dispositions remain deliberate overrides; they do not claim successful copyback.

Before publishing terminal export failure, the finalizer atomically records a stop-only intent with the failed run. This includes ephemeral allocations: ordinary release policy cannot delete their unexported files. A crash before cleanup leaves enough exact lease, result, and plugin authority for restart recovery. The same intent remains while export-only retry is active.

Before resuming the retained sandbox, the controller durably records a stop-only cleanup intent on that exact lease and removes the old stopped receipt. If the resume reply is lost, probing fails, or admission changes, it stops and retains the sandbox. A failed stop remains pending_cleanup; a restarted controller's bounded cleanup sweep retries the verified stop without destroying saved files. An in-flight request holds a 15-minute cleanup claim, so a controller crash may delay that sweep until the claim expires. Neither an unconfirmed stop nor a stale receipt grants admission, and a changed lease or competing sandbox owner prevents cleanup from taking ownership. Retry export after the lease has a new confirmed stopped receipt. No provider turn is created by this recovery. Cleanup and its readiness probe use the plugin ID recorded on that lease. Another plugin with the same provider name cannot take over; an unavailable original plugin defers cleanup without consuming an attempt. Stop-only cleanup requires the exact plugin worker to advertise environmentStopLease. Older plugins without that hook receive neither release nor destroy; resume admission also defers until safe compensation is available. New intents use schema v2 with an explicit plugin pin. A v1 intent created before that field existed remains recoverable using only the plugin ID already recorded on its exact lease; an explicit mismatched pin is still rejected.

The opt-in native-workspace-export-resume.live.test.ts is a provider-boundary fault integration, separate from the browser Product E2E. After building the Daytona plugin, run that exact Vitest file with PAPERCLIP_LIVE_EXPORT_RESUME=1, DAYTONA_API_KEY, and PAPERCLIP_LIVE_EXPORT_RESUME_IMAGE set to an immutable image digest. It creates one disposable ephemeral sandbox and database, injects probe and stop transport failures, and verifies a fresh runtime can stop the sandbox while preserving exact nonce bytes. It also injects three transient failures at the production finalizer boundary and verifies retained work plus export-only retry admission. This boundary test does not claim physical copyback or result commitment; historical browser Product E2E supplied that proof before automatic unsafe-export recovery. It deletes only that owned fixture after proof.

Historical unsafe exports

The reconciliation sweep automatically recovers accepted results that an older controller terminalized with native_workspace_sync_out_unsafe_archive. It omits the already-rejected export without accessing the old provider, so a stopped, unavailable, or deleted sandbox cannot require user repair. The omission barrier and result re-admission are atomic under finalization ownership. The normal status arbiter still enforces current ownership, contracts, and gates.

This works with active, incorrectly resolved, or missing old repair actions. It clears the matching stale unsafe notices instead of restoring them. Newer runs, changed task ownership or contracts, another active recovery action, and explicit operator dispositions prevent replay of old results. No provider turn is created. Diagnostics appear only in the local run log; no unsafe-export activity notice, repair card, or recovery chip is created. Existing stop-only allocation intents retain their exact ownership and cleanup protections.

Daytona stop-only preservation disables provider auto-delete and refreshes the provider record to confirm the disabled policy before stopping. An unavailable or unconfirmed policy leaves cleanup pending; it never falls back to stop or delete. The original ephemeral destroy policy applies only after exact accepted-result copyback and commitment.

New ephemeral native allocations receive an acquisition-time workspace sentinel bound to their run and provider allocation. Export-only resume requires that proof and the unchanged durable intent. A legacy ephemeral allocation without this proof remains blocked; recovery never creates a sentinel or accepts a replacement during resume. The reusable workspace identity hash is unchanged.

Disabling auto-delete retains provider storage while repair waits. No automatic lease-age sweep deletes these released, confirmed-stopped allocations. Storage costs can continue until committed copyback applies the original cleanup policy or an operator explicitly deletes the allocation.

Generic stop-only cleanup

An explicit sandbox stop_and_retain also requires the dedicated provider hook when no export repair is involved, including successful per-turn reusable runs and startup cancellation. Before dispatch, the controller stores a separate sandboxStopAndRetain intent bound to the company, run, lease, provider allocation, and original plugin. The initial cleanup and restart sweep both require that plugin to advertise environmentStopLease. Missing capability or failed stop leaves pending cleanup; ordinary release and destroy are never fallback methods.

A matching stopped receipt clears the pending intent, leaves the lease released and resumable, and saves sandboxStopAndRetainReceipt. Its request identity, original plugin and method: "environmentStopLease" attest this dispatch route. The accepted-result export intent and its commitment requirements are unchanged.

The built-in fake provider uses its explicit stopLease operation rather than a plugin RPC. Its intent pins the registered built-in provider and its receipt says builtin.stopLease. This provider owns no real process or filesystem; the receipt models its lifecycle. Missing built-in stop support or an unconfirmed receipt also remains pending through restart, without calling release or destroy.

Legacy copy-back after a confirmed stop

A legacy adapter can report failed workspace copy-back after cancellation has already stopped and released its sandbox lease. The host records the exact lease snapshot from before adapter dispatch. For an originally ephemeral source, the recorder can preserve the released allocation for repair only while the current lease is still ephemeral and its company, run, issue, workspace, provider, allocation, acquisition time, plugin, and realized root still match. It requires both the dedicated stop-and-retain receipt and the matching stopped-execution receipt. A competing owner or changed source fails closed. The recorder leaves release status and receipts intact, excludes the allocation from reuse, and creates the existing board-owned file-repair obligation without replaying work or changing a newer run or the task's status.

This late-recording path does not admit reusable leases. Provider resume can precede the database handoff, so an old stop receipt and a database row lock cannot prove that reuse has not started. Existing active-source and previously recorded recovery paths retain their behavior. A missing or rejected original snapshot does not authorize adopting another released lease.

A retained source receipt records control-plane evidence; it does not prove the provider still holds the original bytes or that copy-back succeeded. Operators must verify and recover the exact source separately. Later successful runs and completed tasks do not certify recovery of earlier workspace files.