## Thinking Path
> - Paperclip runs Codex locally and in remote sandboxes.
> - The runner must preserve startup configuration and session identity.
> - Missing project trust can disable repository configuration.
> - Full-history requests use deprecated provider fields.
> - Resume usage describes old work and must not become new run usage.
> - This change corrects startup trust, state reads, and usage
classification.
## Linked Issues or Issue Description
**What happened?**
Normal Codex runs could show repository-trust and history-deprecation
warnings.
Resume could report the preceding turn's token snapshot as a late-turn
warning.
The historical last-usage value could also be attributed to the new run.
**Expected behavior**
Trust the server-selected startup root in isolated configuration. Read
lightweight
provider state and paginated evidence. Use historical cumulative usage
as a
baseline without a new charge or user-facing warning.
**Steps to reproduce**
1. Start a native Codex task in a selected repository.
2. Finish the turn and resume the provider thread.
3. Inspect provider notices, history requests, and per-run usage.
4. Repeat startup and cold resume inside a Daytona sandbox.
**Paperclip version or commit**
Codex CLI 0.153.4 is the pinned runtime and reproduced baseline.
Replayed onto master at 6abeb6733. Related authority work: Refs #13092.
This PR retains its startup cleanup and protocol-integrity checks.
**Deployment mode**
Local source checkout and disposable Daytona sandbox.
## What Changed
- Classify the exact historical resume usage event before the generic
stale-turn warning.
- Persist cumulative usage baselines across recovery of the same run.
- Use excludeTurns on resume and lightweight thread reads.
- Page turn metadata and selected turn items with cursor and identity
validation.
- Reject unsupported or incomplete history instead of guessing that
execution is idle.
- Trust the startup execution root on its host, including Git worktree
trust keys.
- Start Codex in that root and retain the selected sandbox profile on
later turns.
- Keep unrelated isolated configuration and Codex's separate hook trust
policy.
- Add Rust, TypeScript, accounting, native integration, and local
run-log documentation.
## Verification
- Codex and native-transport TypeScript: 333 passed before PR replay.
- Adjacent OpenCode/ACPX driver and accounting tests: 49 passed.
- Rust library, serialized: 226 passed. Native Codex integration: 72
passed, 1 ignored, plus two pagination regressions.
- Repository typecheck and build passed. All repository test groups have
passing coverage after fixture and resource retests; the initial
monolithic command was not clean.
- Fresh real Codex native browser tasks returned correct answers without
the three targeted notices. Answers persisted after refresh and restart.
- Real same-thread TypeScript driver tests passed locally and in
Daytona, including cold resume, configuration, skills, and an approved
harmless hook.
- Local usage summed to 64,607 tokens. Daytona usage summed to 42,737
tokens. Each sum matched its final session total exactly.
- See doc/plans/2026-09-09-codex-integration-acceptance.md for the scope
and limits of the live tests.
- After replay onto current master and review fixes: 334 Codex, backend,
and live-session tests passed, including checkpoint serialization and
real-runner process restart. TypeScript checks passed.
- The native Codex integration run passed 83 tests; the large lineage
test passed separately with the release runner (its debug build exceeded
the test deadline).
- All GitHub checks passed on the final PR head. Greptile is 5/5 with no
unresolved review threads. CI regenerates the lockfile for the added
TOML dependency, per repository policy.
- The first server shard hit a timing-dependent duplicate-key failure in
the unchanged artifact-document concurrency test. Its focused 11-test
suite passed locally. One CI retry on the same head passed all 103 files
and 1,405 tests (2 skipped): [retry
result](https://github.com/paperclipai/paperclip/actions/runs/34398832930/job/102631274667).
## Risks
- Trust applies only to the server-selected startup root and isolated
configuration. Sandbox and tool permissions remain authoritative.
- Codex still requires approval of individual hook hashes. This change
does not bypass that policy.
- Providers without the required history APIs fail explicitly.
- Daytona acceptance used the production TypeScript driver. Remote
Paperclip UI and remote Rust execution were not tested.
- No new public API, database state, recovery policy, or UI control is
included.
## Model Used
OpenAI Codex, GPT-6 (`gpt-6-astra`). Used for reasoning, code edits,
tool use,
and test execution. The exact context-window limit is not exposed in
this
session. Real-provider acceptance used Codex CLI 0.153.4 with
`gpt-5.6-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
#` 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>
Make task recovery durable and preserve the latest user request across native and legacy continuations. Keep routine recovery quiet and prevent replay when action outcomes are uncertain.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The Paperclip Runner keeps durable run and provider state outside
one server process.
> - A server restart can leave that runner alive or can interrupt it
after a provider checkpoint.
> - The old startup path used handoff intent and PID evidence, but it
did not reconstruct native ownership.
> - That gap could block the issue, create a replacement run, or start
duplicate provider work.
> - This pull request adds durable same-run recovery for coordinated and
uncoordinated restarts.
> - The benefit is exact recovery of the run, runner, session, provider,
steering, and finalization state.
## Linked Issues or Issue Description
Refs #9628. That pull request added earlier local-adapter hot-restart
work. This change adds native PRP authority reconstruction and same-run
provider resume.
Refs #10935. That pull request handles missing hot-restart snapshots.
This change also supports hard restarts with no snapshot.
Refs #11624. That pull request prevents unsafe retry after an adopted
legacy process exits. This change reconciles native terminal evidence
before provider recovery.
Refs #12070. That pull request improves process liveness checks. This
change also binds recovery to a process-start fingerprint and fails
closed on ambiguity.
**What happened?**
The server could record hot-restart intent, but startup did not rebuild
native runner ownership. A live runner could not re-register its PRP
authority. A dead runner could not resume the exact native and provider
session on the same heartbeat run. Generic recovery could then block the
issue or create replacement work.
**Expected behavior**
A live native runner must reconnect with the same PID and logical
identities. A dead runner must resume the same durable session and
heartbeat run with only a new operating-system PID. A proposed or
terminal result must finalize once before any provider turn starts.
Ambiguous process or session evidence must stay blocked without a signal
or duplicate spawn.
**Steps to reproduce**
1. Start a Paperclip Runner heartbeat and wait for an active provider
turn.
2. Restart only the Paperclip server, with or without a hot-restart
marker.
3. Observe that the old startup path does not reconstruct the native
control-plane authority.
4. Kill both the server and runner after a provider checkpoint.
5. Observe that the old path cannot resume the exact native session on
the original heartbeat run.
**Paperclip version or commit**
The defect was reproduced from commit
`1991f31fd53e7f7794d5c2e4b93be384ade2b41d`. This branch is rebased onto
the current `master`.
**Deployment mode**
Local development and self-hosted server deployments that use the local
Paperclip Runner.
## What Changed
- Added correlated hot-restart requests and version-compatible native
handoff fields.
- Added controller boot identity, process-start identity, controller
generation, recovery state, request id, and bounded history to the
native finalization ledger.
- Added transactional recovery claims for live-runner reattach,
dead-runner resume, and incomplete bootstrap.
- Added fail-closed ownership takeover rules and process identity
validation.
- Added live runner adoption to the local runner transport without a
duplicate spawn.
- Added same-run provider checkpoint resume and legacy retry-row
compatibility.
- Reconciled proposed and terminal results before runner or provider
recovery.
- Bound the HTTP and PRP listener before startup recovery and delayed
scheduling and generic reapers until classification completes.
- Added restart-aware health diagnostics, run-log recovery transitions,
durable runner diagnostics, and bounded shutdown finalizer draining.
- Moved restart-survivable diagnostics into runner-owned, pre-redacted
bounded writes; raw stdout and stderr are never persisted.
- Added process-start fencing for controller, runner, and provider PIDs;
startup classifies every candidate without an implicit cap.
- Added crash-recoverable, contention-safe development restart-request
coordination and failed-startup listener cleanup.
- Added a credential-free real-process restart suite for eight restart,
scale, and identity scenarios.
- Documented native restart operation, persistence, diagnostics, and
verification.
## Verification
- The documented native restart commands passed. They ran eight
real-process/database recovery scenarios and the live runner adoption
transport test.
- Native executor tests passed: 111 tests.
- Heartbeat recovery tests passed: 124 tests.
- Hot restart, health, and shutdown tests passed: 52 tests.
- The broader affected server suite passed: 350 tests.
- Focused native recovery and startup tests passed: 49 tests.
- Runner transport and control-plane tests passed: 63 tests.
- Runner-owned diagnostic tests passed for write-time bounding,
credential redaction, private file modes, and raw stream
non-persistence.
- Development restart coordination tests passed: 11 tests.
- Database migration checks and the partial-application/replay
regression test passed.
- Server, database, and Paperclip Runner typechecks passed.
- `git diff --check` passed.
- Full Paperclip PR CI passed, including build, canary, all five general
server shards, all five serialized server shards, all three browser E2E
shards, workspace suites, and release-registry verification.
- Greptile completed at 5/5 with no outstanding findings,
recommendations, follow-ups, or open review threads.
## Risks
- Moderate risk. This changes startup ordering and ownership transfer
for active native runs.
- The migration adds nullable columns and does not rewrite existing
rows.
- Recovery fails closed when process or durable session identity is
incomplete or contradictory.
- The first implementation supports the local Paperclip Runner. Remote
targets keep their existing behavior.
- The real-process suite covers cleanup and asserts that no runner or
provider process survives each test.
> 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
- OpenAI Codex with GPT-5. The runtime did not expose a more specific
model revision or context-window size. Repository editing, shell
execution, database tests, and real-process test execution were 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
- [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
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The Paperclip Runner needs a narrow server trust boundary before an
adapter can start it.
> - The package has durable runner transport, but the server does not
host or authorize that transport.
> - Native persistence exists, but no writer connects PRP events to
those records.
> - A direct adapter must not enter this path by accident.
> - This pull request adds a hidden, run-bound PRP server coordinator.
> - The benefit is a recoverable server boundary that remains
unavailable to normal execution.
## Linked Issues or Issue Description
Refs #11962
Refs #12129
Refs #12169
**Subsystem affected**
Cross-cutting. The change affects the runner package and server
orchestration.
**Problem or motivation**
The server cannot authenticate runnerd, commit PRP events before ACK,
authorize semantic tools, or enter native finalization from a durable
runner result. The application must have this hidden boundary before a
guarded adapter can use the runner.
**Proposed solution**
Add an authenticated PRP WebSocket authority and register it only for
one exact persisted native Codex run. Bind each connection and event to
the company, issue, agent, run, runner, session, turn, item, and
verified runner identity. Commit each event before its cumulative ACK.
Project only authorized same-task read tools. Rebuild the accepted
result and finalization record from durable result and terminal events.
**Alternatives considered**
The server could expose a broad runner API key or route semantic calls
through existing adapter endpoints. Those options grant too much
authority and weaken replay recovery. The server could also add the
user-facing adapter in this pull request. That option would mix rollout
selection with the transport trust boundary and make legacy
compatibility harder to review.
**Roadmap alignment**
This work supports the shipped enforced-outcomes, governed-tool, and
self-healing-run milestones. It does not add a new roadmap surface.
## What Changed
- Add the durable PRP server authority with one-use bootstrap tickets,
reconnect leases, encrypted frames, bounded state, cumulative ACKs, and
idempotent commands.
- Add `/api/runner/v1/connect/:runId`. Derive its `ws://` or `wss://`
URL from the configured Paperclip API URL.
- Register one authority only after the coordinator verifies the
complete native Codex run binding.
- Commit validated PRP events to `heartbeat_run_events` before ACK.
Reject source gaps and conflicting replays.
- Rebuild accepted results and finalization records from durable result
and terminal events. Enforce finalization owner leases and retry times.
- Project five same-task read operations. Recheck run, agent, task, and
company authority for each call.
- Keep the route hidden. No adapter selects this coordinator, and no
code starts runnerd.
- Vendor the compiled runner TypeScript runtime into the server package
while keeping the workspace package development-only for the server.
- Document the package, database writer, run-log payload, and credential
exclusions.
## Verification
- Run `pnpm --filter @paperclipai/paperclip-runner check:all`. All
TypeScript protocol checks and 69 Vitest tests pass, including
commit-before-ACK crash recovery. All 43 Rust unit tests and 13 Rust
integration tests pass. Conformance and replay parity pass.
- Run the focused server WebSocket, coordinator, package-build, and
startup-wiring suites. All 26 tests pass, including a clean-checkout
reproduction with the runner `dist` directory absent.
- Run `pnpm -r typecheck`.
- Run `pnpm test:run`.
- Run `pnpm build`.
- Confirm that the diff contains 19 files. Confirm that it contains no
workflow or `pnpm-lock.yaml` change.
## Risks
- The server installs the WebSocket route at startup. An unregistered or
malformed run path fails closed and creates no native record.
- Bootstrap tickets are one use. The private state directory uses mode
`0700`, and the state file uses mode `0600`. The file stores derived
authentication verifiers and never stores raw tickets or lease tokens.
- The journal has explicit frame, command, event-window, and file-size
bounds. A bound violation closes the runner connection or rejects the
command.
- A runner event reaches the database before its ACK. A crash between
event commit and ACK causes a byte-equivalent replay, not a second
logical effect.
- The coordinator accepts only an existing queued or running native
Codex row with exact company, task, agent, runner, session, and
completion-contract ownership.
- Existing direct adapters do not call this service. They keep their
current execution, transcript, result, and finalization paths.
- The server has no production dependency on the private runner package.
Its build copies the compiled runtime into `server/dist`; the workspace
link is development-only. This adds no external package and does not
change the lockfile.
> 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
- OpenAI Codex with GPT-5. The exact deployment ID and context-window
size are not exposed. The model used agentic reasoning, repository
tools, code execution, and 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
- [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
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Paperclip records first-party events, OpenTelemetry data, and local
run-log events
> - The code and documents used one term for these three data paths
> - This naming made the required review level unclear
> - This pull request names each data path in the module names,
documents, and code comments
> - The benefit is a clear review rule without a runtime change
## Linked Issues or Issue Description
**Issue type**
Unclear or confusing.
**Where is the issue?**
`packages/shared/src/telemetry/README.md`, `doc/observability.md`,
`doc/run-log-events.md`, and the duplex instrumentation modules.
**What's wrong?**
The repository used Telemetry for first-party events, OpenTelemetry
data, and local run-log events. This usage made the data path and review
level unclear.
**Suggested fix**
Use Telemetry only for Paperclip first-party events. Use Observability
for OpenTelemetry data. Use the run log for rows in
`heartbeat_run_events`.
Related public pull requests: #8476 and #9672.
## What Changed
- Rename the duplex instrumentation modules and identifiers from
`Telemetry` to `Observability`.
- Move the Observability and run-log contracts out of the Telemetry
README.
- Add `doc/observability.md` and `doc/run-log-events.md` as the
canonical documents.
- Add a file-path review rule to `AGENTS.md`.
- Correct the remaining code comments that name the wrong data path.
- Keep all event names, payloads, database records, spans, configuration
keys, environment variables, and runtime paths unchanged.
## Verification
- `npx vitest run packages/shared/src/telemetry/readme-contract.test.ts`
passes.
- `npx vitest run packages/adapter-utils/src/published-exports.test.ts`
passes.
- `npx vitest run
packages/adapter-utils/src/acpx-engine/startup-timing.test.ts` passes
with 42 tests.
- `pnpm --filter @paperclipai/adapter-utils typecheck` passes.
- `pnpm --filter server typecheck` passes.
- The old module name does not remain in TypeScript or JSON files,
except for the intentional publication guard.
- CI and Greptile checks remain pending after PR creation.
## Risks
- The old duplex module subpath no longer has a compatibility shim. The
board accepted this intentional hard break.
- The new duplex module subpath stays blocked from package publication.
- The change has no runtime effect. The main risk is an incorrect
document or module reference.
## Model Used
OpenAI GPT-5 Codex, exact model ID `gpt-5`, with tool use and code
review support.
## 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 described the issue in-PR with the documentation issue
fields
- [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
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
Dotta
Nicky Leach