## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - The runner package is useful only when the application can start, observe, and recover a native Codex run safely. > - Existing direct adapters must keep their current execution and finalization paths. > - The application boundary therefore needs additive persistence, authorization, coordination, and recovery behind an explicit experimental adapter. > - This pull request adds that Codex-only boundary without activating generalized providers, remote environments, or the later task/SDK surfaces. ## Linked Issues or Issue Description **Subsystem affected** Shared contracts, database persistence, adapter utilities, server native-runtime services, and the experimental Paperclip Runner adapter. **Problem or motivation** The already-landed runner package has a qualified Codex path, but the application needs durable native-run state, guarded runtime selection, authenticated coordination, tool security, finalization, and recovery before the experimental adapter can be exercised safely. **Proposed solution** Add a Codex-only `paperclip_runner` application path behind the existing default-off native-runner setting. Bind native state and coordination to company/run identity, preserve persisted-run recovery, and leave every direct adapter on its existing legacy execution path. **Alternatives considered** The earlier stack boundary introduced a generalized executor and remote-environment lifecycle here. That made this PR depend on implementations in higher PRs and changed reusable sandbox behavior globally. Those pieces are now deferred together to #12592. **Roadmap alignment** ROADMAP.md does not list a conflicting native-runner integration project. This change adds the application boundary for the existing Runner architecture. ## What Changed - Added native run/result/finalization/provider-trace persistence, shared validators, and idempotent migration/replay coverage. - Added guarded Codex-only runtime selection, authenticated PRP coordination, recovery, finalization, and interaction services. - Added run/company-bound tool-gateway authorization, credential redaction, SSRF protections, and replay-safe behavior. - Added the explicit `paperclip_runner` adapter behind the default-off rollout setting. - Preserved legacy answered-question wake projection and direct-adapter execution/finalization paths. - Hardened cancellation so only owned in-memory child processes are signaled; persisted recycled PIDs/process groups are never trusted. - Retained the narrow Claude ACPX isolated-context security follow-up discovered after #12590. - Deferred the generalized executor, provider ingress, remote lifecycle, SDK/lab/eval work, release-process changes, and lockfile. ## Verification - Changed-file delta against `master`: 133 files. - GitHub Actions is the authoritative verification environment for this PR. - Full CI, security, and Greptile review will run on this lowest unmerged stack PR. - Local tests/build/typecheck were not run because this checkout is resource constrained. - Static diff/reference checks pass, and `pnpm-lock.yaml` is unchanged. ## Risks - This touches central heartbeat and agent-route code, so legacy compatibility is the primary risk. - Runtime selection remains Codex-only and explicit; direct Codex, Claude, OpenCode, process, HTTP, and plugin adapters remain on their existing paths. - Fresh native starts fail closed while the rollout flag is off; persisted native records remain readable and recoverable. - Cancellation, company/run binding, tool calls, status decisions, and completion writes are guarded or replay-safe. > 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. ## Model Used OpenAI Codex, GPT-5.6, with repository tools, code execution, and parallel agent review. ## 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 linked existing issues or described the issue in-PR following the relevant issue template - [x] I have not referenced internal or instance-local Paperclip issues or links - [x] My branch name describes the change and contains no internal Paperclip ticket id - [ ] I have run tests locally and they pass — GitHub Actions is authoritative for this resource-constrained checkout - [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 risks above - [ ] All Paperclip CI and security gates are green - [ ] Greptile is 5/5 with no open actionable findings - [x] I will address all Greptile and reviewer comments before merge ## Stack - Position: 3 of 5 overall; lowest of 3 currently unmerged - Base: `master` - Previous: [#12590](https://github.com/paperclipai/paperclip/pull/12590), qualified Claude ACPX runtime — merged - Next: [#12592](https://github.com/paperclipai/paperclip/pull/12592), generalized Codex executor, task experience, and developer SDKs --------- Co-authored-by: Dev Agent <dev@paperclip.ing>
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Durable continuation scheduling
Paperclip does not keep an agent process alive between turns. A heartbeat run is finite: it starts, performs work, records a terminal result, and exits. If work must continue later, Paperclip represents that intent in database state and creates another heartbeat run when the continuation becomes eligible.
“Durable continuation scheduler” is a useful umbrella term, but it is not the name of one class or queue. Two related mechanisms provide the behavior:
- Explicit continuation effects are written by native status arbitration.
- Stranded-issue reconciliation is a startup and periodic safety net for an assigned open issue that has no live execution or durable wait path.
The second mechanism produced the repeated issue_continuation_needed runs on
DOT-2.
When it runs
The heartbeat scheduler is enabled unless
HEARTBEAT_SCHEDULER_ENABLED=false. Its interval is configured with
HEARTBEAT_SCHEDULER_INTERVAL_MS and defaults to 30,000 ms. The configured
value is clamped to a minimum of 10,000 ms.
Continuation recovery runs:
- once during server startup, after orphaned runs are reaped, due retries are promoted, and already-queued work is resumed; and
- on every heartbeat scheduler tick, after the same orphan/retry/queue cleanup.
The periodic tick calls reconcileStrandedAssignedIssues(). Consequently, a
new recovery run normally appears within one scheduler interval. The interval
is polling cadence, not a promise that every continuation waits exactly that
long.
Explicit native continuation effects do not need to wait for this scan. The
native status-decision committer writes an idempotent agent_wakeup_requests
row directly. The normal queued-run machinery then claims it.
What is durable
The system reconstructs intent from persisted control-plane records rather than an in-memory timer owned by an agent:
- the issue status and assignee;
- the issue execution lock/run identity;
- heartbeat run status, context, retry ancestry, and terminal timestamps;
agent_wakeup_requestsrows;- native status decisions and their materialized effects;
- pending interactions, approvals, monitors, blockers, and execution stages;
- scheduled retry timestamps and recovery actions.
Because these records survive a process restart, startup reconciliation can resume queued work or repair an issue whose previous execution disappeared.
Explicit continuations
A native result can report yielded with a continuation containing:
- a kind:
same_agent,retry,delegated_issue,response_wake, ormonitor; - a summary; and
- an idempotency key.
The native status arbiter keeps the issue in_progress and emits an
enqueue_continuation effect. The status-decision committer materializes that
effect as an idempotent wake request. A monitor continuation uses
monitor_due; other continuation kinds use issue_status_changed at this
boundary.
This is intentional continuation: the result explicitly says more work is needed and leaves a persisted execution path.
Stranded-issue reconciliation
reconcileStrandedAssignedIssues() scans agent-owned issues in todo,
in_progress, and relevant in_review states. Before creating work, it checks
for reasons not to wake the agent, including:
- an active or queued execution path already exists;
- a pending interaction or durable wait path exists;
- the issue or its tree is paused;
- a provider-quota monitor is pending;
- the run was explicitly cancelled by an operator;
- the assigned agent is not invokable;
- invocation budget or retry/backoff policy prevents a run; or
- recovery has failed enough times that the issue should be escalated instead.
For an eligible in_progress issue with no live path, it creates an automated
wake/run with:
wakeReason: issue_continuation_needed
retryReason: issue_continuation_needed
source: issue.continuation_recovery
This is a liveness repair, not evidence that the previous model requested another turn. Its invariant is: an assigned open issue should have either a live execution path, a durable reason to wait, or a visible terminal/blocking disposition.
Why DOT-2 looped
DOT-2's runner repeatedly produced a successful result that reported done.
The native evidence classifier did not accept the model's evidence references,
so status arbitration preserved in_progress and created another continuation
path. After each run exited, the periodic reconciler saw:
assigned + in_progress + successful terminal run + no live/wait path
It therefore queued issue_continuation_needed again on the next approximately
30-second tick. The new run received the original task title because the native
model envelope also omitted the wake-comment text, so it repeated the same
answer.
The fix has two parts:
- native model input now contains the redacted server-authored task prompt, including the current wake comment; and
- ordinary low-risk issue completion can accept a schema-valid completion claim, while tools, governed effects, interactions, and approvals keep their independent authorization gates.
Thus a completed one-shot task becomes done; it is no longer a candidate for
stranded-issue reconciliation.
How to diagnose a suspected loop
Inspect the latest runs for the issue and compare these fields:
invocationSource— recovery-created runs useautomation;contextSnapshot.wakeReason;contextSnapshot.retryReason;retryOfRunId;- terminal run status and
resultJson.authoritativeDecision; resultJson.issueStatusAfter;- issue
status,executionRunId, and pending interactions/monitors; - lifecycle events explaining enqueue, suppression, escalation, or cleanup.
Repeated successful runs with wakeReason: issue_continuation_needed, an
authoritative decision of in_progress, and no durable wait path usually mean
the result/disposition contract is failing to converge. Fix the status or
continuation decision; increasing the polling interval only hides the bug.
Primary implementation locations
server/src/index.ts— startup recovery and periodic heartbeat scheduler.server/src/config.ts— scheduler enable flag and interval.server/src/services/recovery/service.ts—reconcileStrandedAssignedIssues()and recovery wake creation.server/src/services/issue-rewake-throttle.ts— repeated state-wake throttling and progress detection.server/src/services/native-runtime/status-arbiter.ts— native terminal disposition and explicit continuation decisions.server/src/services/native-runtime/status-decision-committer.ts— durable, idempotent materialization of native continuation effects.server/src/services/heartbeat.ts— run lifecycle, immediate recovery, queue promotion, and wake execution.