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DottaandClaude Opus 5.5 2539004201 fix(ephemeral): start a restarted volume-free server over the Runner controller files it wrote itself (#20952)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Cloud servers run volume-free (`PAPERCLIP_EPHEMERAL_SERVER=true`).
Postgres and object storage hold the durable state. A startup gate
refuses legacy volume data that was not migrated.
> - The gate reads one family of data from disk: Runner controller files
under `runtime/paperclip-runner/durable-sessions/`. It treats a
controller file that the database does not prove as legacy data.
> - A volume-free server also writes these files during normal work. A
warm follow-up restores the previous run's checkpoint as a full
`durable.control-plane-state.v2` file. The file stays full until the new
controller registers its database checkpoint writer.
> - When the server crashes in that window and restarts on the same
filesystem, the gate finds its own file and refuses to start. Every
later start refuses the same way. This is a full outage that no Retry
can fix.
> - This pull request gives the gate a durable marker. A volume-free
server claims an empty state directory before any controller can write.
Files in a claimed directory belong to a volume-free server and do not
block startup.
> - The benefit is that a crash restart of a volume-free server starts
again. Genuine legacy data keeps its protection, and the refusal now
names the run, task and file.

## Linked Issues or Issue Description

**What happened?**
The first restart-chaos waves in volume-free server mode (harness flag
`--ephemeral-server`, #20930) found this outage. Wave
`w-20261111T212429-s6402` (Claude through ACPX, Daytona warm sandboxes)
did a fresh-home deploy and then a `kill -9` of that server. The
replacement server exited with `Volume-free server data is not eligible:
native_controllers_require_migration`. A second start at +608 s exited
the same way. The server stayed down.

**Root cause**
`hasLocalNativeControllerObligations` in
`server/src/services/native-runtime/native-controller-migration.ts`
scans every Runner session in the state directory. The kept instance
shows the cause. The session's newest run `4a4d7ca1` was `running`
(admitted 3 s before the kill). Its controller root held the full
`paperclip.runner.durable.control-plane-state.v2` file of its warm
predecessor `9c13b7f8`. A controller writes that full file when it opens
and replaces it with the `external-control-plane-state.v1` marker only
in `setCheckpointPersistence`. `preservedActiveCheckpoint` accepts only
the marker, so the gate returned `true`. A Codex wave with the same
fault sequence passed because no warm follow-up was in this window at
the kill. Claude W2 cells start a new warm follow-up every 15 to 35 s,
so the window is open much more often.

**Can staging hit it?**
Yes, with a restart that keeps the container. Railway documents that a
manual Restart "restarts the process within the deployment's container",
so the filesystem stays. Railway does not document whether an automatic
crash restart reuses the container. A redeploy makes a new container, so
it does not hit this.

**Expected behavior**
A volume-free server starts again after any restart. State that it wrote
itself is disposable, because the database checkpoint is the durable
record. Data that a volume-backed server wrote keeps its current
protection.

## What Changed

- Add
`server/src/services/native-runtime/volume-free-controller-state.ts`.
`claimVolumeFreeControllerState(true)` writes `.volume-free-owner.json`
atomically (temporary file, fsync, rename, directory fsync) when the
state directory is absent or empty. It returns `owned` for a directory
that has the marker and `unclaimed` for a directory with other files.
`claimVolumeFreeControllerState(false)` removes the marker.
- `server/src/index.ts` calls the claim right after the volume-free
configuration check. This is before any controller or recovery can
write. A server started without volume-free mode releases the claim,
because it may write files that exist only on its disk. An `unclaimed`
result logs a warning.
- `hasLocalNativeControllerObligations` ignores the marker entries. It
returns no obligation for a claimed directory. It now delegates to
`findLocalNativeControllerObligation`, which returns the run, task and
file (or `database_checkpoint`).
- `assertEphemeralServerData` adds that detail to the
`native_controllers_require_migration` refusal. The error says which run
and file the database does not prove and why startup refuses.
- Document the marker in `doc/DEVELOPING.md` ("Runner controller state
on a restarted volume-free server").

## Verification

- Red, before the gate reads the marker: `pnpm --filter
@paperclipai/server exec vitest run
src/services/native-runtime/native-controller-migration.integration.test.ts
-t volume_free_owner` failed with `AssertionError: expected true to be
false` at the first gate check. The fixture is a running warm run whose
root holds a full `durable.control-plane-state.v2` file, the same shape
as the incident.
- Green: the same test passes. It checks: claimed directory gives no
obligation; release gives the obligation back; a non-empty unclaimed
directory stays blocked; the refusal names the run; the controller file
is never changed or removed.
- `ephemeral-server-data.test.ts`, `ephemeral-server-contract.test.ts`
and all 57 cells of `native-controller-migration.integration.test.ts`
pass. Server `tsc --noEmit` passes.
- Probe on a copy of the kept instance database and the killed server's
state directory: the unmodified gate returned an obligation for run
`4a4d7ca1` (source file
`.../7dbf2d5c.../control-plane/control-plane-state.json`).
- Chaos: the s6402 shape (`--ephemeral-server --adapters claude
--workloads W2 --faults K1,K2,K15 --k15-fresh-home --seed 6402`) runs on
this branch merged with #20930. The result is added in a comment.

## Risks

- A filesystem that a volume-free server claimed and that a pre-marker,
volume-backed server then wrote is not detected. This needs a downgrade
and a mode change on one disk. A current server in volume mode removes
the marker, which closes the normal path.
- A volume-free server on a directory written before this change (no
marker) keeps today's refusal. A new deploy makes a new container, so
staging claims the empty directory on first start after this deploy.
- Other scanners of the state directory filter on the 64-hex session
pattern, so the marker file does not change them.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, through Claude Code
with tool use (shell, file edit, test runs). Default context window,
extended reasoning on.

## 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>
2026-11-11 17:59:57 -06:00
DottaandClaude Opus 5.5 34f71f7d57 fix(server): defer a run that meets a busy agent directory instead of failing it (#20829)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Each run of an agent with managed agent files gets a private copy of
the agent directory. Remote copies serialize their prepare, checkpoint,
collect, and release operations through one Postgres advisory lock per
agent, taken with `pg_try_advisory_xact_lock`
> - When the lock is busy, the operation fails at once with "Agent
directory operation is already active"
> - On staging, a deploy restarted the controller while three runs of
the same agent were active. When one run resumed, another run of that
agent was checkpointing its directory. The resume failed, used its last
attempt, and the task became blocked with "Retry or send a message"
> - A run must not fail because another run of the same agent is briefly
using the agent directory
> - This pull request keeps the fail-fast lock and, when it is busy
during preparation, puts the same native run back on the existing
same-run retry schedule a few seconds later
> - The benefit is that lock contention delays a run by seconds instead
of ending it as failed

## Linked Issues or Issue Description

**What happened?**
A task's run failed with `native_continuation_requires_reconciliation`
and the error "Agent directory operation is already active". The task
was blocked and asked the user to retry. The same error ended at least
two other runs of the same agent within one day.

**Steps to reproduce**
1. Use an agent with managed agent files in a remote sandbox.
2. Let one run of the agent checkpoint or collect its agent directory.
3. At the same time, let another run of the same agent prepare (for
example, a same-run resume after a controller restart).
4. The second run fails immediately with "Agent directory operation is
already active".

**Expected behavior**
The second run waits until the first operation is done, then continues.
It does not end as failed.

## What Changed

- `server/src/services/agent-directory-working-copies.ts`: The busy lock
now throws `AgentDirectoryOperationBusyError`, still a 409 with the same
message. Lock behavior is unchanged from `master`: a fail-fast
`pg_try_advisory_xact_lock` held for the life of the holder's
transaction.
- `server/src/services/heartbeat/agent-directory-busy.ts`:
`prepareWithAgentDirectoryDeferral` wraps only instruction preparation
and turns the busy error into `AgentDirectoryPreparationDeferral`
("Another run of this agent is still using its files"). A busy lock met
while collecting files after a turn is not wrapped and keeps its
existing path.
- **Before native admission** (a brand-new run, such as the first run of
a task): `server/src/services/heartbeat/retries.ts`
`finalizeAgentDirectoryBusyDeferral` cancels the run as an expected
control-plane wait (`providerWorkStarted: false`) and schedules an
`agent_directory_busy` retry 5–15 seconds later. The task keeps its
execution lock on the retry. The lane spends no failure retries
(`execution-recovery-attempt.ts`), its count is the retry run's
`scheduledRetryAttempt`, and it stops after 30 attempts.
`pre-dispatch-execution-evidence.ts` classifies this wait like the
existing workspace and AI-connection waits, so retry scheduling does not
ask for reconciliation.
- **A resumed native run**:
`server/src/services/native-runtime/native-controller-recovery.ts`
`deferNativeRunForBusyAgentDirectory` keeps the same run on the existing
same-run retry schedule without spending an attempt. It uses the same
guards as `deferNativeControllerRecovery`: it locks the task, requires
the task's execution run to be this run, requires the current lease
owner, and refuses after a Stop, a startup cancellation or a pending
native cancellation, so those settle normally. Its count is stored in
the run's `contextSnapshot`, which a resume claim does not clear, and it
stops after 30.
- `server/src/services/heartbeat.ts`: routes a preparation deferral to
the same-run path or, before admission, to the scheduled-retry path.
After the bound it follows the normal failure path with the plain
message.
- No schema or migration. Postgres releases a dead holder's advisory
lock with its session. The staging evidence showed a live holder
(another run's checkpoint), not a stale one.
- `doc/DEVELOPING.md`: Documented both paths and the bound.

Earlier revisions of this PR waited on the lock and added idle-session
expiry, keepalive, ownership fences, fenced remote removal and attempt
slots. This revision removes all of them.

### How the directory-wait retry keeps the original wake

The retry no longer replaces the wake. `scheduleBoundedRetryForRun`
takes `preserveWakeContext` for this wait: the retry keeps the original
`wakeReason`, `retryReason` and the whole wake context (interaction,
comment, continuation and admission fields), and its wake request keeps
the original reason. The wait is recorded separately as
`preparationWait: { kind: "agent_directory_busy", attempt, nextAttemptAt
}`, next to the carried `executionRetryAccounting`. Gates that key on
the wake reason therefore treat the retry exactly as they treated the
original wake.

| # | Site | Treatment for the directory wait | Why |
| --- | --- | --- | --- |
| 1 | `heartbeat/retries.ts` `scheduleBoundedRetryForRun` | Changed:
`preserveWakeContext` keeps the original wake context and reason and
adds `preparationWait` | Root cause: the retry overwrote the wake reason
|
| 2 | `run-dispatch/domain/wake-context.ts`
`isResolvedInteractionContinuationWakeContext` /
`PREPARATION_WAIT_RETRY_REASONS` | Special case removed | The original
wake context is kept, so the continuation is classified from it |
| 3 | `heartbeat/retries.ts` `interactionRunnerWait` | Special case
removed | The interaction fields are kept in the context |
| 4 | `run-dispatch/adapters/postgres.ts` scheduled-retry dependency
facts | Changed: a preparation-wait retry whose original wake was
admitted as a dependency-blocked interaction
(`dependencyBlockedInteraction`, recorded at wake time) is admitted the
same way | Without the wait the original wake would have run; this gate
is only met because of the wait |
| 5 | `run-dispatch/domain/wake-context.ts`
`isNonAssigneeWorkspaceBusyRetry` + `heartbeat/retries.ts`
`finalizeAgentDirectoryBusyDeferral` | Kept:
`preparationWaitDeferredWhileAssignee`, derived only from the recorded
admission authority | The scheduled-retry ownership gate has no
wake-reason path; the workspace and AI waits use the same recorded flag
|
| 6 | `heartbeat/retries.ts` explicit user continuation admission |
Kept: admits the `agent_directory_busy` scheduling reason | The
successor needs its own authorization receipt |
| 7 | `execution-recovery-attempt.ts` uncharged lane and
`agentDirectoryWaits` | Kept | Cap and accounting |
| 8 | `pre-dispatch-execution-evidence.ts` (`isPreDispatchResourceWait`,
`isAgentDirectoryPreparationWait`), used by
`legacy-execution-recovery.ts`, `cancelled-native-startup.ts`,
`explicit-native-continuation.ts` | Kept | Describe the cancelled
pre-provider parent run, not the retry's wake |
| 9 | `explicit-native-continuation.ts`
`undeliveredLegacyUserCommentIds`, `run-dispatch/adapters/postgres.ts`
`unstartedUserTurnOrigin` | Kept | The cancelled parent did not consume
the user's comment |
| 10 | `execution-projection.ts` label and saved accounting,
`task-interruption-presentation.ts`, UI toast and chat suppression |
Kept | Presentation of the wait |
| 11 | `run-dispatch/domain/policy.ts` AI-wait lock requirement;
AI-subscription lock recheck; AI wait detection
(`execution-configuration.ts`, `provider-limit-wait.ts`, `heartbeat.ts`,
`ai-connections.ts`, `ai-connection-runtime.ts`, `local-ai-login.ts`) |
Not applicable | AI-subscription specific |
| 12 | `workspace-busy-wait.ts`, `environment-selection.ts`,
`workspace-preparation.ts`, UI workspace-holder banners | Not applicable
| Workspace holder parking; the directory wait is a timed retry |
| 13 | `cancelled-native-startup.ts` paused workspace-retry repair;
`failureRetriesBefore*Wait` | Not applicable | Historical workspace and
AI records only; every directory wait saves its ledger |
| 14 | `failedRunRetryBudgetSpent`; storage-wait exhaustion escalation;
`status-relevance.ts` `isAdmissionWait` | Not applicable | A directory
wait never fails the run, stops at its own bound, and its run has
started |

## Verification

- Original wake kinds after a directory wait
(`heartbeat-agent-directory-busy.test.ts`, real heartbeat): an
assignment runs; a plain user comment on a dependency-blocked task is
answered with `dependencyBlockedInteraction`; an accepted interaction
continuation keeps its parked-task and reassignment gates; a user
message continuation runs with its comment; an accepted non-assignee
mention runs; and a reassignment during preparation does not let the
previous assignee restart. Each retry keeps the original `wakeReason`
and records `preparationWait`. With `preserveWakeContext` off, five of
these fail. Restart recovery keeps its attempt credit
(`native-runner-restart-recovery.integration.test.ts`).

- Non-assignee wake: an accepted mention for an agent other than the
assignee meets a busy directory; its retry records
`preparationWaitDeferredWhileAssignee: false`, survives promotion, runs
and succeeds once the directory is free. Without the shared clause in
`isNonAssigneeWorkspaceBusyRetry`, promotion cancels it.

- Interaction continuations: `heartbeat-agent-directory-busy.test.ts`
runs an accepted interaction continuation into a busy directory. The
retry keeps `mutation`, `interactionId`, `interactionKind` and
`interactionStatus` and is still classified as a continuation. If the
task is moved to todo, or reassigned, while the retry waits, the retry
does not run and the task stays parked or with its new owner. With the
old explicit storage/Runner lists, both cases fail.

- Red/green, new run:
`server/src/__tests__/heartbeat-agent-directory-busy.test.ts` runs a
real heartbeat for a new assignment whose first instruction preparation
meets a busy lock. Without the preparation wrapper, the run ends failed
(red). With it, the first run is cancelled as a wait, an
`agent_directory_busy` retry is scheduled with the task still locked to
it, the retry runs and succeeds, and no run of the task is failed
(green).
- Red/green, same-run: with the deferral as a no-op, the same-run
deferral tests failed (`expected false to be true`); they now pass.
- `native-controller-recovery.integration.test.ts` covers repeated
claim-and-defer cycles of a resumed run: each cycle keeps the attempt
count, cannot be claimed before the delay, stores the count on the run,
and the fourth deferral past a bound of 3 is refused. It also covers
Stop after the busy error, a foreign lease owner and a moved task (each
refused, nothing changed), a run before admission, and that a raw busy
error (as from collection) is never deferred.
- Focused suites: 232/232 passed (`agent-directory-working-copies`,
`instruction-working-copy`, `heartbeat-agent-directory-busy`,
`native-controller-recovery.integration`, `heartbeat-retry-scheduling`).
`tsc --noEmit` for `server` reports no errors in the changed files.
- Staging evidence (read-only): the failed run had a graceful restart at
07:25Z, then same-run resumes. Its third attempt failed at 07:31:08Z.
Another run of the same agent recorded a warm checkpoint receipt at
07:31:37Z. A second run of the same agent failed the same way at
07:59:46Z.

## Risks

- A deferred run waits 5 to 15 seconds per deferral, up to 30 times. If
the holder is still busy after that, the run fails as before with a
plain message.
- Before admission, deferral cancels the run and creates a retry run,
like the existing workspace-busy wait.

## Model Used

- Claude Opus 5.5 (claude-opus-5-5), Anthropic, with tool use and code
execution in Claude Code.

## 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>
2026-11-11 13:56:45 -06:00
DottaandClaude Fable 5.2 1d52436bf8 fix(config): detect the tailnet bind host only when the bind reads it, one time per process (#20843)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The server reads its configuration through `loadConfig()` in
`server/src/config.ts`. Runtime code calls it often:
`getStorageService()` calls it on each use, and the native runtime calls
it for backup storage, response delivery and attachment reuse
> - `loadConfig()` called `detectTailnetBindHost()` on each call. That
function runs `tailscale ip -4` with `execFileSync`, which is a
synchronous child process. The event loop stops until the child process
ends
> - A CPU profile of a busy hosted server showed this cost on the main
thread, on a server that does not bind to a tailnet
> - The tailnet address is an input only to the bind host, and only the
listener that the server binds at startup uses the bind host. Most bind
configurations never read the address
> - This pull request makes `loadConfig()` detect the address only when
the bind configuration reads it, and keeps the result for the life of
the process
> - The benefit is that a `loadConfig()` call no longer starts a child
process on runtime paths, so the event loop stays free for requests

## Linked Issues or Issue Description

No public issue exists. I searched open and closed pull requests for
`tailscale loadConfig` and `detectTailnetBindHost` and found no related
work.

**What happened?**
Each `loadConfig()` call started `tailscale ip -4` as a synchronous
child process. A 30 second CPU profile of the main thread of a hosted
server (commit 556b249897, Node 24, main thread at 96% of one core)
showed `detectTailnetBindHost` ← `loadConfig` at 3.1% inclusive and the
native child-process spawn at 3.6% self. The callers in the profile were
`getStorageService`, `durableNativeHarnessStorage`,
`restoreDurableHarnessForExecution` and
`createRunnerdBackendWithinSessionClaim`. The server process was about
4.4 GB resident, which makes each spawn more expensive. The cost is the
same when the `tailscale` command is not installed, because the spawn
still runs.

**Expected behavior**
`loadConfig()` starts `tailscale` only when the bind configuration reads
a tailnet address: `server.bind=tailnet`, or a host without a bind mode
that is not loopback and not all interfaces. It starts it at most one
time per process. A change to `PAPERCLIP_TAILNET_BIND_HOST`, to another
environment variable or to the config file is still visible to the next
`loadConfig()` call.

**Steps to reproduce**
1. Run `pnpm --filter @paperclipai/server exec tsx
scripts/benchmark-config-load.ts --calls=200` on the parent commit. The
benchmark puts a counting `tailscale` stand-in first on `PATH`, so it
does not need Tailscale.
2. Read the `tailscale execs` column. Each scenario shows 200 execs for
200 calls.

**Paperclip version or commit**
`master` at e2cf9a670f. The profile is from 556b249897.

**Deployment mode**
All modes. The profile is from an `authenticated` hosted server. The
benchmark covers `bind=lan`, the default loopback bind and
`bind=tailnet`.

**Node.js version**
Profile: Node 24. Local benchmark: Node 26.4.0 on darwin arm64.

## What Changed

- `server/src/config.ts`: `loadConfig()` calls `detectTailnetBindHost()`
only when the bind configuration reads the address. With a configured
bind mode, that is `tailnet` only. Without one, it is a host that
`inferBindModeFromHost` cannot resolve to loopback or all interfaces
without the address.
- `server/src/config.ts`: the result of `tailscale ip -4` is kept for
the life of the process, also when the command fails.
`PAPERCLIP_TAILNET_BIND_HOST` is not kept: each call reads it first, as
before.
- `server/src/__tests__/config-tailnet-bind-detection.test.ts` (new):
regression tests that count `tailscale` starts.
- `server/scripts/benchmark-config-load.ts` (new): the reproduction and
benchmark.
- `doc/DEVELOPING.md`: removed the advice to set
`PAPERCLIP_TAILNET_BIND_HOST` for local fixtures to prevent repeated
discovery. The server no longer repeats discovery.
- `cli/src/config/server-bind.ts` has its own copy of the detection. It
is not changed: it detects only for `bind=tailnet` and runs in short CLI
commands, not on a server runtime path.

## Verification

Regression test, red then green:

- `cd server && pnpm exec vitest run
src/__tests__/config-tailnet-bind-detection.test.ts`
- Parent commit: 11 of 11 tests fail. Examples: `expected 1 to be +0`
for `bind=lan` (the command ran when it must not), `expected 3 to be 1`
for `bind=tailnet` (the command ran on each call).
- This branch: 11 of 11 tests pass.
- The tests assert the number of `tailscale` starts and the resolved
bind host. They do not assert time. They cover `bind=loopback`, `lan`,
`custom`, loopback and all-interfaces hosts without a bind mode,
repeated `getStorageService()`, `bind=tailnet`, bind inference from a
host, `PAPERCLIP_TAILNET_BIND_HOST` (used without the command, each
change visible), a bind mode change in the environment and in the config
file, and the unchanged refusal when no tailnet address exists.

Benchmark, same machine, 200 calls per scenario, 3 runs each (ranges
shown):

| Scenario | Before: `tailscale` execs | Before: ms per call | After:
`tailscale` execs | After: ms per call |
| --- | --- | --- | --- | --- |
| `loadConfig()`, `bind=lan` | 200 | 4.5 to 6.0 | 0 | 0.063 to 0.069 |
| `getStorageService()`, `bind=lan` | 200 | 4.0 to 4.5 | 0 | 0.043 to
0.060 |
| `loadConfig()`, default loopback | 200 | 4.0 to 4.5 | 0 | 0.046 to
0.053 |
| `loadConfig()`, `bind=tailnet` | 200 | 3.8 to 5.1 | 1 | 0.74 to 0.92 |

- Command: `pnpm --filter @paperclipai/server exec tsx
scripts/benchmark-config-load.ts --calls=200`
- Each call is synchronous, so the time per call is time that the event
loop is blocked. For 200 calls the block went from about 750 to 1200 ms
to about 9 to 14 ms where the bind does not read a tailnet address.
- The `bind=tailnet` row after the fix contains the one detection (about
150 ms for the first start of the new stand-in file on macOS). The other
199 calls start no process.
- `loadConfig()` also reads and validates the config file on each call.
After the fix a full call costs about 0.05 ms locally, so the file read
is not a material cost and this pull request does not change it. A
hosted server reads a stored snapshot from memory, not a file.

Other checks:

- `cd server && pnpm exec vitest run
src/__tests__/managed-runtime-public-url.test.ts
src/__tests__/native-harness-backup-expiration-config.test.ts
src/__tests__/chat-webhook-public-url.test.ts
src/__tests__/managed-cloud-prerequisites.test.ts
src/__tests__/managed-loopback-auth.test.ts
src/__tests__/cloud-runtime-config.test.ts`: 84 tests pass.
- `tsc --noEmit` over the three changed TypeScript files: clean.
- `pnpm verify` exits 2 (broader verification required, because of the
new file in `server/scripts`). Required CI supplies that coverage.
- Not verified: the benchmark on Linux with a multi-gigabyte process,
and the hosted server after deploy. The local numbers come from a 200 MB
process, where a spawn is cheaper than on the profiled server.

## Risks

- Low risk. The resolved `bind`, `host` and `customBindHost` are the
same as before for each configuration. A configured bind mode other than
`tailnet` never used the detected address, and a loopback or
all-interfaces host resolved before the address was read.
- Behavior shift: a server process detects the Tailscale address one
time. If Tailscale starts, stops or changes its address later,
`loadConfig()` in that process still returns the first result until
restart. The server binds its listener one time at startup, so the
listener already had this property. From the code (not reproduced):
before this change, a `bind=tailnet` server whose Tailscale stopped
after startup threw from each later `loadConfig()` call on runtime
paths. It now continues with the address from startup.
- A failed detection is also kept. With `bind=tailnet` the server
refuses to start, as before, and the next start detects again.
`PAPERCLIP_TAILNET_BIND_HOST` overrides a kept result at once.

## Model Used

- Claude Fable 5.2 (Anthropic, model ID `claude-fable-5-2`), in Claude
Code with tool use (shell, file edits, GitHub CLI).

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Fable 5.2 <noreply@anthropic.com>
2026-11-11 09:59:09 -06:00
DottaandPaperclip 5f38226290 fix(build): report compiler signals in server typecheck layers (#20603)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Its development checks help contributors verify changes.
> - The server typecheck runs the compiler once for each source layer.
> - A compiler child can stop on a signal before it reports type errors.
> - The wrapper returned failure without the signal or the affected
layer.
> - This pull request reports the signal, layer, command, and working
directory.
> - Contributors can identify an interrupted check from its output.

## Linked Issues or Issue Description

**What happened?**

The server typecheck returned exit 1 after a layer banner when a
compiler child stopped on a signal. The wrapper did not report that
signal. Related layer work: #18737, #18738, and #18739. A search of open
and closed PRs found no duplicate signal-reporting fix.

**Expected behavior**

Report the actual termination signal and affected layer. Keep compiler
output visible and return failure. Do not infer a memory failure from
SIGKILL alone.

**Steps to reproduce**

Run a controlled compiler child that sends SIGTERM or SIGKILL to itself.
Run it through typecheckLayers and the real runTsc subprocess path. The
added tests do this without memory pressure or timed waits.

**Paperclip version or commit**

Reproduced on 7368a0b15c.

**Deployment mode**

Source checkout on Linux with Node v25.9.0.

## What Changed

- Print a stderr diagnostic before the existing early return for a
compiler signal.
- Include the layer, signal, compiler command, and working directory.
- Add real subprocess regressions for SIGTERM in below and SIGKILL in
cycle.
- Check that child stdout and stderr remain visible and later layers
stop.
- Document the diagnostic and the limit of what a signal proves.

## Verification

- Red: the two new subprocess tests failed because stderr omitted the
signal and layer.
- Green: `cd server && pnpm exec vitest run
scripts/typecheck-layers.test.mjs` passed all 47 tests. This includes
real compiler success, declaration output, and compiler error
diagnostics.
- `git diff --check` passed.
- `pnpm verify` returned exit 2. The wrapper is a broad input, so CI
must supply broader coverage.
- Preflight installed dependencies and built shared/plugin-sdk. It could
not build Rust outputs because cargo is absent. Rust builds are outside
the focused local test scope.
- Final head: `fdd68d7e13751573c661e80a285be86f1a1420bc`.
- [CI
passed](https://github.com/paperclipai/paperclip/actions/runs/42867062133).
Typecheck, build, test suites, and all eight E2E shards passed.
- [Greptile gave
5/5](https://github.com/paperclipai/paperclip/pull/20603#issuecomment-6774642345)
for this head. No actionable findings or open review threads remain.

## Risks

- Low risk. Only the existing signal branch gains a diagnostic. Failure
propagation and compiler output handling stay the same.
- The controlled signal tests require POSIX signal behavior. Local
verification used Linux.

## Model Used

- OpenAI Codex, based on GPT-6, with reasoning, repository tools, and
code execution. The exact deployment model ID is not exposed in this
session.

## 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>
2026-11-11 08:39:15 -06:00
DottaandPaperclip 556b249897 fix: preserve exact Markdown in native document writes (#20605)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agents save Markdown documents through native tools and REST routes.
> - The native write_document handler trims the supplied body.
> - This removes final newlines and can change Markdown whitespace.
> - This pull request preserves the original body after required-content
validation.
> - Agents can now write and read the same Markdown string across these
paths.

## Linked Issues or Issue Description

**What happened?**

The native write_document tool removes leading and trailing whitespace.
A body with one final newline loses that newline on read-back. The REST
document PUT and write_task_document preserve it.

**Expected behavior**

The native write_document tool must preserve the supplied Markdown body
exactly. Required-content checks and key and title normalization must
stay in place. REST-backed paths retain surrounding whitespace and keep
their existing escaped-line-break conversion for single-line payloads.

**Steps to reproduce**

1. Write a disposable document through write_document with a final
newline.
2. Read the document and compare the full body with the supplied string.
3. Repeat through write_task_document and REST. These paths preserve the
string.

Related work: Refs #18824. That change aligns document keys. This change
preserves body strings. A search of open and closed PRs found no
duplicate fix.

## What Changed

- Use a separate untrimmed required-string helper for the document body.
Keep the existing requiredString callback signature and all other field
normalization.
- Add real tool-handler, database, and authenticated HTTP tests for
create, update, read-back, and replay. Cover leading spaces, hard
breaks, blank lines, final newlines, no final newline, Unicode, and
mixed line endings.
- Keep blank and invalid bodies rejected. Document whitespace
preservation and the existing REST escaped-line-break exception.
- Fix the Runner support archive-scanner shutdown defect exposed by CI:
rejected ZIP scanners now receive SIGKILL so an ignored SIGTERM cannot
leave publication waiting for process closure. Keep all secret and
archive limits unchanged. A real child-process regression fails before
the change and passes afterward.
- Address all three initial review findings: callback type
compatibility, contribution comment policy, and the REST documentation
limit.

## Verification

Final tested head: `c9ff8cf3f83aa19e5d8313c65816a3a2e6562368`.

- All applicable [CI
checks](https://github.com/paperclipai/paperclip/actions/runs/43019885807)
passed. This includes typecheck, build, Runner support, Rust, native
Runner, general tests, serialized suites, all eight E2E shards, and the
required aggregate gates.
- [Greptile
review](https://github.com/paperclipai/paperclip/runs/130520170309)
passed on this head with confidence 5/5. All three review threads are
resolved. The independent Paperclip review also reports 5/5 with no
findings.
- Red at `7368a0b15c2f02107778a961144d86e2eb59a952`: `pnpm --dir server
exec vitest run
src/services/native-runtime/task-document-body.integration.test.ts`
failed because write_document removed the final newline. Cross-task and
REST cases passed.
- Green on the final source: 176 tests passed across the document body,
document key, native tool authority, task scope, document service, and
document route suites. The tests cover create, update, exact read-back,
replay, blank rejection, revision guards, and company scope.
- The ZIP shutdown regression failed before repair with “scanner did not
stop”. After repair, 54 tests passed across zip-inspection-shutdown,
private-reporter-artifacts, manual-private-cell-report-assets, and
private-evidence-budget. The regression uses a real process that ignores
SIGTERM.
- Earlier CI runs had two archive-related timeouts. The source repair
above replaces blind reruns. The Runner support suite and aggregate
verify gate now pass.
- A disposable live native document reproduced the original whitespace
loss. REST preserved the same string. The fixed handler passed local
integration tests. The running service has not been deployed.
- Local environment: Linux x64, Node 25.9.0, Vitest 5.0.3, and embedded
PostgreSQL. Local Rust preparation was unavailable because cargo is
absent. Final-head CI passed Rust verification. `pnpm verify --explain`
requested broad CI because evidence.ts is a global input. Required CI
supplied that coverage.

## Risks

Low risk. The change retains required-content validation. The product
change affects document body whitespace handling. The CI repair
forcefully stops only already-rejected archive scanners; it retains
fail-closed publication and all existing scan limits. It does not change
schema, authorization, revision guards, receipts, or persistence.

## Model Used

CI repair continuation: GPT-6.1, using repository tools and code
execution.


OpenAI Codex, GPT-6 (the exact serving model ID and context window were
not exposed in this session). Used reasoning, repository tools, and code
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

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-11 06:38:32 -06:00
DottaandPaperclip 7f72ea7534 fix(links): retain PR status across page reloads (#20654)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Task messages contain GitHub pull request links.
> - A hover loads PR status into a shared memory cache.
> - A page reload clears that memory and returns each link to an unknown
state.
> - The browser already saves selected reads for each user and company.
> - This pull request adds learned link previews to that cache.
> - Reloads show the saved status. Only user interest can refresh stale
previews.

## Linked Issues or Issue Description

**What happened?**

After a user loaded PR status, a page reload removed the learned state.
The browser persistence rules excluded link-preview queries. Related
implementation: #20593. Searches of open and closed PRs found no
duplicate reload-cache fix.

**Expected behavior**

Keep learned PR status across reloads for the same account and company.
Do not load every PR on page render. Reuse fresh results and refresh
stale results on hover or keyboard focus.

**Steps to reproduce**

1. Open a task with repeated GitHub PR links.
2. Hover one link and wait for its status.
3. Reload the page.
4. Before this fix, both links return to unknown until another hover.

**Paperclip version or commit**

Reproduced against master source at
`30403781b9418355c78dc0ed978366af77036e76`.

## What Changed

- Add link-preview queries to the existing user and company persistence
rules.
- Keep at most 100 previews across accessible companies. Use the
existing 24-hour retention, build boundary, and sign-out cleanup.
- Keep the original read time and freshness when restoring previews.
Other query types keep their existing restore behavior.
- Add regressions for saved status, negative results, bounds, age,
account changes, membership loss, and sign-out.
- Add a production-component Storybook example and browser reload
checks. Update the cache documentation.
- Use one query-key definition for the component, persistence rules, and
cache tests.

The browser read-cache module owns persistence and account cleanup. This
change extends that owner. The link service and provider API contracts
stay the same.

## Verification

- Red: the new reload and retention tests failed because a fresh client
had no saved PR data.
- Green: 102 focused UI tests passed across the cache, sign-out,
account-query, and query-client suites.
- UI typecheck passed.
- Storybook catalog generation and the static Storybook build passed.
- All 21 browser checks passed with retries disabled. They prove status
and negative-cache restoration after real reloads, no eager requests, no
fresh-hover refetch, and one stale-interest refresh shared by duplicate
links. Existing light/dark and narrow PR states, keyboard access, exact
URLs, and card positioning also pass.
- The first browser attempt could not launch because this session lacked
Chromium. Chromium was installed before the complete passing run; that
first attempt supplies no test verdict.
- `pnpm verify --explain` returned exit 2. The browser test path
requires broad CI coverage. No full local suite is claimed.
- The supplied staging page was not accessible through the web tool. No
deployed acceptance is claimed.
- CI on the first head failed in a Slack long-publication timeout and a
font-loading-frame browser check. Both files are outside this change.
The two publication cases passed when run locally in isolation. The font
case also passed locally against the built UI. [Final-head
CI](https://github.com/paperclipai/paperclip/actions/runs/42909433167)
passes on `e19d5b8bb1a910b1cbb9bb9a62ab87cdf684737f`. Typecheck, build,
tests, E2E, and Rust checks pass. There are 58 successful check runs,
three expected skips, and one neutral Paperclip Review check. The legacy
Snyk status passes.

Both Greptile and the supplemental Paperclip review report 5/5 on the
final head. No actionable findings or unresolved review threads remain.
The Paperclip Review check itself has a neutral conclusion.

## Risks

- PR display data now remains in browser local storage until expiry,
build change, or sign-out. Each query requires the matching user and an
accessible company.
- A stale saved status can remain visible for up to 24 hours. Hover or
keyboard focus refreshes it after the provider freshness window.
- Storage restrictions retain the existing memory-only fallback. No
schema migration is required.

## Model Used

OpenAI Codex, based on GPT-6, with reasoning, repository tools, code
execution, and browser automation. The runtime does not expose the exact
serving model ID or context-window size. No subagents were used.

## 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>
2026-11-10 17:43:06 -06:00
DottaandPaperclip 89ec4e7614 feat(links): add cached GitHub pull request previews (#20593)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Task conversations contain links to pull requests and other work.
> - A URL alone cannot tell the operator whether a PR is open, merged,
or blocked by conflicts.
> - Fetching every link at render time wastes API calls and can expose
private data through a shared cache.
> - This pull request adds a demand-driven links service and a GitHub PR
adapter.
> - Each viewer and company has a separate cache. Repeated links share
one request and result.
> - Operators get context when they hover or focus a link. Normal links
stay useful when a provider is unavailable.

## Linked Issues or Issue Description

**Subsystem affected**

Task Markdown links, shared link metadata, and the server GitHub API
boundary.

**Problem or motivation**

PR links have compact labels and neutral icons. They do not provide a
rich hover card or a common status source across repeated mentions. A
background resolver cannot borrow a person's GitHub connection because
it has no viewer identity.

**Proposed solution**

Recognize supported links locally. Request metadata after a delayed
hover or keyboard focus. Show a card at the first line of the link,
aligned with its icon. Share the result across all mentions in the
current viewer and company. Keep the exact original navigation URL.

The first adapter supports GitHub pull requests. Open is green, merged
is purple, and merge conflicts are orange. Draft, closed, unknown,
loading and unavailable states remain quiet.

**Alternatives considered**

Eager page scans would spend API quota on links the operator does not
inspect. Company-wide caching of personal GitHub results would cross the
credential boundary. This change uses neither approach.

**Roadmap alignment**

ROADMAP.md was checked. This extends existing task links and the GitHub
resolver. It adds no deployment adapter or new background worker.
Searches of open and closed PRs for link previews and PR hover cards
found no matching implementation.

## What Changed

- Add host-owned link recognition and a normalized preview contract. The
service selects an adapter by provider.
- Add a board-only company read endpoint. It checks company access
before cache reads and sends a private, no-store response.
- Use the current viewer's eligible GitHub connection. A configured
connection that cannot supply credentials fails closed. With no managed
connection, reuse existing company credentials or public access.
Instance credentials retain the public-repository check.
- Reuse the GitHub external-object resolver for API transport and
response parsing. Add title and mergeability to its normalized snapshot
without changing its existing state contract.
- Coalesce requests by company, viewer and canonical PR URL. Bound
cached entries and concurrent work. Cache success for one minute and
failures for a short period or the provider retry window.
- Add an abortable request deadline. Timed-out work stays in the
concurrency budget until it settles. No periodic worker or idle polling
is added.
- Add a shared browser query and anchored preview card. Repeated
Markdown links observe the same result. There are no automatic retries,
window-focus refreshes, toasts or connection prompts.
- Add ten production-component Storybook examples and real
pointer/keyboard browser checks. Document the API and verification
route.

## Verification

- Linux source checkout: 233 focused tests passed in nine suites. They
cover recognition, fixed API destinations, provider states, access
failures, credential selection, viewer/company isolation, request
coalescing, expiry, cache bounds, concurrency bounds and mounted OpenAPI
coverage.
- A live public GitHub smoke returned this PR's correct title and open
state. Two equivalent URLs shared one real network request. Personal
connection access was not part of that smoke.
- A controlled HTTP server stalls a real response body. The test proves
cancellation while another lookup completes.
- UI typecheck and the server layered typecheck passed. The UI
production build passed.
- Token gates and query policy gates passed. All 30 map/catalog support
checks passed. The three new server test files also passed a focused
TypeScript check.
- All 27 focused browser checks passed on the reviewed source tree. They
cover light/dark themes, narrow layouts,
open/merged/conflict/draft/closed/loading/unavailable/failed states,
fixed positioning during pointer movement, exact navigation and keyboard
access. A real browser HTTP interception counts one deferred lookup for
two equivalent PR links.
- The first browser attempt lacked Chromium. A later combined build/test
attempt exhausted the sandbox's 8 GiB memory limit and killed Storybook.
Those attempts supply no pass evidence. Chromium is installed, and the
final browser checks run with the build stopped. One initial Storybook
dependency reload interrupted a streaming check. All eight existing
inline-link cases passed on the warmed server, followed by a complete
27-case pass.
- Synthetic Storybook pointer events did not exercise the native hover
boundary. The assertions now run through real Playwright pointer and
keyboard actions. The fixture stories retain the production components.
- Review fixes preserve the Draft label when GitHub reports both draft
and conflicts. They also preserve neutral link colors in dark mode. The
25 affected service checks pass, including the added combined-state
regression. Browser checks compare unknown, draft and closed links with
the muted theme color.
- The first CI policy run rejected a literal retry opt-out. The code now
uses the existing explicit zero-retry helper. A new test-spy type error
was also corrected. These failures are fixed; their earlier runs remain
failed.
- `pnpm verify --explain` returned exit 2 because the browser test path
selects broad CI. No full local suite is claimed. The final CI run
supplies that coverage.
- The previous head `437913c797963aa113bb82e2ae8b836969317ef9` passed CI
and received a 5/5 Greptile score. All four review threads are resolved.
Master then advanced. The current head
`ae2a1c2adbd61a621cca9bdd160561952613df6e` resolves the source-manifest
conflict against master `9b21dcbdda01296349f3cfe0a3a6891e79df6130`.
Fresh CI and review are running.
- The previous CI run found a lost class on decorated PR links and a
stale SDK source manifest. Both are fixed. The existing CommentThread
integration test and 26 focused link service tests pass. All 45 SDK
source/privacy tests pass. All eight source-manifest helper tests pass.
The manifest helper changed only source identities and added the two new
shared files. Runtime, compiler, parser and library pins stay unchanged.
- A later review found that expired timeouts could reuse a settled
promise. The service now removes settled requests from its
shared-request map and counts unfinished provider work separately. The
new regression failed before the fix and passes after it. The
concurrency-bound and real stalled-HTTP tests also pass.
- UI typecheck and token gates pass after these fixes. The browser rerun
needed Chromium in the new session. That first attempt did not exercise
the UI. The complete 27-case browser rerun passed before the master
merge with retries disabled. All 27 browser cases also passed on the
merge revision with retries disabled.

- After the master merge, all 84 focused link, OpenAPI and integration
tests pass. All 55 SDK source/privacy/manifest tests pass. UI typecheck
and token gates pass again. The source manifest retains master's
reviewed runtime pins and includes both sets of source changes. GitHub
confirms the PR can merge cleanly. The preflight helper rebuilt the
shared package and plugin SDK; Cargo is unavailable locally. Final CI
supplies Rust coverage.

- The latest master update changed the reviewed report-lock policy but
left the SDK lock hash at its previous value. The SDK source/evidence
checks reproduced the mismatch. This change sets only the SDK lock hash
to the authenticated output of the existing master policy and patch.
Compiler, parser and Zod pins stay unchanged. All 56 SDK
source/evidence/manifest tests now pass. All 84 focused
link/API/integration tests, UI typecheck and token gates also pass on
the updated source.

## Risks

- This cache is process-local. Separate server replicas can make
separate GitHub requests.
- A cached result can remain visible for its short lifetime after GitHub
changes. A later hover refreshes expired data.
- GitHub can report unknown mergeability. The UI shows conflicts only
when GitHub explicitly reports them.
- Personal preview data stays in viewer/company caches. It is not
written to company external-object records or persisted browser query
storage.
- Stories simulate the API. They do not prove a live GitHub login or
private-repository access.
- No schema migration is required.

## Model Used

OpenAI Codex, based on GPT-6. The runtime does not expose the exact
serving model ID or context-window limit. Used reasoning, repository
inspection, source editing, shell execution and browser tools. No
subagents were used.

## 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

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-10 19:32:51 +00:00
DottaandClaude Opus 5.5 9b21dcbdda refactor: remove SPEC docs and repoint spec citations (#20565)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Contributors and agents read the docs under `doc/` before they
change code
> - `doc/SPEC.md` and `doc/SPEC-implementation.md` were out of date.
`doc/SPEC-implementation.md` became an append-only log: in 60 days it
got about 1,645 new lines and lost 181, across 140 commits
> - #20557 changed `AGENTS.md` so the code and its tests are the source
of truth, and the specs are only background
> - This pull request removes the two spec docs. It moves only the
sections that live code comments cite into focused docs, and it repoints
all other references
> - The benefit is one less stale document that agents read and append
to

## Linked Issues or Issue Description

Refs #20557 (merged). This PR is the follow-up that removes the docs. It
is based on `master`, which already contains #20557.

**Issue type**
Outdated content. The docs are out of date and conflict with the code.

**Where is the issue?**
`doc/SPEC.md`, `doc/SPEC-implementation.md`, and the code comments and
docs that cite them.

**What's wrong?**
`doc/SPEC.md` and `doc/SPEC-implementation.md` are out of date, but
agents still read them and append a paragraph with each fix.

**Suggested fix**
Delete both files. Move the sections that code cites into focused docs.
Repoint the references.

## What Changed

- Deleted `doc/SPEC.md` and `doc/SPEC-implementation.md`.
- Moved these spec sections, because live code comments cite them:
- §9.3.1 "Shared default-open issue writes" → new section in
`doc/agent-permission-defaults.md`.
- §9.8.1 "Issue-thread interaction resolver contract" →
`doc/execution-semantics.md`, "Issue-thread interaction resolution".
That section already had most of the contract. I added only the missing
parts: the `supersedeOnUserComment` default, the canonical policy list,
the addressee and cap rules, the rule that surfaces show the server's
effective audience, and the cross-issue budget charge. The short policy
summary at the top of the section now points to the list, so the
definitions occur one time only.
- §9.9 "Task Watchdog Authority Contract" → new "Authority contract"
section in `doc/TASK-WATCHDOG.md`. It holds the allowed and disallowed
mutation lists and the deferred capabilities. The atomic recovery batch,
restoration verification, and interaction rules were already in
`doc/execution-semantics.md` §11, so the new section links there and
does not repeat them. I did not move the "Downstream acceptance
criteria" checklist or the sentence about the CTO and Security sign-off.
These were implementation-time notes; the tests now hold that coverage.
- §9.10 "Company Skill Policy Contract" → new
`doc/company-skill-policy.md`. No focused doc had this contract. I did
not move the "Required regression tests" phase checklist.
- Did not move any other part of the specs.
- Repointed code comments that cited spec sections:
- `packages/shared/src/issue-write-denial.ts` (§9.3) →
`doc/agent-permission-defaults.md`
- `server/src/routes/issues.ts` (§9.9) → `doc/TASK-WATCHDOG.md`,
"Authority contract"
- `server/src/routes/issues.ts` (§9.3, §9.8.1 cross-issue budget) →
`doc/agent-permission-defaults.md`
- `ui/src/lib/interaction-audience.ts` and
`ui/src/components/InteractionGovernancePanel.tsx` (§9.8.1) →
`doc/execution-semantics.md`
- `ui/src/lib/skill-policy-denial.ts`, `ui/src/pages/CompanySkills.tsx`,
`ui/src/pages/CompanySkills.production.tsx`,
`ui/src/pages/SkillStudio.tsx` (§9.10) → `doc/company-skill-policy.md`
- `server/src/services/recovery/ownership-invariant-report.ts` (monitor
deadline wait path) → `doc/execution-semantics.md` §8. That section
already lists the one-shot monitor as a valid wait path.
- Resynced the git blob pin for
`packages/shared/src/issue-write-denial.ts` in
`tests/runner-e2e/source-sdk-public-inputs.json`. The comment edit
changed the file's hash, and the Runner support suite checks that pin. I
used `node tests/runner-e2e/source-sdk-public-inputs.mjs <HEAD>
--write`; only that one pin changed.
- Updated `AGENTS.md` §1 so it does not name the deleted files.
- Removed the links to the deleted files from
`doc/plugins/PLUGIN_SPEC.md`.
- Updated the `doc-maintenance` agent skill
(`.agents/skills/doc-maintenance/`) so it no longer audits or stages
`doc/SPEC.md`.
- Removed or replaced references in `maps/README.md`,
`maps/feature-map/README.md`, `maps/storybook-map/README.md`,
`doc/PRODUCT.md`, `doc/CLIPHUB.md`, `doc/DEPLOYMENT-MODES.md`,
`doc/DEVELOPING.md`, `doc/evals.md`, `doc/spec/agent-runs.md`,
`doc/AGENTCOMPANIES_SPEC_INVENTORY.md`,
`doc/connections/CONNECTOR-PLAYBOOK.md`,
`doc/plugins/ideas-from-opencode.md`, `doc/execution-semantics.md`,
`doc/TASK-WATCHDOG.md`, and `.devin/wiki.json`.
- In `doc/execution-semantics.md`, the "admission is independent of
cleanup and accounting" reference now states the rule inline: only a
hard stop, an explicit pause, or an inactive company refuses admission.
- Kept these references as they are: dated plans in `doc/plans/` and
`docs/plans/`, the dated log
`doc/logs/2026-05-24-cli-api-parity-e2e-log.md`, `releases/`, the
transcript fixture `ui/src/fixtures/runTranscriptFixtures.ts` (it uses
the filename only as sample text), and
`docs/specs/external-task-protocol.md` (it refers to the Symphony
project's own `SPEC.md`).

## Verification

- `git grep -n "SPEC-implementation\|SPEC\.md"` (without `releases/`,
and ignoring `PLUGIN_SPEC.md` citations) finds only the kept references
listed above.
- `grep -rn "§9\.\(3\|8\|9\|10\)" ui/src server/src packages/shared/src`
finds no results.
- `node scripts/check-maps.mjs`: "Maps aligned: 35 areas, 192 capability
IDs".
- `pnpm check:token-gates`: "All gates clean".
- `pnpm exec vitest run --config tests/runner-e2e/vitest.config.ts
tests/runner-e2e/source-sdk-public-type.test.ts
tests/runner-e2e/source-sdk-evidence.test.ts`: 45 passed. These failed
in CI before the pin resync.
- `pnpm verify`: exit 2 ("Broader verification required") because
`AGENTS.md` is a global CI input. Required CI supplies the broad
coverage for this revision.
- All code changes are comments only. No runtime behavior changes. The
title uses `refactor:` because comments in source files changed.

## Risks

- Low risk. The change removes docs and edits comments only.
- A reader can lose context from spec sections that I did not move. The
text stays in git history. The code and its tests are the source of
truth.
- External links to the two deleted files will return 404.

> 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

- Anthropic Claude Opus 5.5 (`claude-opus-5-5`), in Claude Code with
tool use (shell, file edits). Standard context window.

## 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 (focused checks above; CI
supplies broad coverage)
- [x] I have added or updated tests where applicable (not applicable:
docs and comments only)
- [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>
2026-11-10 13:07:59 -06:00
Nicky Leach 17136a6c25 fix(runtime): persist managed Runner credential refreshes across execution targets (#20580) 2026-11-10 10:15:29 -08:00
DottaandClaude 94cfb84150 fix(scripts): build the plugin SDK in the agent worktree preflight (#20473)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Contributors and agents prepare each new git worktree with `node
scripts/agent-preflight.mjs`
> - The server imports `@paperclipai/plugin-sdk` through its built
`dist`. The preflight did not build that `dist`.
> - On a fresh worktree, the server and the restart-chaos harness stop
at startup with `ERR_MODULE_NOT_FOUND` for
`server/node_modules/@paperclipai/plugin-sdk/dist/index.js`
> - The SDK exports `dist` on purpose: plugin workers load it under
plain Node. CI, `paperclipai run` and the typecheck scripts already
build it with `scripts/ensure-plugin-build-deps.mjs`.
> - This pull request makes the preflight run the same builder as a step
> - The benefit is that one preflight command gives a worktree that can
start the server and the harness

## Linked Issues or Issue Description

**What happened?**
After `node scripts/agent-preflight.mjs` on a fresh worktree, `node
cli/node_modules/tsx/dist/cli.mjs tests/restart-chaos/main.ts ...` stops
at startup. The error is `ERR_MODULE_NOT_FOUND` for
`server/node_modules/@paperclipai/plugin-sdk/dist/index.js`, imported
from `server/src/services/reusable-sandbox-resume-error.ts`. The
workaround is `pnpm --filter @paperclipai/plugin-sdk build`.

**Expected behavior**
The preflight prepares everything that the server needs to start. The
server and the harness import their modules without a manual build.

**Steps to reproduce**
1. Make a new worktree from `origin/master`.
2. Run `node scripts/agent-preflight.mjs`.
3. See that `packages/plugins/sdk/dist` does not exist.
4. From `server/`, import
`./src/services/reusable-sandbox-resume-error.ts` with tsx. The import
fails with `ERR_MODULE_NOT_FOUND`.

**Paperclip version or commit**
`origin/master` at a5e01634f6.

## What Changed

- `scripts/agent-preflight.mjs`: add a `plugin-sdk` step after install.
It runs `scripts/ensure-plugin-build-deps.mjs`. That script builds
`@paperclipai/shared` and `@paperclipai/plugin-sdk`, and it skips them
when their content fingerprints match the last build. The step reports
`built` or `skipped`. It fails when the builder fails or when a
completion marker is missing after the build.
- The SDK build does not use the shared cross-worktree cache. Both
packages compile in about 1.6 s with the native compiler, so a cache
clone does not save time.
- `scripts/__tests__/agent-preflight.test.mjs`: new tests. They use the
real builder script with a stand-in compiler. They cover a fresh build,
a skip when sources do not change, a rebuild after a source change, a
rebuild when only the SDK `dist` is missing, a failed build, and missing
outputs. The file is added to `test:release-registry` next to
`agent-build-cache.test.mjs`.
- `doc/DEVELOPING.md`: the "Agent worktree preflight" section describes
the new step.

I checked the other option: change the SDK exports to `src`, as most
sibling packages do. I did not do that. Plugin workers load the SDK
under plain Node, and other tools already depend on the built `dist`. I
also checked the other workspace packages that the server and the
harness import. Only `@paperclipai/paperclip-runner` and
`@paperclipai/paperclip-eval-kernel` also export `dist`, and the
preflight already builds them. The harness builds its sandbox plugin
fixtures itself (`tests/restart-chaos/plugin-build.ts`).

## Verification

- Reproduced on a fresh worktree from `origin/master`: after the
preflight, `packages/plugins/sdk/dist` did not exist and the tsx import
of `server/src/services/reusable-sandbox-resume-error.ts` failed with
`ERR_MODULE_NOT_FOUND`.
- On a second fresh worktree with this change: the preflight printed
`plugin-sdk: built in 1.6s`. A second run printed `plugin-sdk: skipped`.
A tsx import of `reusable-sandbox-resume-error.ts` and
`server/src/app.ts` passed. A tsx import of every module that
`tests/restart-chaos/main.ts` imports passed. I did not run a harness
wave.
- `node --test scripts/__tests__/agent-build-cache.test.mjs
scripts/__tests__/agent-preflight.test.mjs
scripts/__tests__/ensure-plugin-build-deps.test.mjs`: 23 pass.

## Risks

- Low risk. The change affects only the local agent preflight. A fresh
preflight takes about 2 s more. A current worktree adds one fingerprint
check (about 0.1 s).
- The step uses the builder's lock. If another build in the same
worktree holds the lock, the step waits for it, as the other callers do.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, with tool use (shell
and file editing) in Claude Code.

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude <noreply@anthropic.com>
2026-11-10 08:03:56 -06:00
DottaandPaperclip b09f17fbfd fix(agents): repair queued setup through task connection cards (#20361)
## Thinking Path

> - Paperclip manages AI agents doing work for people.
> - Agent verification must finish before an accepted task can start.
> - A missing AI account default can prevent verification before a
provider starts.
> - Lifecycle policy treated that owned configuration refusal as a
temporary failure and retried each minute.
> - The accepted turn remained Queued without explaining the
prerequisite.
> - Park account configuration failures and reuse the task's existing
inline connection card.
> - Successful repair rechecks verification and releases the original
queued turn under its original authority.

## Linked Issues or Issue Description

**What happened?** An OpenCode agent selected the responsible user's
OpenRouter default, but that default did not exist. Verification retried
unchanged configuration indefinitely and its accepted task stayed
Queued.

**Expected behavior:** Preserve accepted work, explain the setup
prerequisite, and let the appropriate person repair it using the
existing task connection UI. Completion must verify the agent before
starting the same queued turn. Genuine pause, approval and access gates
remain effective.

**Reproduction:** Create an OpenCode Runner agent with a
responsible-user OpenRouter binding and no personal default; assign a
task while verification is pending. The base retries verification and
shows an unexplained queue.

Related: #18702 handles pending task connection recovery after account
repair. This PR handles the earlier agent-verification boundary. #20330
addresses a separate Codex governed-wait timeout and is already merged.

## What Changed

- Share owned account-selection failure evidence through a pure library
contract. Lifecycle policy parks those configuration failures with
fixed, redacted guidance; temporary infrastructure errors retain their
retries.
- Batch setup-state reads for unstarted queued turns. Distinguish manual
repair from automatic setup retries and preserve Stop, started/history
state and lifecycle holds.
- Reuse the existing `connection_intent` card, account selection and
completion APIs. Its controller-only `agentSetup` marker accepts only
never-started legacy turns; runtime tokens still require a running run.
- Address the card to the lifecycle verifier's account owner, preserving
the task's execution principal and private-task visibility. Attach
missing cards on admission, verification, startup and full recovery,
including retained retries and continuations. Repeated delivery and
publication remain bounded. A new queued turn supersedes the setup card
of a stopped turn; generic connection cards retain cross-run reuse.
- Recheck lifecycle verification after usable-account completion, then
release the existing turn through the normal readiness path. Preserve
decline, Stop, reassignment and changed setup-owner gates. Fence an
in-flight verification failure from overwriting a repair; add no
provider wake or recurring worker.
- Park owned account refusals during resume as well as initial
verification. Bind setup cards to the lifecycle operation, settle
obsolete deliveries, and keep explicit Retry guidance accurate.
- Reuse the router’s existing lifecycle pin for setup repair without
rerouting the task, advancing the pool cursor, or replacing its saved
binding. Legacy direct-account cards remain readable.
- Hide the incorrect Resume banner during setup, retaining genuine
manual/budget pause controls. Document the execution and retry contract.

## Verification

- Red: eight original behavior assertions failed on the base, including
the real selector's retry decision and the real batched queue
projection. Six owned selection cases failed classification.
Temporary-error presentation, different task/verifier users, retained
retry/continuation recovery and the setup Resume banner also have
failing-before/passing-after regressions.
- Green: 430 affected backend, lifecycle, shared-contract and UI tests
passed before the final review corrections. Subsequent focused runs
cover one inline card, real account selection/completion, duplicate
delivery/publication, verification before readiness, unchanged run
authority, private tasks, no extra provider wake,
decline/Stop/reassignment, company isolation, invalid runtime tokens,
transient retries and redacted diagnostics.
- Final setup/card and generic connection-service suites: 49 tests
passed. The stopped-turn case failed before the correction, then passed
with real account completion, the stopped source remaining cancelled,
and the replacement source remaining queued.
- After rebase, all 129 focused assertions passed. The local queue
suite’s 88 execution assertions passed repeatedly, but its
database-fixture teardown exceeded both 30-second and 120-second hooks.
An isolated queue case completed, and the setup/connection suites fully
passed. The original queue test and cleanup remain unchanged; broad CI
supplies the full-suite result.
- Server/UI typechecks, module boundaries, token gates and diff checks
passed. `pnpm verify --explain` requested broad CI because the
execution-contract document changed; no redundant full local suite was
substituted.
- Real source acceptance: macOS arm64, Node 26.4.0, isolated embedded
PostgreSQL and local board identity. Created an OpenCode/OpenRouter
agent and task through the API with no default. Admission retained one
unstarted turn and produced the existing inline Connect OpenRouter card.
The browser opened its credential form and closed it without entering
credentials. The same card/run persisted after server restart and
reload, with the setup label and no incorrect Resume. The browser also
reproduced Stop followed by a new queued turn retaining the stale card
on the prior head. On `12f609c98372fd1e50644028db75cfcc8deb210d`,
startup superseded the stale card and retained the same replacement
turn, with the original turn still cancelled and no provider execution.
- The earlier CI case-search failure also reproduces on exact base
`0e3fdebea8257bdff11573081c76b306f12db230` without this PR. Its repair
is now in master via #20371; this branch is rebased onto it and contains
no API-search changes.
- Staging's actual Runtime test returned “Connect an account and choose
your personal default” before provider startup. The original turn later
started independently on deployed code, then hit a separate
workspace-export failure. Automatic file recovery subsequently marked
that run successful; its task remains Blocked and the trial’s useful
output is unverified. This PR is not deployed; provider authentication
through its card and downstream publication remain unverified. No
account, credential, default, permission or binding was changed during
diagnosis.
- Previous revision review: Greptile 5/5 on
`12f609c98372fd1e50644028db75cfcc8deb210d`, with all four inline
findings addressed and resolved. [Full CI
passed](https://github.com/paperclipai/paperclip/actions/runs/42713494508)
on that revision: 59 successful checks, one neutral check and three
intentional skips, with no pending or failed checks.

- Latest revision `976bcae993805a8a2222395bbff9394f6791b424`: resume,
router and Retry-copy regressions failed before repair. Green: 92
lifecycle/setup/shared tests, 83 setup/generic-connection/router tests,
and 137 UI/shared tests. Server/UI typechecks, module boundaries and
token gates passed. [Full CI
passed](https://github.com/paperclipai/paperclip/actions/runs/42720731137)
on this exact revision: 59 successful checks and three intentional
skips, with no pending or failed checks. Greptile reviewed this head at
5/5; all six review findings are addressed and resolved. Real Stop/retry
acceptance retained the same replacement turn and current-operation card
through two actual server restarts, with no provider execution.

## Risks

- Known account configuration failures now require repair or explicit
Retry. Temporary failures keep automatic retries; accepted work and
authority remain intact.
- The projection adds one company-scoped batch read only for unstarted
queued turns. Card attachment examines at most 100 active candidates and
adds no timer, worker, schema or migration.
- The optional stored setup-card marker requires an aware reader during
rollback. No run/session/checkpoint identity format changes. Setup
presentation grants no access and cannot bypass verification or other
gates.

## Model Used

- OpenAI GPT-6 (Codex), with reasoning, tool use, code editing and test
execution. The exact serving model identifier and context-window size
are not exposed in this session.

## 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>
2026-11-09 17:49:34 -06:00
Nicky LeachandPaperclip 1838de8c6c Pause agents automatically when moving to a plugin environment (#20375)
## Thinking Path

> - Paperclip manages AI agents and their execution environments.
> - Core owns agent lifecycle state and controls when work can run.
> - A plugin environment can need a computer that belongs to the agent.
> - Moving a ready agent to that environment currently requires manual
pause and resume actions.
> - Saving the environment is sufficient intent to perform those routine
steps.
> - This change records the pause with the environment update and uses
the existing lifecycle worker.
> - Work can resume only after execution stops, the plugin starts its
resources, and verification passes.

## Linked Issues or Issue Description

Related: #19173 introduced environment-scoped plugin selection and the
manual-pause requirement. I searched for related pull requests and found
no duplicate fix. No separate issue is linked.

**What happened?**

Saving a ready agent with an environment whose lifecycle plugin is not
selected returns a conflict. The error tells the user to pause the
agent, change its environment, and resume it.

**Expected behavior**

Saving the environment change starts the required pause, resource setup,
and verification automatically. Existing manual, budget, and company
holds still block resume.

**Steps to reproduce**

1. Use an agent in `ready` on an environment without an agent-owned
plugin.
2. Select an agent-owned plugin environment in the agent configuration.
3. Save without first pausing the agent.

Before this fix, the save fails. With this fix, the agent moves through
`pausing`, `resuming`, and `verifying` before `ready`.

## What Changed

- Save the new environment and automatic pause in the same transaction.
Keep the existing plugin selection during stop.
- Use the existing completion of a pause without holds to resume
automatically. Set the saved resume target to `verifying` so the new
environment must pass its test.
- Preserve independent pause holds, lifecycle version checks,
notifications, resource status events, and worker recovery.
- Add migration tests for idle and running agents, real process-stop
proof across a worker restart, added holds, failed verification, and
route authorization.
- Update the lifecycle and development docs. Keep the feature maps
unchanged, as required for a small behavior fix.

## Verification

- Current revision: `300f57539bce9b198406c3793ab3c2de46492659`.
- Lifecycle and case API discovery suites passed after updating the
branch to master. The final environment-plugin suite passed all 22
tests, including four real-route authorization cases for users and
agents. Coverage includes real process-stop proof across worker
replacement, independent holds, and failed migration verification.
- Server typecheck: passed on the current base. All workspace typechecks
and `pnpm build` passed before the base update; fresh CI covers the
updated base.
- `node scripts/check-module-boundaries.mjs`, `node
scripts/check-maps.mjs`, and `git diff --check`: passed.
- Reviewed the diff for secrets, personal data, private addresses, and
run artifacts before each push.
- [Current
CI](https://github.com/paperclipai/paperclip/actions/runs/42714733533):
passed on `300f57539bce9b198406c3793ab3c2de46492659` (52 successful
jobs; the optional test-selection optimization was skipped). Standard
Greptile: 5/5 on the current revision, with no unresolved findings. The
security scanner accepted the documented configuration-authority policy.
- Earlier CI failed the `case-history-api-discovery` assertion for the
query `case for task`. It also failed locally. The branch now includes
master's fix #20382, and that test passes. The migration implementation
did not change. The superseded CI attempt was cancelled after recording
the failure.
- Full local `pnpm test:run`: incomplete; stopped after two passing chat
partitions. The focused suites passed, and required CI supplies broad
coverage, as specified in the repository instructions.
- Local target: isolated source checkout on macOS ARM64, Node 26,
disposable PostgreSQL, fixture lifecycle plugin. Initial database
startup failed because the bundled macOS PostgreSQL package lacked dylib
aliases. Temporary dependency aliases repaired startup; the focused
database tests then passed. The installed Rust toolchain also needed to
be added to PATH.
- The pending-stop test retains a live process ID in the cancelled run.
The real host stop check blocks plugin setup. After stop acknowledgment
and worker replacement, the saved migration reaches readiness.

## Risks

- Saving this environment change can stop current execution. The system
performs that pause as part of the requested migration.
- A failed stop, plugin call, or verification keeps the agent blocked
and uses existing retry behavior.
- Editing a shared environment or the instance default still uses its
existing conflict checks. This change covers the individual agent
environment update.
- Configuration permission authorizes the temporary system pause needed
for the resource move. Separate manual-pause authority is not required
for this configuration operation. Real route tests cover authorized and
denied users and agents.
- No schema migration or deployment is included. A fixture plugin does
not prove live computer provisioning or model execution.

## Model Used

OpenAI Codex, based on GPT-6, with code execution and tool use. The
exact runtime model ID and context limit are not exposed in this
session.

## 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>
2026-11-09 15:02:54 -08:00
DottaandPaperclip a3a25ce6c9 fix(workspaces): stop running Paperclip's worktree setup before every agent turn (#20269)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Before an agent turn starts, the harness prepares the task's git
worktree
> - The harness runs a repository's `scripts/provision-worktree.sh` when
the project sets no `provisionCommand` and the file exists
> - The harness runs it on every turn, both when it creates the worktree
and when it reuses it
> - In the Paperclip repository, that script writes the worktree's
isolated instance config and runs `pnpm install`
> - Its "install needed" check compares against every `node_modules`
directory in the base checkout, including other worktrees, so it
reinstalls on every turn
> - This pull request renames the Paperclip script so that the harness
default does not find it in this repository
> - The benefit is that Paperclip agent turns no longer wait on a 6–9
second install. Other repositories keep the harness feature.

## Linked Issues or Issue Description

**What existing behavior does this improve?**
Time to first token for agent turns in managed worktrees of the
Paperclip repository.

**Subsystem affected**
Execution workspace provisioning
(`server/src/services/workspace-runtime.ts`) and the repository script
`scripts/provision-worktree.sh`.

**Current behavior**
Every agent turn in a Paperclip worktree first runs `bash
./scripts/provision-worktree.sh`. In a local test, a `pnpm install
--frozen-lockfile` with nothing to change took 6.1 s and 6.3 s, and a
full install from a warm store took 9.0 s. The script's fingerprint skip
does not prevent this, because the script also requires every
base-checkout `node_modules` path (up to depth 4) to exist in the
worktree. On a developer machine that list had 1,735 entries, including
other worktrees under `.claude/worktrees/` and `.worktrees/` and pnpm's
internal `node_modules/.pnpm/*/node_modules`. A managed worktree never
contains the other worktrees' paths, so the script always decides to
reinstall.

**Proposed behavior**
The Paperclip repository does not ship a file at
`scripts/provision-worktree.sh`. The setup script becomes
`scripts/setup-paperclip-worktree.sh`. People can run it by hand or set
it as the project `provisionCommand` to opt in. The harness default
stays for other repositories.

**Reason and benefit**
Agents install dependencies when they need them (`node
scripts/agent-preflight.mjs`, as `AGENTS.md` says). Many turns never run
code. Instance setup stays available on demand:
`scripts/provision-worktree-runtime.sh` runs the setup script when a dev
server starts in a worktree that has no config. Database seeding was
already deferred.

**Breaking changes**
A project that explicitly sets `provisionCommand` to `bash
./scripts/provision-worktree.sh` for this repository will fail with
"file not found". Change it to `bash
./scripts/setup-paperclip-worktree.sh` or clear it.

## What Changed

- Rename `scripts/provision-worktree.sh` to
`scripts/setup-paperclip-worktree.sh`. The content is unchanged.
- `scripts/provision-worktree-runtime.sh` calls the new name when the
worktree has no config.
- Tests read the real script from its new path
(`provision-worktree-self-heal`, `workspace-runtime`,
`worktree-seed-server-spawn`). Server fixtures still copy it into their
test repositories as `scripts/provision-worktree.sh`, so the harness
default stays covered.
- `doc/DEVELOPING.md` says that the Paperclip repository deliberately
has no `provision-worktree.sh`, and tells people how to opt in.

## Verification

- `node --test scripts/__tests__/provision-worktree-self-heal.test.mjs`:
33 passed, 1 skipped (the skip already existed).
- `cd server && npx vitest run src/__tests__/workspace-runtime.test.ts
src/__tests__/heartbeat-workspace-source-trust.test.ts
src/__tests__/execution-workspace-reopen.test.ts`: 242 passed on the
rebased head.
- `cd server && npx vitest run
src/__tests__/worktree-seed-server-spawn.test.ts`: 2 passed.
- Manual: in a Paperclip worktree, start an agent turn. The run log does
not show a `workspace_provision` operation for the script.

## Risks

- Explicit `provisionCommand` settings that name the old path will fail.
See "Breaking changes".
- Open pull requests that edit `scripts/provision-worktree.sh` (for
example #16213, #11335, #11733, #19764) will conflict on the rename. Git
rename detection should carry most edits over.
- An agent that runs tests in a new worktree without first running
preflight will see a missing-module error. `AGENTS.md` already tells
agents to run `node scripts/agent-preflight.mjs`.
- The script's install check still has the bug described above. It now
runs only on demand. A separate fix can address it.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, through Claude Code
with tool use (shell, file edits). Standard context window.

## 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: Paperclip <noreply@paperclip.ing>
2026-11-09 14:03:24 +00:00
DottaandClaude Opus 5.5 fc6e1b0346 perf(native): keep local Codex and OpenCode runners warm by default (#19888)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - When someone messages an agent, the turn must start fast. Time to
first token (TTFT) is a first-class metric.
> - The Phase 0 baseline (#19846) found that every local turn launches a
new runner and loads the provider session again, because `per_turn` is
the default lifecycle. That made a follow-up message slower than a new
task.
> - Warm runners keep the runner and provider session alive between
runs. #19874 fixed the defect that broke warm OpenCode follow-ups, and
#19879 bounds an idle warm runner whose controller dies.
> - This pull request makes warm the default for local Codex and
OpenCode agents, and migrates existing agents that only carried the old
creation default.
> - The benefit: follow-up TTFT p50 drops from 12.0 s to 4.7 s (Codex)
and from 21.7 s to 4.2 s (OpenCode), with no new restart-chaos failures.

## Linked Issues or Issue Description

Refs #19846 (TTFT baseline), #19852 (startup sub-spans), #19874 (warm
completion contract), #19879 (warm reconnect grace).

**What existing behavior does this improve?**
The default runner lifecycle for native agents, and how a follow-up
message starts.

**Current behavior**
Agent creation writes `lifecycleMode: "per_turn"` into every native
agent. Every follow-up launches a new runner and restores the provider
session: 4.2 s (Codex) and 16.3 s (OpenCode) at p50 before the turn
starts.

**Proposed behavior**
New native agents store no lifecycle. On a local target, an unset
lifecycle resolves to `warm` with the default 5-minute idle window for
Codex and OpenCode. Other harnesses, remote targets and managed
providers without warm support stay `per_turn`. An explicit choice
always wins. Migration 0443 clears the stored creation default from
existing agents, except where an edit set "Turn by turn" explicitly.

**Reason and benefit**
Measured locally (`doc/plans/2026-11-07-warm-follow-up-ttft.md`). Warm
follow-ups are 2.6–5× faster for Codex and OpenCode, and restart
recovery latency is equal or lower.

## What Changed

- `native-lifecycle.ts`: an unset `agentMode` resolves to warm (5-minute
idle window) for local `codex_app_server` and `opencode_server` agents.
`runtime-selection.ts` passes `localTarget`. Explicit `per_turn` or
`warm` wins. An admitted session keeps its persisted policy. ACPX Claude
stays `per_turn`: it relaunches its provider process on every follow-up
by design, so warm did not shorten its follow-up (10.7 s warm vs 10.5 s
per_turn).
- Creation and configuration writes no longer store `lifecycleMode:
"per_turn"` for Codex, Claude or OpenCode. This covers
`normalizePaperclipRunnerAdapterConfig` (runs on every create and
update), `paperclipRunnerTransitionConfig` (switching to the native
runner), `agent-runner-selection.ts`, `codex-local` `build-config.ts`,
and the simplified new-agent setup (`paperclipRunnerCreationLifecycle`
in `@paperclipai/shared`). Grok, Pi and Cursor keep their explicit
value.
- Agent form: the Runner lifecycle field shows the unset state as
"Automatic". "Turn by turn" and "Warm session" remain.
- Migration `0443_native_warm_follow_up_default.sql`: clears
`lifecycleMode = 'per_turn'` from native Codex, OpenCode and Claude
agents unless `agent_config_revisions` shows an edit that set it to
`per_turn`. Each migrated agent gets an `agent.updated` activity entry
with the old value (`actor_id =
migration:native-warm-follow-up-default`). Creation records no revision,
so a "Turn by turn" pick made at creation cannot be told apart from the
old default. The product owner approved migrating those agents. Claude
agents follow the default, which is `per_turn` today.
- Restart chaos harness and TTFT driver: `--lifecycle
per_turn|warm|default` (saved in the wave plan). `default` removes the
catalog's pinned lifecycle, so a wave exercises the real default path.
- Docs: `doc/DEVELOPING.md` "Runner lifecycle default", and the results
in `doc/plans/2026-11-07-warm-follow-up-ttft.md`, which also documents
baseline finding 4 (Claude's resumed turn-start gap is ACPX's per-turn
process generation, not the provider).

## Verification

- `server`: `native-lifecycle.test.ts` (new default cases: local Codex
and OpenCode warm, Claude, remote, unknown target, unmeasured harness,
managed Claude, admitted per-turn session, explicit choices, non-native
adapter), `agent-runner-selection.test.ts`, `runtime-selection.test.ts`
(335 pass).
- `packages/db`: `native-warm-follow-up-default-migration.test.ts` on
embedded Postgres. Default agents are cleared, the explicit edit is
kept, other harnesses and legacy adapters are untouched, audit rows are
written once, and a rerun is a no-op. Without the explicit-edit filter
the test fails. `check:migrations` passes.
- `codex-local` `build-config.test.ts` (65), `ui`
`config-fields.test.tsx` (40), restart-chaos unit tests (134), `tsc
--noEmit` for `server`.
- `adapter-utils` `paperclip-runner-lifecycle-default.test.ts`:
configuration writes and adapter conversion store no lifecycle for
Codex, OpenCode and Claude, keep `per_turn` for the others, and preserve
explicit choices. It fails without the fix.
- End-to-end default check on this branch (`ttft-baseline.ts --lifecycle
default`, codex and opencode, 2 samples): the agents read back with no
stored lifecycle, and every follow-up reused the runner and provider
session (no `runner.process.launch`). Follow-up TTFT was 3.6–4.8 s. This
check found the per-write `per_turn` injection fixed here.
- Restart chaos (codex and opencode, A1/B1/B5, K1/K2/K6, seed 4242), 8/8
PASS each with no open signatures: forced warm, forced per_turn, and
`--lifecycle default` on this branch (agents created without a
lifecycle).
- `pnpm verify` selects broader CI (harness config is a global input),
so required CI supplies the broad coverage.

## Risks

- Behavior change: local Codex and OpenCode agents keep a runner and
provider process for up to 5 minutes after a run. Instance sleep waits
for that idle window. The process is reaped by the idle timer, by
graceful shutdown, or by the #19879 reconnect grace if its controller
dies.
- Migration: agents whose "Turn by turn" was chosen at creation become
Automatic. The activity entry records the old value; choosing "Turn by
turn" restores it.
- Previous-release story (`rules/upgrade-safe-run-state.mdc`): a task
session keeps the lifecycle policy it was admitted with, so sessions
saved before this change stay `per_turn`. New sessions get the default.
No run, checkpoint or launch state changes shape.

> 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

- Anthropic Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with
tool use (shell, file edit, 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
- [ ] 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>
2026-11-07 14:37:36 -06:00
DottaandClaude Opus 5.5 76994c5027 fix(native): bound failover backup restores by inactivity, not total time (#19906)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - A native per-turn session that continues an earlier conversation
first restores its failover backup from durable storage. This happens
before the coordinator claim, so no provider has started.
> - That restore ran under a fixed 300 s total deadline
(`AbortSignal.timeout(300_000)`). The deadline covers the download and
the local decrypt, digest, extraction and provider-artifact steps.
> - On staging, restore time for resumed sessions grew during the day.
It reached 300 s, and then every resumed run of one review agent failed
with the generic "The operation was aborted". Fresh sessions were not
affected.
> - A failure at this point also enters the saved-work reconciliation
path, so the user request stopped.
> - This pull request bounds each durable read by inactivity instead of
total time. A slow transfer continues while bytes arrive. A read that
stops sending bytes fails with a named code.
> - The benefit is that resumed sessions no longer fail only because
their backup is large or the store is slow.

## Linked Issues or Issue Description

Refs #19894 (adds the same idle-deadline rule for workspace snapshot
reads; this PR covers the separate native failover-backup reads).

**What happened?**

On staging, a PR-review agent had 17 runs fail in about 80 minutes. Each
failure had the message "The operation was aborted" and the code
`native_continuation_requires_reconciliation`. Every failing run resumed
an existing session (`sessionIdBefore` set, per-turn lifecycle). Every
fresh-session run in the same window succeeded. In each failing run, the
error came 304–309 s after the `environment.startup` span, and no
`native.coordinator.claim` span was recorded. The run result had
`executionRecovery: { kind: "bootstrap", providerWorkStarted: false }`.
Earlier resumed runs of the same agent show the time from
`environment.startup` to `native.coordinator.claim` growing from about
30 s to about 200 s before the failures started. The only fixed 300 s
deadline on that path is the failover-backup restore in
`restoreDurableHarnessForExecution`.

**Expected behavior**

A resumed session restores its backup when the store keeps sending
bytes, even when the total time is more than five minutes. A read that
stalls fails with a named, diagnosable code. A failed restore publishes
no partial backup and keeps the saved backup.

**Steps to reproduce**

1. Persist a native failover backup with provider artifacts.
2. Restore it through a storage reader that sends bytes slowly, so the
full restore takes longer than the deadline.
3. Before this change, the restore fails with "The operation was
aborted". A reader that stops sending bytes, with no caller deadline,
waits indefinitely.

## What Changed

- `native-harness-backup-storage.ts`: add `downloadIdleTimeoutMs` to
`restoreDurableNativeHarnessBackup` and
`verifyDurableNativeHarnessBackup`. When set, each durable `getObject`
(the backup object and the provider artifacts) runs under an idle timer.
Each received chunk renews the timer. The timer is active only while a
read is in flight, so local decrypt, digest, extraction and copy are
never timed. On expiry the whole restore aborts and throws
`native_harness_storage_download_stalled`. Caller cancellation keeps its
own error.
- `verifyRecoverableNativeHarnessBackup` and the executor's
`restoreDurableHarnessForExecution` use the five-minute idle limit
(`NATIVE_HARNESS_DOWNLOAD_IDLE_TIMEOUT_MS`) instead of
`AbortSignal.timeout(300_000)`.
- The whole restore or verification keeps a 30-minute outer limit. It
fails with `native_harness_storage_restore_deadline_exceeded`, so a hung
local step stays bounded and named.
- The executor passes the startup Stop signal
(`providerPackSourceAbort`) into the restore, so Stop (also a Stop that
came before the restore began) ends it. Only a startup that already
completed does not reuse its signal. The restore checks the signal after
the local copy and before it publishes `current`.
- The wrapped storage is a `Proxy` that replaces only `getObject` and
forwards every other member to the real service.
- `doc/DEVELOPING.md`: document the idle limit and the named code.

Previous-release story (`rules/upgrade-safe-run-state.mdc`): no
persisted shape changes. Backups, artifact rows, receipts and
checkpoints saved by the previous release restore unchanged. A deploy
that lands during a restore stops the process. The new process starts
the restore again from the saved durable backup under the new limit. The
existing hash, size, encryption and atomic publication checks are
unchanged.

## Verification

Run from `server/`:

- `pnpm exec vitest run
src/services/native-runtime/native-harness-backup-download-deadline.integration.test.ts`
— 4 tests passed (embedded PostgreSQL, local-disk storage, an OpenCode
backup with provider artifacts). The tests are in a focused suite, so
the existing 990-line storage suite does not grow.
- `pnpm exec vitest run
src/services/native-runtime/native-harness-backup-storage.integration.test.ts`
— 68 existing tests passed.
- New: "keeps restoring a backup whose download outlasts the idle window
while bytes keep arriving". With the former total-deadline policy, the
same slow transfer fails with "The operation was aborted" and publishes
nothing (the staging message). With the idle limit, the restore
completes after more than twice the window, restores the session and the
OpenCode launch artifacts, and verification also completes.
- New: "names a download that stops sending bytes and publishes no
partial backup". It checks restore and verify, checks that no `current`
backup is published, and then restores the same saved backup
successfully.
- New: "stops at the outer bound during local copy and publishes
nothing".
- New: "lets Stop end a progressing download with its own reason,
including a Stop before it starts".
- RED: with the production files reverted to `origin/master`, the stall
test does not finish and times out after 10 s, because no stall is
detected. The other two tests pass on the old code, because the total
deadline was the executor's caller policy. The first test reproduces
that policy directly.
- `pnpm exec vitest run` on `native-harness-online-preservation`,
`native-harness-filesystem-independence` and
`native-controller-migration` integration suites passed.
`native-warm-checkpoint-ownership.integration.test.ts` fails locally on
master as well, because the local Rust `paperclip-runnerd` binary is not
built.
- `node scripts/typecheck-layers.mjs` passed for all layers.

Not verified: a live resumed run on staging with this build. The staging
evidence shows where the time goes (before the coordinator claim, on
resumed sessions only) but does not show which restore step was slowest.
The fix removes the total deadline for every step on that path.

## Risks

- A restore that progresses very slowly can now take longer than five
minutes. Before, it failed. The run still stops on caller cancellation.
- A local step that hangs (for example a stalled disk) is now cut off by
the 30-minute outer limit instead of 5 minutes. A stalled local writer
also pauses the read through backpressure, so it can be reported as
`native_harness_storage_download_stalled`.
- A failure before the coordinator claim still enters the existing
saved-work reconciliation path. This PR does not change that
classification. It removes the cause of these failures.

## Model Used

- Provider: Anthropic. Model: Claude Opus 5.5 (`claude-opus-5-5`), with
tool use (shell, file edits, read-only browser for API inspection) in
Claude Code.

## 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>
2026-11-07 14:34:57 -06:00
DottaandPaperclip 57ae2fc309 perf(workspaces): reduce snapshot stream scheduling overhead (#19900)
Use bounded 1 MiB filesystem buffers during workspace archive hashing, encryption, and restore. Preserve integrity, ownership, cancellation, and snapshot format guarantees.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-11-07 14:24:42 -06:00
Devin FoleyandPaperclip c9959814ba fix(workspaces): cancel stalled snapshot reads and preserve restore refusals (#19894)
Cancel encrypted snapshot reads after five minutes without incoming bytes.
Renew the deadline on progress, preserve caller cancellation, settle the
physical request and private scratch, and retain saved snapshots for normal
retry admission. Keep Node warnings out of server-owned helper refusal labels.

Verified both complete owner suites (145 tests), the prior unchanged storage
and transport coverage, server typechecks, final-head CI and Greptile 5/5.
The earlier CI cancellation-signal assertion failure was reproduced locally
and corrected with checks for abort state, reason, stream closure and cleanup.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-11-07 12:06:18 -08:00
DottaandClaude Opus 5.5 0189fedffc fix(native): bound an idle warm local runner whose controller died (#19879)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - A warm runner (`lifecycleMode: warm`) keeps runnerd alive between
runs so a follow-up turn starts fast. The follow-up default flip (next
PR) makes warm the default for local Codex and OpenCode agents.
> - The controller owns a warm runner's idle window. Runnerd ignores the
idle timeout itself.
> - A graceful controller shutdown suspends idle warm sessions. A
controller that dies (SIGKILL, crash) does not. Local runners launch
with no process reconnect grace, so the idle runner kept running until
its 1-hour connection lease ran out, owned by nobody.
> - This pull request gives warm local runners the 7-minute reconnect
grace that remote runners already use.
> - The benefit: idle runners are reaped by proof within a bounded time,
never left orphaned, before warm becomes the default.

## Linked Issues or Issue Description

Refs #19874 (warm completion contract), #19846 (TTFT baseline), #19852.

**What existing behavior does this improve?**
Ownership of an idle warm local runner after its controller dies.

**Current behavior**
`runnerProcessReconnectGraceMs` is `undefined` for local targets, so
runnerd launches without `--reconnect-grace-ms`. An idle warm runner
whose controller was killed stays alive until its connection lease (one
hour) expires. The restart-chaos harness cannot show this: its K1 kills
the controller's whole process tree, runner included.

**Proposed behavior**
`localRunnerProcessReconnectGraceMs(policy)` returns the remote grace (7
minutes) for a warm policy and `undefined` for per-turn. After the
grace, runnerd records `transport_reconnect_grace_exceeded`, stops its
provider, keeps durable state and exits. The next run resumes cold.

**Reason and benefit**
The restart plan requires idle runners to be reaped by proof, never
orphaned. Seven minutes is far longer than a controller restart (13–20 s
locally) and the long-outage fault holds (3–5 minutes), so a live turn
still reattaches.

## What Changed

- `native-runner-recovery-contract.ts`:
`localRunnerProcessReconnectGraceMs`.
- `native-session-executor.ts`: the local runnerd transport passes it as
`runnerProcessReconnectGraceMs`. Remote targets keep `null`
(lease-owned).
- `runnerd-warm-idle-orphan.test.ts` (new): real runnerd and fake Codex.
An idle warm runner, after its turn completed, whose controller
detaches.
- `doc/DEVELOPING.md`: the grace and its bound.

## Verification

- `pnpm --filter @paperclipai/paperclip-runner exec vitest run
src/live/runnerd-warm-idle-orphan.test.ts`: with a process grace, the
idle runner exits with `transport_reconnect_grace_exceeded` and the next
transport resumes the same provider session cold. With no grace (`null`,
today's local launch), the runner is still alive after the controller
left.
- `cd server && npx vitest run
src/services/native-runtime/native-runner-recovery-contract.test.ts`:
warm gets the remote grace; per-turn keeps none; the grace outlasts a
controller restart and a long outage.
- `tsc --noEmit` passes for `server` and `packages/paperclip-runner`.
- Local restart measurement with warm runners (K1/K2, codex, claude,
opencode, n = 3 each): every interrupted run recovered, with recovery
latency equal or lower than per-turn. The chaos waves with this change
are in the default-flip PR.

## Risks

- A warm local runner whose controller stays down for more than 7
minutes exits. A turn in progress then resumes through
`resume_dead_runner`, the same path as a controller crash that kills the
runner. Remote runners already behave this way.
- Previous-release story (`rules/upgrade-safe-run-state.mdc`): no
persisted state changes. A warm runner launched by the previous release
keeps the launch arguments it started with (no grace) until it exits.

> 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

- Anthropic Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with
tool use (shell, file edit, 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
- [ ] 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>
2026-11-07 13:11:18 -06:00
DottaandPaperclip c740cb9ded fix(ui): dismiss skipped confirmations when sending a message (#19496)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Tasks and Agent Chat show saved requests above the message composer.
> - A person can send a separate message while a confirmation is open.
> - The old code closed only question forms, after the message save
finished.
> - A confirmation could stay open or open again after a refresh.
> - This change closes the form when sending starts and keeps the
request in the feed.
> - People can open the request later and make the original decision.

## Linked Issues or Issue Description

**What happened?**

A confirmation stayed open when a person sent a separate message.

**Expected behavior**

The form closes immediately. The request stays in the feed. A person can
open it later. Sending a message does not record an approval.

**Steps to reproduce**

1. Open a task with a pending confirmation.
2. Send a separate message below the form.
3. Observe the form while the message save is pending.
4. Reload the task and open the request from the feed.

**Paperclip version or commit**

Reproduced at a434edf991.

**Deployment mode**

Source checkout and isolated Storybook fixtures.

## What Changed

- Close the composer request before the message save finishes.
- Keep earlier saved requests in history after a newer human message.
- Save browser dismissal IDs in one batch after a successful send.
- Restore the previous form after a failed send, including a reopened
request after an optimistic comment changes automatic selection.
- Track deliberate selection changes separately from automatic
filtering. Keep a newer request open when an earlier send fails.
- Allow a new request to open while an earlier message is being saved.
- Add tests for confirmation and checkbox forms in task and Agent Chat
modes.
- Add Send Instead Of Confirming and Reopen Skipped Confirmation
stories.
- Update the existing answer-later story to check the current answer
receipt.
- Update the behavior and Storybook documentation.

## Verification

- TDD: Six new cases failed before the main fix. Four more cases
reproduced the review finding before the recovery fix. They cover failed
sends with an optimistic comment and its rollback in both task and Agent
Chat modes.
- Component checks: 518 passed, one existing test skipped. Run `pnpm
--filter @paperclipai/ui exec vitest run
src/components/TaskChatThread.test.tsx
src/components/task-chat/TaskChatComposer.test.tsx`.
- UI typecheck passed after preparing the local plugin SDK dependency.
- Token gates passed.
- Catalog structure checks passed. The three catalog test files passed
all 30 tests.
- Six Playwright cases passed in an owned Storybook server. They cover
the initial form, sending, manual reopening, light theme, mobile, and
answering later. Play assertions passed. Accessibility reports had zero
violations.
- The stories use the production thread with simulated saves and
decisions. Existing optional fixture endpoints return 404. These do not
prevent the selected journeys.
- No visual baseline comparison was possible. The baseline manifest has
no published snapshots.
- `pnpm verify --explain` requested broader CI coverage. [Required
CI](https://github.com/paperclipai/paperclip/actions/runs/42253585800)
passed on fda44f2648.
- Greptile and Paperclip Review both report 5/5 with no findings on the
final head.
- The remote commit tree matches the tested local tree:
7e22201513.

## Risks

- Older pending requests now stay in history after a newer human
message. People must select the feed entry to open them.
- Dismissal changes presentation. Server approval checks and request
decisions keep their existing behavior.
- Browser fixtures do not prove live provider continuation or staging
behavior.

## Model Used

OpenAI GPT-6 Codex. The exact backend model identifier and context
window were not exposed to this run. Used reasoning, repository
inspection, edits, shell tools, component tests, and browser tools.

## 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>
2026-11-07 08:34:14 -06:00
Devin FoleyandPaperclip 51ab7ebdc6 fix(recovery): admit recovered scheduled preparation retries (#19802)
Allow explicit Retry after a recovered scheduled setup failure.

Recognize the exact host scheduled-retry promotion only when its saved
parent, attempt, deadline and reason match the source run and context.
Keep changed, extra or foreign evidence held. Preserve the existing
provider-absence, stopped-source, recovered-file and authorization gates.

Keep refusal tests receipt-only until they change saved proof, then
invoke the real retry handler. Positive tests retain real HTTP delivery.

Verification: 217 unique tests passed across five recovery suites. The
12-test affected suite and its typecheck layer passed again after the
test-race fix. All applicable CI passed; exact-head Apex review was 5/5.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-11-07 02:20:02 -08:00
131b566ca4 fix(workspaces): report safe Git restore diagnostics (#19736)
Return the restore stage and failure category with the existing HTTP409 rejection. Preserve the unsaved comment and editable draft. Keep nested saved-commit and clone-timeout diagnostics through preparation wrappers, and distinguish local Git file errors from authentication failures. Retain only safe process flags privately; no raw command cause is exposed.

All seven affected local suites pass (288 tests) and the layered server typecheck passes on supported Node25.6.1. Reviewed head 022eb7c2eb has Greptile Apex5/5, zero unresolved findings and all applicable CI passing (55 successful checks and4 intentional skips).

Co-Authored-By: Sentry Bot <sentry-bot@paperclip.invalid>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-11-06 21:33:59 -08:00
18be7ac696 fix(server): retire idle native sessions before tenant sleep (#18988)
## Thinking Path

> - Paperclip lets people manage AI agents and their work.
> - Native agents can retain a warm session between useful turns.
> - That owner must close and save its files before the tenant can
sleep.
> - A failed close must keep the owner visible until retirement
succeeds.
> - This PR prepares idle resources under the exact current admission
hold, then takes a fresh safety snapshot.
> - Busy turns, uncertain closure and changed holds still prevent sleep.
> - CI also exposed a chat authorization race. The fix repeats full
authorization after the exact delivery commits.

## Linked Issues or Issue Description

Refs #18639 for local work and incoming wake boundaries. Related #18829
covers suspension receipts after admission.

**What happened?**

Idle preflight did not retire warm Native owners. Three failed-close
paths could forget an owner without proving that its provider stopped.
CI also found a false chat rejection when a delivery changed from
processing to processed between two validation reads.

**Expected behavior**

Retire only idle owners under the exact bounded hold. Wait for closure
and file collection. Retain failed owners. Scan safety after
preparation. Keep diagnostic reads passive. A newly committed chat
delivery must pass the full current authorization checks before
attestation succeeds.

**Steps to reproduce**

Finish a warm Native turn. Start an idle drain and request safety with
its owner ID. Delay or reject provider closure, or replace the hold
during preparation or scanning. The report must keep the instance awake.
For the chat race, commit the exact delivery between the first binding
read and its fallback read.

**Paperclip version or commit**

Current head `7f6f02b611dcf5a9a2b05173a44e9631eaf78058` normally
integrates actual master `1aa0c3639714f4976cfa56f95aae6e2b7d1235ac`. The
merge preserves every unrelated master path. Fresh exact-head CI and
complete review remain required.

## What Changed

- Retain uncertain Native owners after failed restart, idle timeout and
failed-turn closure.
- Prepare Native retirement through the existing heartbeat facade. Reuse
provider closure and stopped-file collection.
- Track preparation under the exact idle owner and expiry. Reject new
activity, changed holds and expired holds before and after awaited work.
- Take the final durable and local safety snapshot after preparation.
Keep diagnostic inspection passive.
- Cover ephemeral workspace retirement and useful next use, supported
plugin drain and SDK persistence, busy owners, failed closure and hold
replacement.
- Keep dedicated recovery storage explicit. Use the same validated
options for support and storage. Probe-free helpers retain the original
implementation bodies and preserve default callers.
- Complete the Native fixture through real retirement and budget
evaluation. Keep its rejection, file, credential, accounting and strict
NONE assertions.
- Repeat the complete chat authorization once if the fallback sees the
exact batch now processed. Preserve owner locks, principal and binding
checks, denial handling and the original retry deadline.

## Verification

- The support-mode regression reproduces one failure with four passes
under the old policy, then passes all five controls. It retains prior
allocation and cleanup cases. The explicit mode does not probe embedded
PostgreSQL or use an admin alias.
- The deterministic chat race baseline reproduces two authorized
failures with all four current-authority denial controls passing. Both
Slack and Discord use real PostgreSQL and the real authorization
function. The negative setup commits before the attestation transaction;
it does not claim to revoke access through a row lock.
- The product fix passes normal own App declaration emission with no
public declaration changes, plus both current normal owning compiler
programs (399 and 611 roots). The same six controls pass after the fix.
The full original file plus these controls passes all 30 tests with no
skips.
- The original controlled Native continuation passes: one test, no
failures or skips, 1.718 seconds in its body and 23.138 seconds in its
launcher. The original 40-second case and 180-second outer bounds are
unchanged. It verifies held closure, strict NONE, an ordinary authorized
comment, saved session/files, useful output, encrypted credentials,
accepted results and settled accounting. All ten observed processes and
groups close; worker connections and listeners reach zero. A separate
post-owner audit finds zero sessions; the successful owned database is
normally removed.
- Earlier preparation, HTTP, lifecycle, workspace and plugin controls
remain source-specific evidence. They are not a claim that every
final-tree test ran locally.
- The original CI assertion log is retained. The controlled race proves
a possible cause; the original CI SQL schedule was not captured. Two
other jobs lost their self-hosted runners and provided no test verdict.
Earlier asset timeouts, readiness failures and unexplained later
recovery remain separately recorded. No timeout, failure predicate or
authority check was weakened.

Focused public commands:

```sh
pnpm exec vitest run server/src/__tests__/idle-sleep-preparation.test.ts server/src/__tests__/instance-settings-routes.test.ts --maxWorkers=1 --no-file-parallelism
pnpm exec vitest run server/src/__tests__/heartbeat-reviewed-chat-binding.integration.test.ts --maxWorkers=1 --no-file-parallelism
```

Local database qualification uses fresh owned test databases on existing
PostgreSQL, bounded pools and one worker. The local allocation adapter
changes only database allocation for this test module; it runs normal
migrations and client cleanup. It is not part of the published source.
No new cluster is created.

Local acceptance measured the `0a69efa6` integration with the same
committed authorization bytes. The later normal master merge adds
startup-timeout classification and recovery changes. Those paths are
outside the controlled healthy-backend witness; retirement and
authorization hunks are preserved. Exact-head remote CI at
`7f6f02b611dcf5a9a2b05173a44e9631eaf78058` has completed with 56
successful contexts and four skips. The complete current Greptile
summary is5/5 with no new actionable findings; all review threads are
resolved. Ponytail’s current turn is explicitly paused without a
current-head verdict; earlier actual findings are fixed and accounted
for. No whole final-tree local repository build/test run, live-provider
restore or deployed suspension is claimed.

Actual master subsequently advanced to
`d5c4f7dd02d408a261cedd9a1926b9900a4aedc4`. Its local normal-merge
projection with this reviewed head preserves all20 owned paths and every
unrelated master blob and mode. Current Runner TypeScript, App
declarations and their full owning compiler programs pass. Focused
Native cleanup and warm-continuation composition checks are being
completed before merge; the new upstream suspension-retry behavior is
not inferred from the older controlled-backend witness. The remote PR
head remains unchanged.

## Risks

- Privileged idle preparation can close idle warm Native sessions. It
requires the exact current hold.
- Failed closure retains its owner and can keep the tenant awake until
normal retry succeeds.
- A changed hold cannot authorize sleep. Started cleanup remains tracked
until it settles.
- The chat repair can perform one extra full authorization read. It
keeps the existing deadline and does not grant authority from the
fallback query.
- Unsupported resources and active work retain their existing blockers.
This PR does not certify every transport, plugin or deployed host.

## Model Used

OpenAI `gpt-6.1-sol` produced the delegated changes and verification.
OpenAI Codex, based on GPT-6, performed managing review and integration.
Both used repository tools and code execution. The coordinator's exact
backend snapshot and context-window limits were not exposed.

## 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 at exact head
`7f6f02b611dcf5a9a2b05173a44e9631eaf78058`
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
at the exact current head
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Codex <noreply@openai.com>
2026-11-06 20:49:30 -06:00
Nicky LeachandClaude Opus 5.5 0b73c805e8 feat(environments): fill an unset instance default with a managed plugin environment (#19551)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A managed instance gets its instance-level environments from the
`PAPERCLIP_MANAGED_CONFIG` document, which can declare plugin
environments next to the managed sandbox
> - A platform that runs managed instances wants a new instance to start
with one of those plugin environments as its default, without changing
the default of any instance that already has one
> - #19632 made boot fill the instance default only when it is unset,
local or deleted, in one locked transaction, and removed the revert, so
every existing managed instance keeps a set default
> - This pull request adds an `instanceDefault` flag to a plugin entry.
That entry fills an unset default through the same locked fill, before
the managed sandbox does
> - The fill follows the same readiness rule as an admin's default
write, so it never moves ready agents onto a plugin that has not
prepared them
> - The platform also needs a way to know whether a release understands
plugin entries, so the release now ships a small capabilities file
> - The benefit: new instances get the plugin environment as their
default, and existing instances and admin choices are never changed

## Linked Issues or Issue Description

Refs #19632 (the locked fill-if-unset rule this builds on), #19508
(plugin entries in the managed config)

**Subsystem affected**
Server environments: the managed config parser and the managed
environment bootstrap.

**Problem or motivation**
The managed config can declare plugin environments, but it can't make
one the instance default on a new instance. An external platform also
has no way to tell whether a given release supports plugin entries
before it sends one.

**Proposed solution**
- Add `instanceDefault: true` to at most one plugin entry. Right after
that entry's boot ensure succeeds, it fills the instance default through
`fillUnsetInstanceDefault`. The managed sandbox fill runs after it.
- On a new instance the plugin environment wins. On an existing instance
the default is already set, so neither fill changes it.
- The fill declines while an active agent that follows the default
hasn't been prepared by that plugin. This is the rule the
instance-settings route enforces. When the plugin fill declines, the
managed sandbox fills as usual.
- Ship `server/src/services/managed-config-capabilities.json`, which
lists `pluginEnvironments`.

**Alternatives considered**
- A recorded one-time decision with a retry worker. It needed pending
states and extra checks for many writer and trigger combinations.
Filling only an unset default, under the existing lock, needs none of
that.
- Rejecting the fill whenever agents exist. That is stricter than the
admin route and blocks harmless cases, such as agents that are paused or
already prepared.

**Roadmap alignment**
This extends existing managed-environment behaviour. It adds no UI.

## What Changed

- `server/src/services/managed-config.ts`:
- `ManagedPluginEnvironmentSpec.instanceDefault` (boolean, default
`false`).
- The parser refuses `instanceDefault` on more than one plugin entry, on
the sandbox entry (even `false`), or as a non-boolean.
- `MANAGED_CONFIG_CAPABILITIES` and
`MANAGED_CONFIG_CAPABILITIES_SCHEMA_VERSION` constants. A plugin entry
is refused unless `pluginEnvironments` is listed.
- `server/src/services/managed-config-capabilities.json`: `{
"schemaVersion": 1, "capabilities": ["pluginEnvironments"] }`. A test
pins it to the constants and to this literal contract.
- `server/src/services/managed-environments.ts`:
- New `fillPluginInstanceDefault`. It runs right after a successful boot
ensure of the flagged entry and logs a fill or a decline. Recovery after
boot never fills.
  - The managed sandbox fill now runs once, after the plugin entries.
- `server/src/services/managed-instance-default.ts`:
`fillUnsetInstanceDefault` runs `agentsNeedSetupForEnvironmentChange`
inside its locked transaction and returns `declined:
"agents_need_setup"`. A sandbox target never needs agent setup, so the
managed sandbox fill behaves as before.
- `server/src/services/plugin-environment-driver.ts`: the readiness
query is factored into `agentsNeedSetupForEnvironmentChange`.
`assertAgentsReadyForEnvironmentChange` wraps it and still throws the
same conflict.
- `doc/DEVELOPING.md`: documents `instanceDefault`, the fill order, the
readiness decline, and the capabilities file.

## Verification

- `cd server && npx vitest run
src/__tests__/managed-plugin-environments.test.ts` (embedded Postgres),
under `instanceDefault (fill only an unset default)`:
  - A new instance gets the plugin row as its default.
  - An existing sandbox default is kept, and so is an admin's choice.
- If the plugin was down at the first boot and the sandbox filled, a
later recovery and boot keep the sandbox default.
- An admin-cleared or local default is declined while a ready or
verifying agent follows the default without the plugin's setup. The
managed sandbox then fills it.
- It fills when the agents that follow the default are paused or already
prepared, or are pinned to another environment.
  - Without the flag, nothing happens.
- A new agent that follows the default gets the plugin in
`requiredPluginIds`.
- `npx vitest run src/__tests__/managed-instance-default.test.ts`
(embedded Postgres): the earlier fill, lock and overlap cases pass. A
sandbox fill also succeeds while active agents follow the default.
- `npx vitest run
src/services/managed-environments-plugin-entries.test.ts`:
  - The fill order is plugin then sandbox.
  - When the plugin is down there is no fill, and recovery never fills.
- A failed ensure gives only the sandbox fill, and a failed fill keeps
the ensure counted.
  - When the plugin fill declines, the sandbox still fills.
- `npx vitest run src/__tests__/managed-config.test.ts
src/services/managed-config-capabilities.test.ts`: parser refusals and
the capabilities contract.
- `npx vitest run src/services/managed-environments.test.ts
src/__tests__/instance-settings-routes.test.ts
src/__tests__/environment-routes.test.ts`: pass. The route still throws
the same readiness conflict.
- `pnpm --filter @paperclipai/server typecheck` passes.
- I did not run the full `pnpm test:run`, `pnpm -r typecheck` or `pnpm
build`. CI covers them.

## Risks

- An instance whose default is unset at the first boot after this
release gets the plugin environment, if its agents are ready for it.
That covers a new instance, and an instance whose admin cleared the
default or chose the local environment. This is the intended behaviour.
- The readiness check doesn't lock agent rows. If an agent becomes ready
during the boot fill, it can miss the check, which is the same race the
admin route has. Agents created after the fill are prepared for the
plugin, because setup reads the current default.
- If the plugin is down at a new instance's first boot, the instance
keeps the managed sandbox default from then on.
- No schema change.

> 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

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, through Claude Code
with tool use (file edits, shell, test runs).

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 16:48:13 -08:00
Nicky LeachandClaude Opus 5.5 fb3cf1a072 feat(ci): retry a failed Vitest case once in PR CI and report each retried pass (#19637)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Contributors wait for PR CI before merge, so CI wall-clock time sets
the pace of work
> - PR CI runs Vitest shards with 4 workers on 4-vCPU runners, so
timing-sensitive tests sometimes time out under load
> - One such timeout fails the whole run, and a re-run costs another 15
minutes or more
> - In one 7-hour window on 2026-11-06, about 30 failed jobs were test
flakes on commits that passed on a later attempt
> - This pull request retries a failed Vitest case once in PR CI only,
and reports every pass that needed the retry
> - The benefit is fewer whole-run re-runs, while each flaky test stays
visible so that we can fix it

## Linked Issues or Issue Description

**What existing behavior does this improve?**

PR CI fails the whole run when one Vitest case fails once because of
runner load.

**Subsystem affected**

CI: the PR Vitest lanes (general, serialized, workspace and Runner
package lanes).

**Current behavior**

Vitest uses `retry: 0` everywhere. One timeout under load fails the run.
A person must notice it and re-run the failed jobs. About 20% of
recently merged PRs needed at least one re-run.

**Proposed behavior**

PR CI retries a failed Vitest case one time. A test that passes only on
the retry gets a GitHub warning annotation and a row in the job summary.
Local runs, release, cloud readiness and master keep `retry: 0`.

**Reason and benefit**

A re-run of one test case costs seconds. A re-run of the CI run costs 15
minutes or more. The report keeps flaky tests visible. Separate pull
requests fix the known flaky tests.

**Breaking changes**

None.

## What Changed

- Add `scripts/ci/vitest-retry.mjs`. It sets 1 retry when
`GITHUB_ACTIONS=true` and `GITHUB_WORKFLOW=PR`, and 0 in other contexts.
`PAPERCLIP_VITEST_RETRY` overrides the value.
- Add `scripts/ci/retry-reporter.mjs`. It writes a `::warning`
annotation and a step-summary table row for each test that passed only
on a retry.
- `scripts/run-vitest-stable.mjs` passes `--retry` to `vitest run`. The
`vitest list` collection step does not retry.
- The root `vitest.config.ts` and
`packages/paperclip-runner/vitest.config.ts` add the retry reporter
beside the existing reporters. The Runner config sets `retry` from the
same gate.
- `.github/workflows/pr-trusted.yml` reads the `CI_VITEST_RETRY`
repository variable. Set it to `0` to turn retries off without a code
change.
- Add `scripts/ci/retry-reporter.test.mjs` to `test:release-registry`,
and document the behavior in `doc/DEVELOPING.md`.

## Verification

- `node --test scripts/ci/retry-reporter.test.mjs`: 11/11 pass. The
tests cover the gate matrix, the reporter output, a real Vitest run with
a test that fails once, the wrapper arguments, and the Runner config.
- `node --test scripts/__tests__/run-vitest-stable-shard.test.mjs`:
39/39 pass.
- `node --test .github/scripts/tests/*.test.mjs`: 744/744 pass.
- Manual check: a temporary test that fails once ran through
`run-vitest-stable.mjs` and through the Runner package config. With the
PR environment it passed and wrote the annotation and the summary row.
With `GITHUB_WORKFLOW=Release` it failed. The temporary test is removed.

## Risks

- A retry can hide a flaky test. The annotation and the summary row
reduce this risk.
- A test that fails for a real reason now runs twice in PR CI, so a
failed run takes slightly longer.
- `pr.yml` loads `pr-trusted.yml` from master, so the `CI_VITEST_RETRY`
switch works only after merge. The retry itself is in the scripts and
starts with this pull request.
- Low risk otherwise: release and master verification are not changed.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with tool use and
code execution. A Claude sub-agent wrote the change, and the parent
session reviewed it.

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 16:43:02 -08:00
DottaandPaperclip 752cb8d3da fix(ui): contain patch previews and highlight diff source (#19478)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Tasks show documents and file attachments in cards and file views.
> - Patch source needs clear added and removed lines in each view.
> - Long patch lines can exceed the width of an inline preview.
> - This pull request keeps the preview inside the card and adds patch
colors.
> - Users can read a compact patch preview and open the full source.

## Linked Issues or Issue Description

**What happened?**
Patch text can exceed the inline document box. Patch files and patch
code blocks show plain text in the document view.

**Expected behavior**
Keep source inside its preview. Show added lines in green and removed
lines in red. Keep headers, source markers, copy controls, line numbers,
and downloads.

**Steps to reproduce**
1. Open a document card with a diff code block that has long unbroken
lines.
2. Open a `.patch` or `.diff` attachment in a task tab.
3. Open the same patch in the workspace file view.

**Paperclip version or commit**
Source checkout based on `e82210386f1e`.

**Deployment mode**
Built from source. The browser checks use Storybook fixtures.

Related work: #19269 adds inline diffs for file edits. This change uses
its line classifier for document and file source views.

## What Changed

- Share the unified diff line classifier with file and document views.
Track hunk lengths so later file headers keep their metadata style.
- Add safe patch source rendering for patch files and `diff` or `patch`
code blocks.
- Clip long lines with an ellipsis in compact cards. Wrap the full
source in file views.
- Add a Preview patch action for small `.patch` and `.diff` attachments,
including generic binary MIME types. Opening a large artifact list does
not fetch patch source. Bound the actual response bytes. Reject remote
preview URLs and redirects. Keep download and retry fallbacks.
- Add patch text colors with sufficient contrast in both themes. Keep
source-line selection visible over patch row colors. Copy the original
patch text without layout line breaks.
- Add five production component stories and browser checks at two widths
in both themes.
- Document the focused Storybook browser command.

## Verification

- Final base qualification at
`a120e0ada3f1eee9746f47a10384b5aa95f79824`: normally integrated the
already-merged #19610 model-fixture repair
(`8621bcf53ee2e4bbefb7d193add42dd544ca06e8`), preserving the reviewed
patch preview changes. Official preflight passes (1.8s); all 129 focused
tests pass again (23.67s), with UI typecheck and token gates passing.
Current revision CI and reviews are pending; prior-head review receipts
below are not current-head approval.

- Conflict qualification at `befc954a6116f7292506200b96623b673f9385b5`:
normally merged current master
`c66b4a55efdc5675b5a5146197078b94de6407da`, resolving the append-only
`ui/src/index.css` conflict by retaining both the patch rules and all
current agent identity rules. No feature behavior was changed during
resolution. Official isolated preflight passes. The seven focused
component/parser suites pass 129 tests; UI typecheck and token gates
pass. Fresh head CI and reviews are pending.
- Qualification setup limits: the first focused command used the
repository root instead of the UI working directory, so setup failed
before any test ran. It was corrected to the UI directory and actual
attachment-test path. The first UI typecheck found the unbuilt local
plugin SDK; building that checkout’s SDK and repeating typecheck passes.
These setup attempts are not test/typecheck passes.

- Focused Vitest run: 139 tests passed in eight files. This includes
source preservation, HTML escaping, large patches, tabs, Markdown
wrapping, line numbers, and transcript diff parsing. A 200-card check
confirms no patch fetch occurs before a preview request. CRLF
regressions cover no-newline markers and added lines that start with
`+++`.
- `pnpm --filter @paperclipai/ui typecheck`: passed after the plugin SDK
build prerequisite.
- `pnpm check:token-gates`: passed.
- Storybook catalog check and 30 map/catalog tests: passed.
- `STORYBOOK_TEST_BASE_URL=http://localhost:6006 pnpm exec playwright
test patch-preview.spec.ts
--config=tests/storybook-visual/playwright.config.ts --project=stories
--workers=2 --retries=0`: 20 passed on Linux Chromium. The checks
include accessibility, theme colors, overflow, opening a document,
wrapping source, exact clipboard contents, and the selected source line.
Screenshots were inspected and saved to the task.
- The first browser runs found contrast failures in diff text and source
gutters. Patch text tokens and patch gutter opacity now fix those
failures. The final run passes without retries.
- `pnpm verify`: exit 2. The new browser spec is a global CI input.
Required CI must supply broad coverage.
- The local full Storybook build was killed with exit 137. This is not a
build pass. External screenshot baselines are not published, so no
baseline comparison was run.
- Reviews found selected-row background precedence, file headers in
unified patches without git separators, eager patch loading across a
collection, and CRLF no-newline markers. Each finding has a focused fix
and regression checks. The Storybook hunk count now matches its source
lines.
- Prior feature commit `b3cb9d6d3c0423315540514b1ad68325a64c1cc2`: [CI
typecheck, build, tests, runner checks, and E2E
passed](https://github.com/paperclipai/paperclip/actions/runs/42247974154).
[Security scan
passed](https://github.com/paperclipai/paperclip/runs/127995160859).
[Greptile is
5/5](https://github.com/paperclipai/paperclip/pull/19478#issuecomment-6688482753),
and [Paperclip Review is
5/5](https://github.com/paperclipai/paperclip/runs/127998788846). All
six inline review threads are resolved.

## Risks

- Compact previews omit the end of long lines. The full document and
downloads keep the source.
- Patch colors apply to unified diff syntax. Other patch formats keep
literal text and do not have full format parsing.
- The shared classifier keeps the existing task chat behavior.
Regression tests cover that consumer.
- No database, API, or access rules change.

## Model Used

- OpenAI Codex, GPT-6, with reasoning, tool use, and code execution. The
runtime did not expose a more specific model ID 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
- [ ] 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

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-07 00:06:50 +00:00
Nicky LeachandClaude Opus 5.5 a2aa69bc62 perf(ci): split the Runner package Vitest lane into three duration-balanced lanes (#19646)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Contributors wait for PR CI before merge, so CI wall-clock time sets
the pace of work
> - The Runner package Vitest lane is the PR CI critical path. It
finishes a median 15.3 minutes after the push
> - That lane runs all 311 package test files in one job with 2 workers:
1,381 seconds of serial work and 727 seconds of wall time
> - Ten files account for 61% of the time. Vitest's `--shard` splits by
file count, not by duration, so it cannot balance this work
> - This pull request splits the package files into three lanes balanced
by duration, and runs the native server group in its own lane
> - The benefit is about 232 seconds of tests per package lane instead
of 727 seconds

## Linked Issues or Issue Description

**What existing behavior does this improve?**

The time that PR CI needs to run the Runner package Vitest tests.

**Subsystem affected**

CI: the `Verify Paperclip Runner` Vitest lanes in `pr-trusted.yml`, and
`packages/paperclip-runner/scripts/run-pr-vitest-lane.mjs`.

**Current behavior**

The `vitest package` lane takes a median of 13.6 minutes. It is the last
job to finish in most PR runs. The lane keeps a 2-worker limit so that
Runner and sidecar processes can start within their deadlines. Average
CPU use is 29%.

**Proposed behavior**

Three package lanes each run about one third of the files, balanced by
measured duration. Each lane keeps the 2-worker limit. The native server
group runs in its own lane, as before.

**Reason and benefit**

The Runner lane stops being the critical path. More workers per lane
would add CPU contention and timeouts, so this change adds lanes
instead. The cost is about 3 runner-minutes per run for the extra setup.

**Breaking changes**

None. The `master` ruleset requires only `ci / verify` and `ci / e2e`,
so the new job names do not change required checks.

## What Changed

- Add `packages/paperclip-runner/scripts/vitest-package-lanes.mjs`.
- It gets the file inventory from `vitest list --filesOnly --json`, so
it follows `vitest.config.ts`.
- It partitions the files with the `partitionGeneralServerSuites`
function from `scripts/general-server-shard.mjs`.
- Add `packages/paperclip-runner/scripts/vitest-lane-durations.json`.
- It uses the same schema as
`scripts/general-server-shard-durations.json`.
- It is seeded from CI run 42290920882. It measures 310 of the 311
files.
- `run-pr-vitest-lane.mjs` accepts two new arguments:
  - `--package-lane=K/N` runs one partition.
  - `--native-server` runs only the native server group.
- The `--shard=1/2` and `--shard=2/2` arguments keep their exact
behavior for the matrix that master still sends.
- `.github/ci-task-matrix.json` and the fallback matrix in
`pr-trusted.yml` have three `vitest package (K/3)` lanes and the `vitest
native server` lane. The labels keep the `vitest` prefix because
`scripts/ci-profile/trace.mjs` matches `Verify Paperclip Runner
(vitest`.
- Tests:
- the lanes cover the inventory exactly once, checked with real `vitest
list`;
  - the old `--shard` commands plan the same commands as before;
  - the manifest schema is correct;
  - bad lane arguments are refused.
- Update the Runner Vitest lane paragraph in `doc/DEVELOPING.md`.

## Verification

- `node --test scripts/__tests__/run-vitest-stable-shard.test.mjs`:
44/44 pass.
- `node --test scripts/__tests__/runner-release-crate-cache.test.mjs
.github/scripts/tests/ci-plan.test.mjs`, together with the file above:
71/71 pass.
- Related workflow, cache, routing and profile tests: 446/446, 153/153
and 14/14 pass.
- Local end-to-end run of `GITHUB_WORKFLOW=PR node
scripts/run-pr-vitest-lane.mjs --package-lane=3/3` on macOS:
- the prep steps ran, and the lane ran 104 of 311 files in 123 seconds;
- 2 tests failed: a macOS `kill EPERM` and a 5-second timeout under full
local load without the CI worker limit;
  - both files pass when run alone (35/35 tests).
- This PR's own CI runs the matrix from master, so it uses the old
`--shard` commands. The new lanes run in CI only after merge. Reviewers
can compare the job durations of the first PR runs after the merge.

| Lane | Files | Serial estimate | Wall estimate with 2 workers |
| --- | --- | --- | --- |
| 1/3 | 103 | 464.9 s | ~232 s |
| 2/3 | 104 | 465.0 s | ~232 s |
| 3/3 | 104 | 465.0 s | ~232 s |

## Risks

- The weights come from one CI log and do not include collection or
setup time. The balance can be uneven until a refresh measures real lane
runs.
- Each lane passes its file paths to Vitest as filters, and Vitest
matches a filter as a substring of the path. A path that is a substring
of another path would run a file in two lanes. No current path does
this. If one does, the script prints a warning, and no file is dropped.
- Each package lane runs `ensure:eval-build-deps` and `build:rust`
again, which adds about 3 runner-minutes per run.
- A comment in `scripts/run-vitest-stable.mjs` (about line 110) still
says that the last Runner shard runs the native group. A follow-up will
correct it.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with tool use and
code execution. A Claude sub-agent wrote the change, and the parent
session reviewed it and ran the local lane check.

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 15:12:05 -08:00
DottaandPaperclip 2e340d6235 fix(ui): show unread message counts in agent chat pickers (#19627)
## Thinking Path

> - Paperclip helps people manage AI agents and their work.
> - People switch between agent chats to read replies.
> - The agent picker does not show how many messages are unread.
> - People need that count before they select a chat.
> - The chat list already has the viewer's read state.
> - This pull request adds numeric badges from that shared list.
> - People can find unread replies without extra requests for each
agent.

## Linked Issues or Issue Description

**What existing behavior does this improve?**

The chat header agent picker and the secondary sidebar's Add chat
picker.

**Subsystem affected**

Agent Chat UI, shared task types, and the chat read-state service.

**Current behavior**

The pickers do not show the unread message count for each agent.

**Proposed behavior**

Show the unread count beside each agent. For example, show 3 for three
unread agent messages. Hide the badge when the count is zero. Keep
switching available while chat data loads.

**Reason and benefit**

People can see which chats need attention before they switch. The count
uses the existing shared request and cache.

**Breaking changes**

The chat response gains an optional `unreadMessageCount` field. Existing
fields and read receipts keep their behavior. There is no database
migration.

**Additional context**

Related: #19425 changes chat structure. This change adds counts to the
current agent pickers. The duplicate search found no PR for these count
badges.

## What Changed

- Count unread agent comments in the existing grouped read-state query.
Keep company and viewer scope.
- Exclude human messages, deleted comments, system notices, and
fast-response receipts.
- Pass memoized count maps to both agent pickers. Use a direct lookup
for each row.
- Show numeric badges and accessible singular or plural labels.
- Test count changes, account isolation, cached opens, search, and large
agent lists.
- Update the chat stories, fixture data, and development guide.
- Make the Slack owner retry-deadline test deterministic after
reproducing its CI failure.

## Verification

- On current head `05f5fa6201`, the [main CI
workflow](https://github.com/paperclipai/paperclip/actions/runs/42305845930)
passed, including build, typecheck, all applicable test shards, browser
shards, and final verification. The prior server shard 2, 6, and 7
failures do not recur.
- [Greptile's current-head
review](https://github.com/paperclipai/paperclip/pull/19627#issuecomment-6696161631)
is 5/5, its check succeeded, and both previous review threads are
resolved. Current head check inventory is complete: 55 successful
checks, three intentional skips, and no pending or failed checks. The
Paperclip application review summary reports paused; no new completed
Paperclip review is claimed. Its existing findings are resolved, and the
independent current-head Greptile review is 5/5.

- Current head `05f5fa6201` merges master `8621bcf53e` to resolve an
import conflict. Master now includes the same model-default test repair.
This branch keeps its upstream import, so that file no longer differs
from master.
- After this merge: all 21 server tests in the Slack owner and
model-default suites pass, all 22 tests in the three picker/sidebar
suites pass, and token gates pass. The standard preflight still cannot
build Rust because `cargo` is absent. Fresh CI must supply the broad
checks.

- Head `7d125fb8c7` replaces the Slack owner test's real timer wait with
the worker's existing clock input. It checks that the intent stays
pending one millisecond before the retry deadline and clears at the
deadline. All 15 Slack owner integration tests pass locally. Runtime
retry behavior is unchanged.
- On `4cfb1e9d55`, both review checks gave 5/5. CI [server shard
2](https://github.com/paperclipai/paperclip/actions/runs/42302458830/job/128183671349)
failed the Slack credential-lease retry test. The same assertion failed
in an unchanged local run. A diagnostic run with added logging passed;
the exact timer deviation was not captured. The new test removes the
real-time wait assumption and checks the clock boundary directly. The
earlier model-default and cleanup failures did not recur in that CI run.

- On `a3378dfc40`, both Greptile and Paperclip Review gave 5/5 with no
open findings. Typecheck, build, all eight browser shards, and most test
shards passed.
- That CI attempt failed two server shards. The model-default test still
expected `gpt-5.6-sol`, while the current default is `gpt-6.1-sol`. I
reproduced both failures locally. Commit `4cfb1e9d55` uses the exported
default-model constant; all six tests in that suite now pass. Production
model selection does not change.
- The retained-cleanup backlog test exceeded its 15-second limit in
[server shard
6](https://github.com/paperclipai/paperclip/actions/runs/42299858777/job/128175193320).
The unchanged test passes locally with the same limit. Its CI timeout
cause is not established. No assertion or timeout was changed. The fresh
CI run must recheck it.

- Review repair: commit `0db631b215` keeps the existing-chat and
unread-agent arrays stable when chat data and the active agent do not
change. A new 500-agent test fails before the repair and passes after
it. The test also checks count refreshes.
- The first CI typecheck failed on duplicate `IMAGE_ONLY` and
`TESTOPS_REQUESTED` keys in `tests/runner-e2e/workflow-target.test.ts`.
This was present in upstream code. Master commit `e482f0f632` removes
the duplicate keys. This branch now includes that commit. All nine
workflow-target tests pass locally.
- After the latest master merge: all 22 tests in the three affected
picker/sidebar suites pass. Before that merge, all 38 focused UI tests
passed.
- The current head is `05f5fa620134ad199a3d85b66fb2eb93d3bb6077`. All
current status checks are complete, the aggregate verify gate succeeds,
mergeability is CLEAN, and no unresolved review threads remain. The
maintainer has instructed normal merge after checks pass.

- After merging current master: 37 focused UI tests pass across
AgentChatPicker, CoordinatorAgentSwitcher, AgentConversationsSidebar,
useAgentChatRead, and SidebarAgentChats.
- After merging current master: all 38 proactive-chat integration tests
pass with a real disposable PostgreSQL database. They check counts of 2,
1, and 0 at exact read cutoffs.
- The prior revision passed UI typecheck and build, shared build,
isolated low-memory server typecheck, token gates, and 30 map/catalog
tests.
- The 500-agent test bounds index work and count lookups. Search does
not rebuild the existing-chat index.
- Browser checks used production components with simulated API data.
Dark, light, mobile, and Add chat cases passed. Counts of 3 and 12
stayed visible through search. Read agents had no badge. Cached opens
made no chat API requests.
- Twenty local cached opens took 34.5–57.6 ms, with a 38.4 ms median.
This is an unthrottled fixture measurement.
- Earlier full local checks could not complete because Rust cargo is
absent and the workspace has limited memory. The standard worktree
preflight also stops at missing cargo. Required CI must supply broad
checks for this PR head.
- The first server typecheck ran out of memory while Storybook was
active. Its isolated low-memory retry passed. No visual baseline
comparison or live provider delivery is claimed.

## Risks

- Low risk. The count replaces a boolean aggregate in the same grouped
query. Very long chat histories still need that existing scan.
- A count can be stale until the existing chat-list cache refreshes.
Read receipts still control the unread cutoff.
- The change adds no polling, per-agent history request, database
migration, or permission change.

## Model Used

OpenAI GPT-6 through Codex, with code editing, terminal tools, and
browser verification. The runtime did not expose a more specific served
model ID 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>
2026-11-06 17:10:56 -06:00
Nicky LeachandClaude Opus 5.5 f2299cb00f feat(ci): re-run failed PR jobs once when every failure was a lost runner (#19640)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Contributors wait for PR CI before merge, so CI wall-clock time sets
the pace of work
> - PR CI runs on self-hosted AWS runners, and these runners are
sometimes lost mid-job
> - On 2026-11-06, 21 of 51 failed jobs on commits that later passed
were runner loss. The losses came in fleet-wide bursts, for example 10
jobs on 10 instances in 51 seconds
> - After each loss, a person must notice the failure and click "Re-run
failed jobs"
> - This pull request adds a workflow that re-runs the failed jobs once,
only when every failure was a lost runner
> - The benefit is fewer manual re-runs and a shorter wait for CI to
pass

## Linked Issues or Issue Description

**What existing behavior does this improve?**

The recovery of PR CI runs that failed only because a self-hosted runner
was lost.

**Subsystem affected**

CI: the trusted PR workflow (`pr.yml` → `pr-trusted.yml`).

**Current behavior**

When an AWS runner is lost, the job fails with "The self-hosted runner
lost communication with the server" or "The runner has received a
shutdown signal". The PR stays red until a person re-runs the failed
jobs.

**Proposed behavior**

When the `PR` workflow completes with a failure on attempt 1, a new
workflow examines the failed jobs. If every failed job lost its runner,
it re-runs the failed jobs one time. If any job failed for another
reason, it does nothing.

**Reason and benefit**

A runner loss is not a code problem. The re-run starts without waiting
for a person to notice the failure.

**Breaking changes**

None.

## What Changed

- Add `.github/workflows/ci-runner-loss-rerun.yml`. It triggers on
`workflow_run` for `PR`, and it acts only on attempt 1 failures of
`pull_request` runs in this repository. It runs on `ubuntu-latest`, so
it does not depend on the AWS fleet.
- Add `.github/scripts/runner-loss-rerun.mjs`. The script:
- lists the attempt-1 jobs and ignores the aggregate jobs `ci / verify`
and `ci / e2e`;
- finds runner loss in the check-run annotations. If the only annotation
is "The operation was canceled.", it reads the `##[error]` lines in the
job log;
- calls `rerun-failed-jobs` only if every remaining failed job lost its
runner;
- does not re-run when the gate job failed, the PR head moved, the PR is
closed, or a newer run exists for the same commit;
- writes the decision and a job table to the step summary. A `--dry-run`
mode never posts.
- Add 16 tests, with trimmed fixtures from four real runs.
- Add a paragraph about the workflow to the "Trusted PR Workflow"
section of `doc/DEVELOPING.md`.

## Verification

- `node --test .github/scripts/tests/runner-loss-rerun.test.mjs`: 16/16
pass. The tests cover:
- re-run when all jobs were lost, including the case where the signal is
only in the log;
- no re-run for mixed failures, real failures, only aggregate failures,
attempt 2, a failed gate, or a stale run;
- pagination, incomplete listings, a cross-host link that is refused,
and the workflow guards.
- `node --test '.github/scripts/tests/*.test.mjs'`: 760/760 pass.
- A read-only dry run against the real GitHub API for six recent runs
classified all six correctly.
- The workflow can run on GitHub only after it is on master. Reviewers
can make sure that the first runner-loss failure after the merge
triggers one re-run.

## Risks

- **Trust:** a re-run of failed jobs uses the outputs of the gate job
that succeeded on attempt 1, including its AWS runner admission. A
person who clicks "Re-run failed jobs" gets the same result. The only
difference is that `github-actions[bot]` triggers attempt 2. The
workflow never checks out or runs PR code.
- **Failed gate:** if the gate job itself failed, the script does
nothing. A re-run by the bot would put all jobs on GitHub-hosted
runners.
- **Profiling:** `scripts/ci-profile/export.mjs` exports only attempts
triggered by authorized users. The bot-triggered attempt 2 is not
exported to Honeycomb. Attempt 1 is still exported.
- **Events:** GitHub may not create `workflow_run` events for attempts
that `GITHUB_TOKEN` started. Then other `workflow_run` consumers do not
react to attempt 2. Required checks still update.
- **Permissions:** `actions: write`, `checks: read`, `contents: read`
and `pull-requests: read`. The last one lets the script confirm that the
run still belongs to the open PR's current head.
- **Cancelled jobs:** a runner loss where the lost jobs end as
`cancelled` and only the aggregate jobs show `failure` is not re-run.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with tool use and
code execution. A Claude sub-agent wrote the change, and the parent
session reviewed it.

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 15:05:42 -08:00
Nicky LeachandClaude Opus 5.5 913102870d fix(environments): fill the managed instance default once, under a lock (#19632)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - On a managed instance under `enableManagedSandboxOnly`, boot points
the instance default at the managed sandbox when nothing deliberate is
set
> - That write read the default and wrote it later without a lock. Two
overlapping boots, or a boot and an admin write, could overwrite a value
the other had just committed
> - A revert path also reset that stamped default whenever the mode was
turned off, so a platform-filled default could change again later
> - A planned plugin-environment default should fill only an unset
default and never change a set one, which needs every instance's default
to stay set
> - This pull request makes the fill one locked transaction and removes
the revert, so a filled default is an ordinary set value
> - The benefit is a single, race-free rule: boot fills an unset default
once, and nothing changes a set default afterwards

## Linked Issues or Issue Description

Refs #19551 (the plugin-environment default that builds on this rule)

**Subsystem affected**
Server environments: the managed environment bootstrap and the instance
settings route.

**Problem or motivation**
`applyManagedEnvironments` read the instance default, decided, and wrote
it in separate steps with no lock, so a concurrent boot or admin write
could be overwritten. When `enableManagedSandboxOnly` was not declared,
a revert reset a default the platform had filled. That needed a
`managedDefaultStamped` marker, plus a marker clear on every admin
default write. A later boot could therefore change a default that had
already been set.

**Proposed solution**
Fill the default in one transaction that locks the instance default row
and rechecks it. Fill only an unset, local or deleted default. Remove
the revert and its marker, so a filled default behaves like any other
set value.

**Alternatives considered**
Keeping the revert and adding locks to it. A revert on a mode change
would still move an existing instance's default later, which a fill-only
plugin default cannot tolerate.

**Roadmap alignment**
This narrows existing managed-environment behaviour. It adds no product
surface.

## What Changed

- New `server/src/services/managed-instance-default.ts`:
`fillUnsetInstanceDefault(db, environmentId)`. In one transaction it
creates the settings row if needed, locks the instance default row (`FOR
UPDATE`), and rechecks the current value. It writes only when the
default is unset, names the local environment, or names a deleted
environment. Any other set default is kept.
- `server/src/services/managed-environments.ts`:
- Under `enableManagedSandboxOnly`, the managed sandbox fill now uses
that helper, through a new `fillInstanceDefault` test seam.
- The mode-off revert and the `managedDefaultStamped` marker are
removed.
- The unused `instanceSettings` seam option is removed, along with the
`getById`, `update` and `findManagedSandboxEnvironment` methods of the
environments seam.
- `server/src/routes/instance-settings.ts`: an explicit default write is
a plain `update` again. The marker clear and its transaction are gone.
- `doc/DEVELOPING.md`: the "Managed environments" section states the
fill rule.

Existing rows may still carry `managedDefaultStamped` in their metadata.
Nothing reads it any more, and it is not part of the managed stock hash.

## Verification

- `cd server && npx vitest run
src/__tests__/managed-instance-default.test.ts` (embedded Postgres):
- The fill writes an unset default, including on a fresh instance with
no settings row. It also writes a default that names the local
environment, or one whose environment was deleted.
- It never changes a default set to an ssh, plugin or other sandbox
environment, and leaves a default that already names the target alone.
- Controlled overlap: an uncommitted admin default write makes the fill
wait, and the fill then keeps the admin's value. This test fails without
the row lock.
  - Two overlapping fills: exactly one writes.
- Real boot pass: the default is filled under managed-sandbox-only and
stays the same after a boot with the mode off. A set default stays on
every boot.
- `npx vitest run src/services/managed-environments.test.ts
src/services/managed-environments-plugin-entries.test.ts`: the fill runs
only under managed-sandbox-only, with the managed sandbox row. It never
runs for a plugin environment. Nothing is written when the mode is off.
A failed fill does not fail the ensure.
- `npx vitest run src/__tests__/instance-settings-routes.test.ts`: an
explicit default write is a plain update that touches no environment
row.
- `npx vitest run src/__tests__/managed-plugin-environments.test.ts
src/__tests__/environment-routes.test.ts
src/__tests__/server-startup-feedback-export.test.ts
src/__tests__/instance-settings-service.test.ts`: pass.
- `pnpm --filter @paperclipai/server typecheck` passes.
- I did not run the full `pnpm test:run`, `pnpm -r typecheck` or `pnpm
build`. CI covers them.

## Risks

- Behaviour change: when `enableManagedSandboxOnly` is turned off for an
instance, a default the platform filled with the managed sandbox now
stays. Local execution is still allowed then, but it is no longer the
default unless an admin picks it.
- No schema change. Stale `managedDefaultStamped` keys stay in some row
metadata and are ignored.
- The fill holds the instance default row lock for one short transaction
at boot.

> 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

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, through Claude Code
with tool use (file edits, shell, test runs).

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 15:01:58 -08:00
DottaandPaperclip fdda02a26e fix(ui): remove stale plan approvals from the composer (#19528)
## Thinking Path

> - Paperclip helps people manage AI agents and their work.
> - A task can ask a person to approve a saved plan.
> - The server refuses approval after a newer plan replaces that plan.
> - The document and request queries can finish at different times.
> - The composer can then keep controls for a plan that is already out
of date.
> - This change removes those controls when a newer saved revision is
known and refreshes the request state.
> - People can review the current plan without an obsolete approval
above the composer.

## Linked Issues or Issue Description

**What happened?**

An old plan approval can stay above the task composer after the plan
changes. Selecting Approve returns a superseded error. The failed action
does not refresh the request list.

**Expected behavior**

Remove the old approval and its pending count as soon as the UI knows
that the plan has changed. Keep a newer approval visible if its document
query still has an older revision. Preserve accepted decisions and
unrelated requests.

**Steps to reproduce**

1. Create a confirmation for a saved plan revision.
2. Save a newer plan revision while the old request remains in the
browser cache.
3. Read the composer before the request query finishes.
4. Try an old approval after the server has expired it.

**Paperclip version or commit**

Source checkout based on `5d25117ffa`.

**Deployment mode**

Source checkout. The regressions use the production React components and
query cache in jsdom.

Related work: Refs #14907 (replaced request receipts) and Refs #15025
(server replacement for requests from board users). This change fixes
the interval between document and request reads, plus the refresh after
a failed resolution. It does not change those server or history rules.

## What Changed

- Remove pending approvals for older saved plan revisions from the task
display and composer.
- Compare revision numbers, or document and request times for targets
that have only a revision ID. Keep newer requests when the document
cache is behind.
- Refresh request queries after document activity and settled approval
errors.
- Use the same plan freshness check for recovery retry. An old hidden
approval no longer blocks Retry agent.
- Test the recovery controls and the guards for missing plans, accepted
decisions, questions, other tasks, other companies, and older document
reads.
- Add regressions for both workspace presentations, task and
conversation modes, revision formats, unrelated requests, and accepted
history.
- Document the display behavior in the development guide.

## Verification

- TDD: five assertions failed before the main fix. Old controls stayed
in the composer, document activity did not refresh requests, and
superseded accept or reject responses did not read the new state.
- The previous session recorded 815 passing focused UI tests after the
recovery retry fix at `d95cf3235ed83dc1f6c7f51372dff408814eb15c`. UI
typecheck, the production UI build, and token gates also passed.
- The main fix at `5147fd29a03413596d5b2445ae3b480352cbff1a` passed all
CI gates. This includes typecheck, build, general tests, and eight E2E
shards. [CI
run](https://github.com/paperclipai/paperclip/actions/runs/42266101662).
- The prior affected local run passed 7,656 UI tests, with one skipped,
and 38 shared tests. Its CLI phase had two file-mode failures under the
agent's `0077` umask and a child-server timeout during first-use builds.
All three CLI files passed after a new check with `umask 022` and warm
build dependencies: 25 tests passed. No CLI source changed. The initial
full command did not pass or store a reusable pass.
- On this continuation, the local test command could not start because
the restored workspace has no installed Vitest dependency. No test
verdict came from this attempt.
- Final
[CI](https://github.com/paperclipai/paperclip/actions/runs/42302544154)
passes all applicable required gates for
`d95cf3235ed83dc1f6c7f51372dff408814eb15c`, including typecheck, build,
general tests, and eight E2E shards. Greptile and Paperclip reviews both
report 5/5 at that exact revision, with no unresolved findings. The
separate advisory review workflow remains queued.
- No live browser acceptance or deployment is claimed.

## Risks

- The UI must distinguish an older approval from an older document
cache. Tests cover both query orders and preserve newer approvals.
- This is a display and cache refresh change. Stored decisions, server
authorization, approval gates, and database schemas are unchanged.

## Model Used

OpenAI GPT-6 through Codex, with reasoning, tool use, and code
execution. The exact deployment model ID and context window size are not
exposed in this environment.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with available 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 following the bug template
- [x] I have not referenced internal/instance-local Paperclip issues or
links
- [x] My remote 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 for the final revision
(scope and initial environment failures are stated above)
- [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>
2026-11-06 16:25:51 -06:00
DottaandPaperclip 44c60c7221 Verify default skill sync through two real cold sleep cycles (#19191)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Automatic skill sources check upstream every five minutes.
> - The domain deadline contract can hand future work to a durable wake
alarm.
> - A saved deadline or a worker unit test does not prove that a stopped
tenant resumes the real producer.
> - This pull request checks the default cadence through the actual app
and a matching service checkout.
> - It checks two cold starts and three distinct persisted skill
revisions with real clocks.
> - The benefit is repeatable local evidence without changing production
timing or authority.

## Linked Issues or Issue Description

Refs: #19001, #17008, #17923.

This is a test and documentation follow-up to #19001. #19001 is now
merged; this PR targets master. Feature code remains in that merged
foundation. #17008 covers the earlier source worker change. #17923
covers separate skill-cache retention; this PR does not change that
behavior.

A scoped search of public PRs and issues found no duplicate
default-cadence cold-cycle acceptance test. No matching public issue was
found. The enhancement fields follow.

**Pre-submission checklist**

This improves checks for an existing feature. It adds no product
endpoint or execution authority. The public related-work search is
complete.

**What existing behavior does this improve?**

Verification of automatic skill-source updates across a durable idle
handoff and cold restart.

**Subsystem affected**

`server/` test fixtures and development documentation.

**Current behavior**

Domain tests cover claims, access and future deadlines. They do not
prove the full default-300-second path from ordinary source attachment
through signed tenant reports, durable alarms, stopped compute and a
changed persisted skill.

**Proposed behavior**

An opt-in launcher checks bootstrap first, then two full real-clock
cycles. Ordinary CI can run the transport controls without the host
fixture. The launcher-specific worker assertion runs only when prewire
is requested, and fails closed in that lane.

**Reason and benefit**

The test can detect an early refresh, a lost deadline, a stale proof, an
ACK after physical stop, a failed cold restart or a producer that does
not publish changed contents.

**Breaking changes**

None to product APIs, schema, cadence, authorization, claims or retry
policy. Existing maintenance-helper defaults stay unchanged.

**Additional context**

The opt-in host flow needs an authorized matching service checkout, its
normal compiled acceptance bridge, Node 22 and two owned PostgreSQL test
databases. The standalone controls do not need that service or
PostgreSQL. Roadmap review places this under existing Skills Manager and
Cloud deployment verification, not a new core feature.

## What Changed

- Add an opt-in default-cadence acceptance test and checked-in launcher.
- Reuse real server startup, managed tenant authority and the ordinary
project attachment route. Control only the remote Git snapshot boundary;
keep actual authorization, scanning, claims and publication.
- Use actual signed tenant routes and the matching service's gate, sleep
controller and PostgreSQL wake-alarm store. Stop and restart real app
children through a controlled local provider.
- Preload the Node transport guard before coordinator, worker and child
module work. Check worker-local and child PID, thread and source-hash
receipts. Keep caught unexpected transport attempts fatal.
- Require both persisted refresh times and actual upstream handler
timestamps to be at or after each original deadline.
- Join physical callbacks during bridge close, stop a late wake-created
child, and preserve the original cleanup budget. Add a real
IPC/HTTP-child counterfactual.
- Accept valid owned HTTP options paths without allowing Unix sockets or
unknown origins. Remove the unused App helper export.
- Add finite transport and launcher controls. Defer only the
launcher-specific parent assertion in vanilla CI. Keep all subprocess
controls default-runnable.
- Add optional child entry, preload and bounded pool settings to the
existing test helper. Preserve its defaults and the real observer test
body.
- Remove added explanatory comments under the contribution policy.
Preserve executable syntax, directives and literals.
- Document pinned setup, fresh owned databases, bootstrap and full
two-cycle commands in `doc/DEVELOPING.md`.

The diff against the intended base contains nine test/helper/launcher
files and this one document. It adds no production feature code or Cloud
source to the App repository.

## Verification

The latest two-file CI repair preserves both original failed jobs. A
newer master workflow introduced two required step inputs absent from
its extracted-step test environment; the faithful false/false inputs now
pass all five existing target-authorization cases, after an actual
missing-input counterfactual failed. A controlled socket case also
reproduces legal reuse of the released runner port; the fixture now
holds that reservation until the preview binds, releases it in finally,
and asserts distinct ports. All original retry/result/accounting
assertions and timeouts stay unchanged. The original Linux listener
owner remains unknown; the control proves this fixture collision
mechanism, not that original attribution. Fresh current-head full CI and
complete reviews are pending.


Current merge-integration candidate:
`f6f686103b7bfd0a4ab83085634c622af3896ecb`, a normal merge after #19001
landed, including actual master
`1c9767d323cf872a266962b9e6b4bd5cbcb57f1c`. All nine acceptance code
files are byte-identical to148a82e5; both parents' documentation
additions survive. Every other path equals actual master. The only
conflict was the old foundation's startup block; current master was
retained in full. Fresh exact-head CI and complete reviews are pending.
The local measurements below belong to their explicitly named revisions;
no fresh full614-second run is claimed.

Current candidate: `148a82e54c502759785407357001c6b50c1439dd`, normally
carrying the current base `8c912e1ba4fc66397a7341ade59373af8075068f`.
All nine acceptance code blobs remain identical to qualified repair
`e092746f4da181c8414c63be71474619a84b97e7`; documentation retains both
parents. The matching built service for the fresh bootstrap is
`389878364b42dd129835d263f91882c5774d5123`, using Node 22.23.4. The App
uses Node 24.22.2 and pnpm 9.15.4.

Use the exact controlled setup and commands in
[doc/DEVELOPING.md](doc/DEVELOPING.md#controlled-default-cadence-sleep-acceptance).
Fresh owned databases and the matching compiled service are
prerequisites; the launcher does not create a cluster or build
dependencies.

- **Current affected semantic check passed**, using actual native
TypeScript 7 and the current generated CI options/references (0.640
seconds). Normal declaration references passed in 11.726 seconds, with
source-matched SDK/shared/kernel/Runner prerequisites and the frozen
current lockfile.
- **Current guarded controls: 44 passed**, plus the same single explicit
real-PG observer deferral, in 4.790 seconds. The executing worker
checked its own global PID/thread/preload source hash and matching
receipt. Guard hash:
`7daf9ae7d2f26e8fcd389b1d560fac1d4e218a8304a2c58e49f646af108165bc`. No
unexpected attempts or PG sockets occurred. Vanilla controls on the
identical repair files passed 22 cases with one explicit launcher-parent
assertion deferral (2.044 seconds).
- **Real cleanup counterfactual:** unchanged old helper failed the
actual endpoint assertion in 1.568 seconds: its late HTTP child remained
reachable after close returned. The same fixed-helper case passed in
1.485 seconds: close waited, the child exited, the port was unreachable
and no IPC error occurred. The isolated driver records only the known
legacy closed-IPC error long enough to inspect cleanup; current helper
requires zero such errors. All recorded processes and ports were
independently checked empty.
- **Fresh current bootstrap passed once**, 16.159 seconds wall / 14.12
seconds Vitest / 12.237 seconds body. The ordinary enabled producer
persisted useful revision 1, cleared its lease and retained exactly
300,000 ms between success and original next deadline. A signed
current-generation report produced the matching
generation/operation-lock SQL ACK before physical child stop (ACK
06:54:02.020 UTC; stop signal 06:54:02.025 UTC). The alarm retained the
original D and D-120 eligibility. Both fixture databases ended with zero
sessions; the coordinator independently audited and normally removed
them. This bootstrap does not execute a due wake or the new v2/v3 timing
assertions.
- **Historical full two-cycle result remains 1/1 passed in 614.213
seconds wall**, at measured App
`74f7c012ca17ad0d7302d76403f5033affb1430b` and service
`2cb54f904031dcf69a32902cd853b43f74d6f301`. Two new processes published
distinct immutable v2/v3 at original D+115 ms and D+98 ms. Exact signed
SQL ACKs preceded both physical stops; real SQL D-120 claims caused both
cold starts. Features, claims and original business deadlines stayed
unchanged.
- Both historical 10.002-second quiet windows kept app SQL, upstream and
outgoing HTTP counts unchanged. Two awake PG sockets remained. Quiet
counts do not mean all connections closed.
- The stronger timing checks are additional assertions, not
retroactively executed results. Offline inspection of the original
receipts confirms persisted successes at D+115/+98 ms and earliest
upstream handler entries at D+44/+30 ms; all five requests in each
refresh group started after D. The exact new pre-sleep request counter
and dispatch-before-handler time were not independently recorded
historically.
- Source review found 19 critical automatic Git producer/runtime files
identical to the measured App. The current active cache helper change
does not run on automatic Git publication and adds no pool. The matching
service carries unchanged measured helper/sleep/controller/alarm seams
through its normal master merge. The current bootstrap and focused
controls qualify the changed cleanup/guard and parent integration. No
fresh current-head 614-second pass or whole-tree identity is claimed.
- Runtime is serialized: worker 1, per-pool limits at most 4, configured
App potential 10 + shared service pool 2 + one observer against server
max 40. Current bootstrap point samples observed at most 3 owned clients
plus the observer; those samples are not a continuous aggregate peak.
App/service guard peaks were 2 each, with zero remaining sockets at
cleanup.

Failures remain accounted for. The first historical bootstrap cleanup
masked an unknown primary error. Later attempts exposed missing
fixture-owned domain metadata and lost origin snapshots; test-only
ownership/cleanup corrections preserved the original assertions and
timeouts. The new causal driver first lacked a final observation, then
encountered sandbox bind EPERM, then exposed the old closed-IPC error;
only the final real endpoint failure above is labeled the cleanup
counterfactual. An offline dependency miss and a generator-cleared
ignored compiler config were retained and corrected without weakening
compiler options. The former inherited policy failure (397 findings) is
resolved by the genuine current-master base/scanner, with zero findings
and seven scanner tests; no unrelated UI site was edited and the gate
was not relaxed.

Historical real TCP observer coverage passed 1/1 in 3.688 seconds.
Comment-only and opt-in-selection carries remain documented in prior
evidence; self-hash changes are metadata exceptions with fresh
executing-worker checks.

The full workspace typecheck, test, build and browser commands were not
run locally for this test-only slice. The current base passes its full
exact-head CI and Greptile 5/5; this leaf now has all 56 exact-head
check runs terminal (54 success, one neutral, one skip), the additional
legacy security status passing, complete current Greptile 5/5 and
Ponytail 5/5 reviews, and all four review threads resolved across all
pages. No live provider or deployed host/database suspension was
exercised.
## Risks

- The host test requires a matching service checkout and compiled
bridge. An unrelated service revision is not a valid substitute.
- Controlled localhost Git, S3 and physical process operations do not
qualify deployed Railway or Neon suspension, external permissions or
provider uncertainty.
- The Node guard does not prove native subprocess transport isolation.
Only finite local Git metadata and Node version commands were needed.
- Two short SQL/HTTP quiet windows do not establish strict 90-second
host acceptance. Separate plugin-host LISTEN, MCP wake and other domain
gaps remain open.
- Explicit test URLs are destructive fixture inputs. Use fresh, owned
`_test` databases. The launcher does not start a cluster or choose a
database implicitly.
- Passing CI and review do not qualify deployed suspension; the current
proof boundaries above still apply.

> For core feature work, check `ROADMAP.md` first and discuss it in
`#dev` before opening the PR. This PR adds verification to the existing
feature in its base.

## Model Used

OpenAI `gpt-6.1-sol` assisted with implementation, repository review and
local code execution. OpenAI Codex, based on GPT-6, performed managing
review and integration. The context-window sizes and exact served
backend snapshots were not exposed.

## 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 and contains no internal
Paperclip ticket id
- [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 — fresh merge-head gates pending
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups —
fresh merge-head review pending
- [x] I will address all Greptile and reviewer comments before
requesting merge


### Current master reconciliation (2026-11-06)

Merged actual master `e28158b353fd274f0322be76d62cd223e0df599f`
normally. All nine qualified acceptance code files and the held-port
repair remain byte-identical. Upstream independently landed the workflow
input fix in #19602; the fixture now uses that exact upstream version
once, avoiding duplicate object keys in a squash merge. All other master
changes are preserved. The earlier two-cycle local evidence remains
source-specific; no fresh 614-second run or deployed suspension is
claimed. This new head requires fresh CI and bot reviews.

### Actual combined-tree typecheck failure and repair

CI job `128156887548` failed with TS1117 at workflow-target.test.ts:22:
two independently landed master fixes declared the same `IMAGE_ONLY` and
`TESTOPS_REQUESTED` keys. The complete original log is retained. A
further normal master merge now removes the duplicate declarations,
retaining exactly one false/false pair and every original assertion. All
nine qualified acceptance code paths and the held-port repair remain
byte-identical; unrelated master changes are preserved. This is a
concrete compiler failure and source repair, with fresh exact-head
CI/reviews required.

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-06 15:55:05 -06:00
DottaandClaude Opus 5.5 02a2299173 feat(codex): default Codex to gpt-6.1-sol, half the gpt-5.6-sol price (#19623)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Codex agents run through Paperclip Runner or the legacy
`codex_local` harness, and the runner E2E suites run paid Codex cells
> - The shared Codex default and many selections preferred `gpt-5.6-sol`
> - The reviewed OpenAI rate card in
`server/src/services/codex-pricing.ts` (`openai-standard-2026-09-30`)
prices `gpt-6.1-sol` at $2 input / $0.10 cached / $10 output per 1M
tokens, and `gpt-5.6-sol` at $4 / $0.40 / $20
> - So every default run and every paid Codex eval cell cost twice as
much as necessary
> - This pull request moves every place that prefers or selects
`gpt-5.6-sol` to `gpt-6.1-sol`, and keeps historical facts, rate cards
and compatibility fallbacks on `gpt-5.6-sol`
> - The benefit is half the token price for new default Codex agents and
for the Codex E2E and TestOps cells

## Linked Issues or Issue Description

**What existing behavior does this improve?**
The default Codex model for new agents and the Codex model that the
runner E2E suites and TestOps plans select.

**Subsystem affected**
Adapters (`adapter-utils`, `codex-local`), server native runtime
fallback, UI AI connection pools, Paperclip Runner devtools and live
evals, runner E2E catalog and TestOps mappings.

**Current behavior**
New Codex agents without an explicit model store `gpt-5.6-sol`. The
runner E2E `runner-codex` profile, the Reliability `queue-steer` plan
cell, the Product regression TestOps mapping and the ACPX Codex
qualification selection all use `gpt-5.6-sol`.

**Proposed behavior**
They use `gpt-6.1-sol`. Existing agents that store a model keep it.
`gpt-5.6-sol` stays selectable.

**Reason and benefit**
`gpt-6.1-sol` costs half as much per token on the in-repo reviewed rate
card. The current OpenAI pricing page (retrieved 2026-11-06) shows the
same short-context rates and also lists long-context rates of $4 / $0.20
/ $15 for `gpt-6.1-sol` against $8 / $0.80 / $30 for `gpt-5.6-sol`.

**Breaking changes**
None for stored configurations. See Risks.

## What Changed

Changed defaults and selections (all now `gpt-6.1-sol`):

- `PAPERCLIP_RUNNER_DEFAULT_MODELS.codex` in
`packages/adapter-utils/src/paperclip-runner-permissions.ts`. This also
changes `DEFAULT_CODEX_LOCAL_MODEL`,
`resolvePaperclipRunnerModel("codex", …)`, runner config normalization,
`codex_local` → Paperclip Runner conversion, the UI new-agent and
agent-config defaults, the composer default model and the public MCP
effort lookup.
- `codex-local` `models`: the 5.6 entry is now the literal
`gpt-5.6-sol`, because it used to be `DEFAULT_CODEX_LOCAL_MODEL`. The
list order and contents do not change.
- AI connection pool: a new OpenAI member profile uses
`PAPERCLIP_RUNNER_DEFAULT_MODELS.codex` instead of a hard-coded
`gpt-5.6-sol`.
- Paperclip Runner devtools ACPX Codex default and preset, the
`runner-codex-sol` local provider smoke, and the `acpx-codex-sol` live
workflow candidate.
- `tests/acpx-qualification-models.ts` Codex selection (runner E2E and
runner acceptance ACPX Codex profiles).
- Runner E2E: the `runner-codex` profile follows the default, so all
native Codex cells move. This includes the `runner-codex` cells among
the 52 standard `everyday-workflows` cells and the seven Codex
reliability cells. `runner-codex-mini` stays on `gpt-5.4-mini`. The
Reliability plan `queue-steer` `steeringProfile` is now
`['runner-codex', 'gpt-6.1-sol']`. Its executionId
(`everyday-workflows.runner-codex.daytona.queue-steer`), its fullName
and its TestOps case identity do not change. No separate profile is
necessary.
- `product-regression-testops.mjs`: the declared model for every
`runner-codex` case is now `gpt-6.1-sol` (it was already that for
`configured-repository`).
- `tests/runner-e2e/installed-cli.ts`: the credential-free installed
startup proof opens a session on the default model.
- `tests/runner-e2e/scheduled-prices.json`: add a `gpt-6.1-sol` price
(`openai-standard-2026-11-06`, including 30m/12h cache writes and
long-context rates from the OpenAI pricing page). The weekly scheduled
Codex cells need an exact price for their model, or admission fails
closed.
- Storybook: the composer model picker fixtures, the connection pool
stories and host, and the agent settings preview show `gpt-6.1-sol` as
the default.
- Docs: `doc/DEVELOPING.md` (the Codex conversion default) and
`tests/runner-e2e/EVERYDAY-WORKFLOWS.md` (local matrix, reliability
extras, `queue-steer` row).
- Tests that assert the default now expect `gpt-6.1-sol`. New
assertions: the default has the `0.159.0` CLI floor, the compatibility
fallback is floor-free, the `queue-steer` plan cell runs `runner-codex`
on `gpt-6.1-sol`, and all native Codex everyday cells (standard and
reliability) use `gpt-6.1-sol`.

Deliberately kept on `gpt-5.6-sol`:

- Rate cards: `server/src/services/codex-pricing.ts` and
`packages/paperclip-runner/src/evals/model-pricing.ts`. Old receipts
need them. (The runner eval rate card has no `gpt-6.1-sol` entry. An
unpriced candidate is reported as unpriced, not as zero. I did not add a
rate there because that card has its own version and source.)
- The remote Codex CLI compatibility fallback. A new
`CODEX_LOCAL_COMPATIBILITY_FALLBACK_MODEL = "gpt-5.6-sol"` replaces the
default in `codexModelFallbackCandidates`. `gpt-6.1-sol` needs Codex
0.159.0 or newer, so it cannot be the floor-free last resort. Fallback
behavior is unchanged.
- `tests/runner-e2e/provider-usage.ts`: the implicit request
cache-policy attribution stays qualified only for `gpt-5.6-sol`. I did
not verify that policy for `gpt-6.1-sol`. A `gpt-6.1-sol` response that
omits the write-TTL split keeps its cache-write cost unknown, which is
the existing behavior for unqualified models.
- `tests/runner-e2e/scheduled-measurements.json`: historical
`gpt-5.6-sol` measurements. They no longer match the current suite
definitions, so the forecast reports them as historical only. The
forecast tests now build their synthetic cohorts on the current
definition hash.
- Model catalogs that list `gpt-5.6-sol` as available (`codex-local`,
`cursor-local`, `opencode-local`, Speko voice diagnostics, Pi picker
fixture).
- The `gpt-5.6` → `gpt-5.6-sol` alias for old stored configs.
- Dated or evidence docs: `doc/plans/*`, `doc/adapter-model-audit-*`,
`QUALIFICATION-*`, `doc/connections/MEMORY.md`,
`doc/connections/TASK-REVIEWS-VERIFICATION.md`,
`tests/runner-e2e/CHAT-FEATURES.md`, the Slack eval evidence, and the
S49 soak signature text (the soak failure happened on `gpt-5.6-sol`).
- Test fixtures that parse, price, migrate or round-trip an existing
`gpt-5.6-sol` value (Rust runner tests, driver tests, pricing tests,
stored-config tests, stories that show an existing agent).

## Verification

- `npx vitest run` on every server, UI, adapter-utils and codex-local
test file that mentions `gpt-5.6-sol` or the default, plus all of
`packages/adapter-utils` and `packages/adapters/codex-local`: 5,483
passed. Three timeouts under load (`sandbox-managed-runtime`,
`acp.quota`) passed when rerun.
- `packages/paperclip-runner`: `vitest run` for `src/eval`, `src/evals`,
`src/drivers/acpx`, `src/drivers/codex`, `src/cli`, `src/contracts`,
`src/backends`: 2,641 passed.
- `node --test tests/runner-e2e/reliability-testops.test.mjs
tests/runner-e2e/product-regression-testops.test.mjs`: 28 passed.
- `node tests/runner-e2e/run-unit.mjs`: all model, catalog, reliability,
scheduled and TestOps tests pass. Failures remain only in
`copilot-protection-flow`, `denied-target-isolation-flow`,
`pi-controls-flow`, `workflow-target` and `unit-launcher`. These five
also fail on unmodified master in this local environment (filesystem
watch and git environment), and they do not touch models.
- `vitest run --config tests/runner-acceptance/vitest.config.ts`: 19
passed.
- `pnpm test:e2e:runner -- --list --suite everyday-workflows --group
reliability`: the seven `everyday-workflows.runner-codex.daytona.<case>`
cells show `gpt-6.1-sol` with `OPENAI_API_KEY,DAYTONA_API_KEY`.
`--matrix-json` gives 16 reliability cells with the same credentials as
before. `--list --all` shows no `gpt-5.6-sol` cell.
- Typecheck: `adapter-utils`, `adapter-codex-local`, `server`, `ui`,
`paperclip-runner` (TypeScript), and `pnpm test:e2e:runner:typecheck`.
- `pnpm check:token-gates`: clean.
- Not run: paid cells, Rust tests (no Rust change), the browser suites,
and the full `pnpm -r typecheck` / `pnpm build` (CI runs them).

## Risks

- Agents without an explicit model change model on their next save or
normalization, and Paperclip Runner rows with a blank model use
`gpt-6.1-sol` at execution. Stored models, including `gpt-5.6-sol`, are
never rewritten. No migration is necessary.
- `gpt-6.1-sol` needs Codex CLI 0.159.0 or newer with ChatGPT sign-in.
The runner pins `@openai/codex@0.160.0`. On a remote target with an
older image CLI, the existing compatibility check falls back to
`gpt-6-sol` and then `gpt-5.6-sol`, and that probe now runs for
default-model agents too. A legacy `codex_local` agent created with the
new default on a host with an older Codex CLI gets the existing
actionable "upgrade Codex" Test result.
- Qualification: the native Codex profile uses `adapter_constant` model
qualification, so it follows the default. No qualification gate is
dropped. The ACPX Codex qualification selection moves to `gpt-6.1-sol`.
Its next qualification run uses the new model. The provider-usage
cache-policy attribution stays limited to `gpt-5.6-sol`.
- Runner E2E history: the Codex cells change their suite definition
hashes, so earlier `gpt-5.6-sol` results are a separate cohort and do
not count as current.
- The `gpt-6.1-sol` scheduled price uses the file's existing `expiresAt`
(2026-11-19). It needs the same review as the other entries before then.
- No `.github/` change. The Reliability queue-steer cell keeps the
`runner-codex` profile id, so the existing workflow credential and setup
steps still match.

> 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

- Claude Opus 5.5 (Anthropic), model ID `claude-opus-5-5`, running in
Claude Code with tool use (shell, file edits, web fetch of the OpenAI
pricing page).

## 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

Related: #19604 (commits the Reliability TestOps identities; this PR
changes only `steeringProfile` in the same file).

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 15:35:34 -06:00
DottaandPaperclip 6148fbd31f feat(ui): distinguish GitHub resources in inline Markdown links (#19476)
## Thinking Path

> - Paperclip helps people manage AI agents and their work.
> - Task conversations and documents use the shared Markdown renderer.
> - GitHub repository, pull request, and issue links currently use the
same icon.
> - Long pasted URLs make these references hard to scan in a
conversation.
> - This change identifies each resource from its URL and shows a
compact label with a distinct icon.
> - The exact destination and custom link text stay intact. Connected
status data keeps its existing behavior.

## Linked Issues or Issue Description

**What existing behavior does this improve?**

Inline GitHub links in rendered Markdown.

**Current behavior**

Repositories, pull requests, and issues all use the GitHub mark. Pasted
resource links show the full URL.

**Proposed behavior**

Pull requests use the pull request icon. Issues use the issue icon.
Repositories and other GitHub pages keep the brand mark. Pasted resource
URLs show `owner/repository#number` or `owner/repository`. Custom labels
keep their text and formatting.

**Reason and benefit**

Readers can identify GitHub resource types and scan references in a
narrow conversation. Full URLs, query strings, and comment anchors stay
available through the link destination. Link rendering makes no remote
metadata requests.

**Breaking changes**

The visible text of a bare GitHub resource URL becomes compact. The
destination does not change. No API, database, or connection changes are
required.

Searches found no duplicate work for GitHub inline resource
presentation. Related work: [same-origin Markdown
routing](https://github.com/paperclipai/paperclip/pull/17864). This
change preserves that route handling.

## What Changed

- Add a pure GitHub URL classifier with exact host checks and resource
labels.
- Move ordinary URL presentation into `MarkdownUrlLink`. Keep internal
references, workspace links, custom resolvers, and connected metadata in
their existing order.
- Add separate icons and accessible resource names. Preserve authored
Markdown titles and formatted labels.
- Add Playground, Narrow, and Streaming Storybook examples that mount
`MarkdownBody`.
- Add parser and renderer tests, eight Chromium browser cases, and the
browser command in the development guide.
- Consider Open Graph loading. Use the existing connected metadata path
for remote status and titles. Add no arbitrary page fetches.

## Verification

- Focused Vitest coverage: 129 passing tests across nine files for
GitHub parsing, Markdown rendering, connected metadata, document
rendering, and workspace-file rendering.
- `pnpm check:token-gates`.
- `pnpm --filter @paperclipai/ui typecheck`.
- `pnpm --filter @paperclipai/ui build`.
- `pnpm build-storybook`.
- Storybook catalog generation/check and 30 catalog/map tests.
- Site-route regression: Stars, Education, and enterprise pages keep
general GitHub branding and their full URL text. Three parser cases
failed before the fix; parser and renderer cases now pass.
- Streaming regression: three resource cases failed before the fix and
pass after it. The fix preserves the generated word span and custom
formatted labels.
- Chromium: `STORYBOOK_TEST_BASE_URL=http://localhost:6106 pnpm exec
playwright test inline-links.spec.ts
--config=tests/storybook-visual/playwright.config.ts --project=stories`.
- Browser scope: eight passing cases for ordinary/streaming modes,
dark/light at desktop and 390px mobile, completed play assertions, exact
comment destinations, safe external attributes, keyboard focus,
wrapping, and no GitHub requests. Screenshots are saved as task
artifacts; no review images are committed.
- The first browser attempt in the resumed environment could not launch
Chromium because its executable was missing. The browser was installed,
and all eight cases then passed.
- The browser cases use synthetic text and one connected metadata
fixture. They do not prove provider authentication or server
persistence. No visual baseline comparison is claimed; the repository
baseline manifest is unpublished.
- Initial typecheck found two unsupported story assertion options and an
unbuilt SDK dependency in the fresh checkout. The options were removed
and the SDK was built before the successful retry.
- `pnpm verify` returned 2 because the new browser spec requires broad
CI coverage. Focused tests and the browser suite supply local evidence.
Required CI supplies broad coverage.

## Risks

- Compact labels hide URL detail from the visible line. The exact href
and default tooltip preserve that detail.
- GitHub site routes can change. Unknown paths retain the general GitHub
treatment. Lookalike hosts and credential-bearing URLs do not get GitHub
resource treatment.
- Connected external-object status and title rendering keeps priority
over URL-derived presentation.

## Model Used

OpenAI Codex, GPT-6 (`gpt-6` family), with reasoning, tool use, browser
checks, and code execution. The exact deployment ID and context window
are not exposed in this run.

## 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
- [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>
2026-11-06 15:26:10 -06:00
DottaandClaude Opus 5.5 24508a8ba5 perf(dev): add agent preflight with a shared content-keyed build cache (#19555)
perf(dev): add agent:preflight with a shared content-keyed build cache

Agent worktrees each built the Runner from nothing: a cold cargo debug and
release build, the Runner TypeScript build and its checks, about 8 minutes
per fresh worktree on a loaded machine.

`pnpm agent:preflight` replaces the manual install + Runner build sequence.
It skips steps whose inputs are unchanged and reuses other worktrees'
results from ~/.cache/paperclip/agent-build:

- Runner and eval-kernel dist, keyed by the Runner build-input digest and
  the toolchain
- Runner debug binaries, keyed by every file the Rust build reads
- a cargo seed with third-party crates only; the Runner crate is scrubbed
  because cargo records its out-of-package includes by absolute path

Entries are written once with an atomic rename and restored as APFS clones.

Also exclude provider-assets from the Runner build inputs. The build writes
that directory itself, so the first build in every fresh checkout saw its
inputs change and never recorded a build stamp.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 14:01:54 -06:00
Nicky LeachandClaude Opus 5.5 7dfdc97b9f fix(deps): let Dependabot update the sandbox providers (#19489)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Sandbox providers (`packages/plugins/sandbox-providers/*`) are
standalone published packages. `pnpm-workspace.yaml` keeps them out of
the root workspace on purpose.
> - `.github/dependabot.yml` watches only `/`, so Dependabot never saw
the providers.
> - Because of this, the Kubernetes provider stayed on zod 3
(GHSA-mrhx-c7xc-m3w5) after the rest of the repo moved to zod `^4.6.6`.
#18839 fixed it by hand.
> - We do not want to keep these versions current by hand in many
places.
> - This pull request lets Dependabot update the providers, and keeps
each provider standalone.
> - The benefit is that a provider dependency that falls behind gets a
pull request that can pass CI.

## Linked Issues or Issue Description

Refs #18839 (adds `scripts/typecheck-sandbox-providers` and fixes
Kubernetes zod by hand).
Refs #18998 (a Dependabot pull request for the Pi distribution that
fails CI by design).

**What existing behavior does this improve?**
Dependabot version updates. They skip every package that the root pnpm
workspace excludes.

**Subsystem affected**
CI and dependency automation: `.github/dependabot.yml`,
`scripts/typecheck-sandbox-providers`.

**Current behavior**
Dependabot does not update the sandbox providers. A provider can stay on
an old or unsafe version, and nobody gets a pull request.

**Proposed behavior**
Dependabot updates the providers each week. Each pull request changes
the provider manifests and the lockfiles that CI installs frozen, so the
pull request can pass CI.

**Reason and benefit**
We stop having to find and fix old provider dependencies by hand.

## What Changed

- `.github/dependabot.yml`: add an npm entry for
`/scripts/typecheck-sandbox-providers`. Dependabot treats this workspace
as one unit. One pull request per dependency changes every provider that
uses the dependency and the shared `pnpm-lock.yaml` together. So the
entry needs no `groups`. One entry per provider would open a separate
pull request for each provider, and each one would fail the frozen
install in CI.
- `.github/dependabot.yml`: add an npm entry for
`/packages/plugins/sandbox-providers/daytona`. Daytona is the only
provider with its own lockfile, and the release build and the Daytona
end-to-end job install it frozen. Each lockfile has exactly one
Dependabot entry, so every pull request changes a manifest and its
lockfile together.
- Take Daytona out of the shared typecheck workspace. This pull request
does not commit `scripts/typecheck-sandbox-providers/pnpm-lock.yaml`:
since #19522, only the lockfile refresh workflow writes it. After merge,
the bot removes Daytona's packages from it (no other version changes;
checked with pnpm 9.15.4). Until then CI resolves it in place.
`scripts/typecheck-test-programs.mjs` now installs Daytona from its own
lockfile (`LOCKED_PROVIDERS`, with `--ignore-workspace`). A stale
lockfile is resolved in place for the run, for both installs.
- `.github/dependabot.yml`: add a comment that tells why the Pi and Kimi
runtime distributions have no entry (see Risks).
- `scripts/typecheck-sandbox-providers/pnpm-workspace.yaml`: list each
provider by its full path. Dependabot does not expand a workspace glob
that starts with `../`, so with the glob it saw no providers.
- `scripts/typecheck-test-programs.test.mjs`: add tests. They check that
the workspace list has no glob and matches `SANDBOX_PROVIDERS` without
`LOCKED_PROVIDERS`, that each locked provider has its lockfile, that a
locked provider installs frozen with `--ignore-workspace`, and that a
stale locked-provider lockfile is resolved in place.
- Add `.npmrc` (`auto-install-peers=true`) in
`scripts/typecheck-sandbox-providers` and in the Daytona provider.
Without it, Dependabot reads the root `.npmrc` (`false`). That rewrites
the lockfile settings, and the frozen install then fails. npm and pnpm
never publish `.npmrc`.
- `scripts/typecheck-sandbox-providers/package.json`: add
`"packageManager": "pnpm@9.15.4"`, the version CI uses. Without it,
Dependabot guesses pnpm 10.
- `doc/DEVELOPING.md`: say that contributors do not refresh or commit
Daytona's lockfile either, and that a new provider goes in both lists.

No provider moves into the root workspace. There is no pnpm catalog. The
root `pnpm-lock.yaml` does not change.

## Verification

I ran the real Dependabot updater on this branch with the Dependabot CLI
(`dependabot update ... --local`, updater image
`dependabot-updater-npm@sha256:c5a9451c…`):

- Before the change, the workspace entry loaded only
`cloudflare/bridge-template` (the one path without a glob). It skipped
all the other providers.
- After the change, `--dep typescript` gave one pull request. It changed
the 9 non-Daytona provider `package.json` files and the shared
`pnpm-lock.yaml`, and did not touch Daytona.
- `--dep wrangler` changed only the wrangler closure in the shared
lockfile. Before the `.npmrc` fix, the same run changed
`autoInstallPeers` to `false` and 757 lockfile lines.
- The Daytona entry (`--dep @daytonaio/sdk`) changed Daytona's
`package.json` and its own lockfile in one pull request, and kept
`autoInstallPeers: true`. It keeps the exact pin exact: `0.203.0`
becomes `0.227.3`.
- Both frozen installs (shared workspace, and Daytona with
`--ignore-workspace`) pass with pnpm 9.15.4.
- Dependabot installed `pnpm@9.15.4` from the new `packageManager`
field.

Other checks:

- `.github/dependabot.yml` passes the SchemaStore `dependabot-2.0`
schema (Ajv). A wrong key fails the same check.
- With pnpm 9.15.4, `install --resolution-only --ignore-scripts
--no-frozen-lockfile` in `scripts/typecheck-sandbox-providers` (the
lockfile bot's command) gives exactly the lockfile that passed the
frozen installs earlier in this pull request.
- The lockfile rule from #19522 allows this pull request's diff: it
changes no lock content.
- `node --test scripts/typecheck-test-programs.test.mjs`: the new test
and the provider tests pass. Two other tests need a root `node_modules`
(`tsc`), which my worktree did not have. CI runs them.

These checks cannot run before merge. GitHub reads `dependabot.yml` only
from the default branch. After merge, open Insights → Dependency graph →
Dependabot and make sure that the two new entries show no errors and run
on Monday.

## Risks

- A dependency in both a non-Daytona provider and Daytona (for example
`typescript`) gets two pull requests: one from each entry. Each one
passes alone, and they can merge in any order.
- The typecheck job now typechecks Daytona's tests against Daytona's own
lockfile instead of the shared one. Its versions are a little older (for
example vitest 4.1.11), so a type difference can show up there.
- Majors of shared dev tools (for example TypeScript 7, Vitest 5) come
as one pull request across all providers. It can need code changes
before it passes. That is the same as the root entry.
- Pi and Kimi get no version updates. Every direct dependency there is a
pinned provider release, and the pins feed the provider's ACPX
`commandDigest`. The Runner checks compare the Pi lock with
`PI_DISTRIBUTION_PINS`, and the Kimi build compares the lock SHA-256
with a pin. So any Dependabot change there fails CI (see #18998), and a
real upgrade starts saved sessions fresh. GitHub security alerts still
cover both lockfiles.
- The Pi zod `3.25.76` pin is still affected by GHSA-mrhx-c7xc-m3w5
(open alert). It is deliberate: `pi-acp@0.0.33` has `zod ^3.25.0` as a
direct dependency, not a peer. A fix needs a `pi-acp` release that
allows zod 4. This pull request does not change it.
- `packages/plugins/examples/plugin-orchestration-smoke-example` is also
outside the root workspace. It uses `workspace:*` dependencies, so it
cannot install alone, and this pull request does not cover it.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude
Code with tool use (shell, file edits, local Docker runs of the
Dependabot CLI).

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 11:08:39 -08:00
DottaandClaude Opus 5.5 7afb57c022 test(runner-e2e): repair restart-cell harness drift (#19538)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The Runner Product E2E suite proves that agent work survives a
control-plane restart
> - A restart chaos campaign found three restart cells that fail in the
test harness, not in the product
> - A harness failure hides the real restart result, so the campaign
cannot classify these cells
> - This pull request repairs the harness drift in those cells and names
the one failure the harness cannot prevent
> - The benefit is that these cells now test restart behavior, or fail
with a clear cause

## Linked Issues or Issue Description

Refs #14811 (connector setup became one screen). Refs #19475
(completion-update restart fixture).

**What happened?**
1. `lifecycle-baseline.runner-codex.local.tool-review-restart` clicked a
"Save and continue" button. #14811 removed that button. The cell failed
during setup. After that fix, the cell also failed after the restart:
the expanded review card does not survive the post-restart reload, so
"Approve & run" was not visible.
2.
`local-session-integrity.runner-acpx-claude.local.structured-question-restart-resume`
failed with `page.goto: net::ERR_ABORTED` after the controller restart.
The old document's Vite client reloads when the replacement server
starts, and this aborts the test navigation. The code tolerated only
`TimeoutError`.
3.
`completion-updates.runner-acpx-claude.local.handoff-completion-restart`
waited for the source agent to run an instructed wait command. Claude
replied without the command (2/2 attempts), so the restart never
occurred. The cell then failed with a generic timeout.

**Expected behavior**
Each cell reaches its restart boundary and tests restart behavior. If
the boundary cannot be reached, the cell names the cause.

**Steps to reproduce**
Run `pnpm test:e2e:runner -- --max-parallel 1 --max-automatic-retries 0
--id <cell>` for each cell above on `master`.

## What Changed

- `tests/runner-e2e/connection-reviews.ts`: accept the one-screen "Check
link" step and the older "Save and continue" step. This uses the same
regex approach as `connection-flow.ts`.
- `tests/runner-e2e/runner.spec.ts` (tool review): click "Review
request" after the restart reload, on the document that acts on the
card.
- `tests/runner-e2e/chat-restart.ts`: add `gotoAfterServerRestart`. It
retries only `net::ERR_ABORTED`, within the caller's deadline and at
most 5 attempts. It still accepts `TimeoutError`. It rethrows all other
errors. The structured-question restart uses it. The existing sentinel
and durable-state assertions still prove the new document.
- `tests/runner-e2e/completion-updates.ts` and
`completion-update-flow.ts`: add `completionRestartGateSkipped` and
`completionRestartGateTimeoutDetail`. The gate poll stops at once with
`restart boundary not reached (agent skipped gate)` when no completion
turn is active and the turn that carries this task's Done facts
(`chatCompletionUpdates`, as in `completionDelivery`) succeeded or
published its reply before the gate reports `waiting`. A failed or
cancelled turn is not blamed on the agent, because delivery can retry
it; the timeout detail names it instead. The post-restart chat
navigation now uses `gotoAfterServerRestart`.
- A fixture-level gate is not possible without a product hook. The
native run finalizer publishes the completion reply inside its own
transaction, through the issue service closure. The isolated-server
entrypoint can patch only class prototypes and HTTP responses, and the
reply uses no tool call or HTTP request.
- `tests/runner-e2e/README.md`: document the skipped-gate failure.
- Docs: use `pnpm --filter @paperclipai/paperclip-runner run
build:runner-binaries` in `tests/runner-e2e/README.md`,
`tests/restart-chaos/README.md`, `tests/restart-chaos/main.ts` and
`doc/DEVELOPING.md`.
- No product code changes.

## Verification

- Unit: `pnpm exec vitest run --config tests/runner-e2e/vitest.config.ts
tests/runner-e2e/chat-restart.test.ts
tests/runner-e2e/completion-updates.test.ts
tests/runner-e2e/connection-reviews.test.ts` (36 passed).
- Typecheck: `node scripts/typecheck-test-projects.mjs tests/runner-e2e`
passed.
- Live cells, local, `--max-parallel 1 --max-automatic-retries 0`,
macOS, load average 35–65:
- `lifecycle-baseline.runner-codex.local.tool-review-restart`: PASS
(first run found the review-card reload drift, fixed in the second
commit).
-
`local-session-integrity.runner-acpx-claude.local.structured-question-restart-resume`:
PASS. A first attempt failed before the restart with `PRP command
session.open timed out` at load ~36 (environment).
-
`completion-updates.runner-acpx-claude.local.handoff-completion-restart`:
FAIL as designed, twice (before and after the review fix), with `restart
boundary not reached (agent skipped gate): completion turn … ended
succeeded without the reference gate reporting waiting`. Claude skipped
the wait both times, so this cell still does not exercise a restart.

## Risks

- Low risk. Test harness and docs only.
- The navigation retry could hide a real abort. It is limited to
`net::ERR_ABORTED`, 5 attempts and the deadline, and the test still
asserts that a new document loaded.
- The ACPX Claude completion restart cell still does not exercise a
restart when the agent skips the gate. It now reports this cause by
name.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, via Claude Code with
tool use (shell, file edit, browser test runs).

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 12:59:54 -06:00
Devin FoleyandPaperclip fd4b197f83 fix(ui): hide runner selection during agent setup (#19517)
## Thinking Path

> - Paperclip lets people manage AI agents for work.
> - Agent setup connects a harness, model, account, and computer.
> - The system already selects a qualified runner for a new agent.
> - Setup still asks users to select that internal runner.
> - The runner dropdown can be the only field in Advanced.
> - This PR removes the dropdown and hides an empty Advanced section.
> - Users keep their saved execution settings and see fewer setup controls.

## Linked Issues or Issue Description

**What existing behavior does this improve?**

Agent creation, onboarding, built-in agent setup, company import, and agent configuration.

**Subsystem affected**

The UI, setup error messages, tests, and Storybook fixtures.

**Current behavior**

Users can select a runner from a dropdown. Some setup screens place only that dropdown in Advanced. Errors can direct users to that control.

**Proposed behavior**

Remove runner dropdowns from setup and configuration. Use the existing automatic selection for new agents. Retain saved runner settings. Show Advanced only when other fields remain.

**Reason and benefit**

Users can configure agents without an extra internal execution choice. Setup also avoids an empty Advanced section.

**Breaking changes**

Users can no longer select a runner through these UI dropdowns. The API and CLI retain their runner options. Existing agents keep their saved execution settings.

**Additional context**

Related: [Default new agents to the qualified runner for their harness](https://github.com/paperclipai/paperclip/pull/15422). This PR changes the existing setup UI. It adds no harness or runtime default. The master merge retains the custom gateway placement from [#19510](https://github.com/paperclipai/paperclip/pull/19510).

## What Changed

- Remove the shared runner dropdown and its setup/configuration callers.
- Hide Advanced when it has no remaining fields. Keep command and argument settings where supported. Preserve custom gateway setup under Advanced on the Claude and OpenAI API key paths.
- Keep setup failures visible and keep the retry action outside the removed control.
- Update errors and documentation that referred to the removed dropdown.
- Update component tests and Storybook fixtures for the new UI states.
- Make Legacy first-task evals resume an API-configured setup record. Record that path separately from fresh automatic onboarding.

## Verification

- Latest master integration (`187c0f6d6e5`): 276 onboarding/provider-connection tests passed across six files. UI typecheck and build passed. Token gates, query-error rendering checks, and the Storybook catalog check passed. The conflict resolution retains master's bounded connection tests and cancellation while removing the obsolete runner instruction. The first test command used the wrong working directory and failed before collecting tests; the corrected invocation from `ui/` passed.
- Earlier branch verification passed: full workspace build and typecheck, 1,037 focused UI/service tests, 49 heartbeat provider contract tests, eval typecheck, and 30 map/catalog tests.
- The full local `pnpm test:run` run passed all six chat integration shards (1,931 tests). It was stopped for the master merge before the complete suite finished. The [complete CI run](https://github.com/paperclipai/paperclip/actions/runs/42264662642) passed on the previous head `72e1699`.
- Current head `a097c8369d079c839e78661a2206cfa62c5210e0`: [full CI](https://github.com/paperclipai/paperclip/actions/runs/42273168268) passed. PR checks total 55 passed and 3 skipped, with none failed or pending. Greptile reviewed this head at 5/5 with no actionable findings or unresolved review threads.
- Live browser/provider evals have not run. The Legacy eval change has no live qualification claim.

## Risks

- Removing the dropdown changes the setup UI. Existing API and CLI runner choices remain available.
- Conditional Advanced sections must retain valid command and argument fields.
- Legacy first-task evals now prove setup resumption. They do not prove the fresh-agent automatic default.
- No schema change or data migration is included.

## Model Used

OpenAI `gpt-6.1-sol`, through Codex in T3 Code. Reasoning effort: `xhigh`. The model used file editing, shell commands, and test tools. The harness does not expose the 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>
2026-11-06 10:58:42 -08:00
Nicky LeachandClaude Opus 5.5 3b3037aab5 fix(ci): run the sandbox provider tests in required CI (#19533)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Sandbox provider plugins (Daytona, E2B, Cloudflare, Kubernetes,
Modal, and others) run agents in remote sandboxes
> - The providers are outside the root pnpm workspace, so `pnpm
test:run` and the CI test lanes never run their Vitest suites
> - paperclipai/paperclip#18839 typechecks those tests, but a test that
fails at runtime still fails nothing
> - The providers have about 1,040 tests, and they finish in about 15
seconds on Linux
> - This pull request adds a required `Sandbox provider tests` job that
runs them when a change can affect them
> - The benefit is that a broken provider, plugin SDK, or shared
contract fails CI on the pull request instead of in a release or a paid
end-to-end run

## Linked Issues or Issue Description

Refs #18839

**What happened?**

No CI job runs the sandbox provider tests. `runner-full-stack-e2e.yml`
builds the Daytona plugin for a paid nightly run, but it does not run
any provider's `pnpm test`.

**Expected behavior**

A pull request that can break a provider runs that provider's tests, and
a failure blocks `ci / verify`.

**Steps to reproduce**

Add `expect(1).toBe(2)` to a test in
`packages/plugins/sandbox-providers/e2b/src`. Open a pull request. CI
stays green.

## What Changed

- Added `scripts/test-sandbox-providers.mjs` and its tests. The script
installs the providers through `typecheckTestPrograms` with no programs,
because that function already owns the provider install and the plugin
SDK link. Then it runs each provider's `pnpm test`, four at a time, and
prints each provider's output as one block. It fails if a suite fails or
if no provider has a test script.
- The script skips `cloudflare/bridge-template`, because Cloudflare's
Vitest config already runs those tests.
- Added the `sandbox_provider_tests` job to
`.github/workflows/pr-trusted.yml`, and made `ci / verify` require its
result.
- Added the `//#ci:sandbox-providers` task to `turbo.json` and its lane
to `.github/ci-task-matrix.json`. The CI planner runs the job only when
a change touches `packages/plugins/sandbox-providers/**`,
`packages/plugins/sdk/**`, or `packages/shared/**`. `packages/shared` is
the plugin SDK's only workspace dependency. Global CI inputs, such as
`scripts/**`, `.github/**`, `pnpm-lock.yaml`, or any `package.json`,
still select every job.
- The job turns off core dumps. A Daytona capacity test kills a process
at a file-size limit inside the exported directory. If core dumps are
on, the core file joins the export, and the test sees 12 files instead
of 11.
- Updated the job lists in `scripts/__tests__/e2e-shard.test.mjs` and
the job count in `.github/scripts/tests/ci-profile.test.mjs`. Added
planner tests to `.github/scripts/tests/ci-plan.test.mjs`. One of these
tests fails if the plugin SDK gets a new workspace dependency that is
not in the job's inputs.
- Added the new test file to `test:release-registry`, and documented the
script in `doc/DEVELOPING.md`.

## Verification

- `node scripts/test-sandbox-providers.mjs` on macOS: 8 of 9 suites pass
in 31.6 s, including the install. Kubernetes fails 12 `file-sync` tests,
because macOS has no `/proc/self/fd`. Some Daytona tests skip, because
they need GNU `tar` and coreutils.
- The same script in a Linux container (`node:24`, a non-root user, core
dumps off): all 9 suites pass, with 1,012 tests passed and 26 skipped.
The script took 15 s after the install.
  - Kubernetes: 205 passed.
  - Daytona: 590 passed and 16 skipped.
- With core dumps on, Daytona's `preserve literal capacity repair` test
fails. The export includes a `core` file. With `--ulimit core=0`, it
passes.
- To look for timing failures under load, I ran the whole script 12 more
times in the container, limited to 2 CPUs (8 runs) and 1 CPU (4 runs).
All 12 runs passed. They took 45 to 76 s on 2 CPUs and 73 to 102 s on 1
CPU.
- `ubuntu-latest` has `zstd`, and my container did not, so some Daytona
tests skipped in those runs. With `zstd` installed, Daytona passed with
598 tests and 8 skipped, and only the live tests skipped. One earlier
`zstd` run failed while the stress runs used the same CPUs, and I did
not capture its output. The next run passed.
- `node --test` on every test that reads `pr-trusted.yml`, the CI
planner, or the task matrix: 816 passed. These include
`.github/scripts/tests/*.test.mjs`,
`scripts/__tests__/e2e-shard.test.mjs`,
`scripts/ci/test-selection-workflow.test.mjs`, and the new tests.
- `pnpm run test:release-registry` on macOS: 251 of 255 pass, including
the new tests. The 4 failures are `wait_for_npm_package_versions` tests
in `scripts/release-lib.test.mjs`. They fail the same way on master on
the same machine, and CI runs this suite on Linux.
- `actionlint` 1.7.7 reports no errors on the changed workflow.
- I called `planTasks` from `.github/scripts/ci-plan.mjs` with one
changed file at a time. `server/src/index.ts` and `ui/src/App.tsx` leave
`sandbox_provider_tests` off.
`packages/plugins/sandbox-providers/e2b/src/plugin.ts` and
`packages/shared/src/index.ts` turn it on.

This pull request cannot run its own new job. `pr.yml` calls
`pr-trusted.yml@master`, so the job first runs on pull requests after
this one merges. After merge, check the first pull request that changes
a provider or `packages/shared`.

## Risks

- **First real run is after merge.** I measured the time on Linux in
Docker, not on a CI runner. CI runners are about 2 times slower than my
machine, so I expect about 2 to 3 minutes for the job, including the
dependency restore. The job runs in parallel with the other jobs, and
the slowest required job takes about 13 minutes. So the job should not
make CI slower.
- **Open provider pull requests.** After this merges, open pull requests
that change a provider run its tests. If those tests fail, `ci / verify`
blocks them until they are fixed.
- **`packages/shared` changes often.** Any change there runs this job. A
Linux-only provider failure would block those pull requests. All suites
pass on Linux today.
- **One unexplained Daytona failure.** One Daytona run with `zstd`
failed under CPU contention, and I did not capture its output. Some
Daytona tests have short deadlines. If the job is flaky after merge,
quarantine the failing test or revert the job, and do not leave `ci /
verify` red.
- **Path rules can be too narrow.** If a provider starts to import
another workspace package, a change to that package does not run this
job. The plugin SDK dependency test covers the SDK. It does not cover a
provider that imports a workspace package directly. Today no provider
does.
- **Overlap with paperclipai/paperclip#19489 and
paperclipai/paperclip#19522.** Both pull requests change the provider
install in `scripts/typecheck-test-programs.mjs`. This pull request does
not edit that file. It calls the same install function, so it uses their
install changes when they merge. All three pull requests edit the same
section of `doc/DEVELOPING.md`, so a small text conflict is possible.

> 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

- Anthropic Claude Opus 5.5 (`claude-opus-5-5`), in Claude Code with
tool use (shell, file edits, GitHub CLI, Docker). Extended reasoning was
on.

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 10:34:03 -08:00
Nicky LeachandClaude Opus 5.5 e3041f5481 fix(ci): let the lockfile bot own the sandbox provider lockfiles (#19522)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The repository has a supply-chain rule: contributors do not commit
lockfiles. A bot and verified Dependabot commits write them.
> - The rule checks only the root `pnpm-lock.yaml`.
> - The sandbox providers are outside the root workspace, so they have
two more pnpm lockfiles. Pull requests edited them by hand, for example
#12791, #18839 and #19489.
> - This pull request makes the same rule and the same bot cover those
two lockfiles.
> - The benefit is one lockfile rule for every managed pnpm lockfile,
and no lockfile edits in contributor pull requests.

## Linked Issues or Issue Description

Refs #19489

**What existing behavior does this improve?**

The lockfile policy and the lockfile refresh bot.

**Subsystem affected**

CI: `.github/scripts/lockfile-trust.mjs`,
`.github/workflows/refresh-lockfile.yml`, and the sandbox provider
installs.

**Current behavior**

`lockfile-trust.mjs` blocks contributor edits to `pnpm-lock.yaml` only.
A contributor can edit
`scripts/typecheck-sandbox-providers/pnpm-lock.yaml` or
`packages/plugins/sandbox-providers/daytona/pnpm-lock.yaml`, and CI
passes. The refresh bot does not update these files.
`typecheck:test-programs` fails on a stale provider lockfile and tells
the contributor to commit a new one.

**Proposed behavior**

The policy blocks contributor edits to all three lockfiles. The refresh
bot regenerates all three after merge. CI resolves a stale provider
lockfile in place for the run, as it does for the root lockfile.

**Reason and benefit**

Lockfile content comes only from the bot or from verified Dependabot
commits. Contributors do not need to run pnpm in special folders.

**Breaking changes**

None. A pull request that edits a provider lockfile now fails the policy
check. Remove the lockfile change from the pull request. The bot commits
it after merge.

## What Changed

- `lockfile-trust.mjs` now exports `LOCKFILES`: the root lockfile, the
shared sandbox provider lockfile, and the Daytona lockfile. The policy
blocks contributor edits to each of them. A Dependabot pull request must
match a verified Dependabot commit for each lockfile that it changes.
The `merged` command and the reporting-lock proof still use only the
root lockfile.
- `check-pr-lockfile.mjs` (advisory check) uses the same list.
- `refresh-lockfile.yml`:
- A job-level `LOCKFILES` env lists the same three files. A test checks
that it equals the policy list.
- A new step regenerates the two provider lockfiles with
`--resolution-only --ignore-scripts --no-frozen-lockfile`.
- The unexpected-changes check, the change check, and `git add` cover
all three lockfiles.
  - The release-age gate checks the added versions in every lockfile.
- A held refresh saves all three lockfiles at their repository paths,
with a `source-locks.sha256` file. The next run reuses them only if
every master lockfile is unchanged. An artifact in the old format is not
reused.
  - The PR title is now `chore(lockfile): refresh pnpm lockfiles`.
- `check-lockfile-release-age.mjs` accepts more than one
`--base`/`--head` pair.
- `scripts/typecheck-test-programs.mjs`: if the frozen install of the
provider workspace fails, the script resolves the lockfile in place and
installs frozen again.
- `scripts/build-standalone-public-packages.mjs`: the same fallback
applies to a package with a committed lockfile (Daytona). `release.sh`
already restores tracked files when it exits.
- `doc/DEVELOPING.md` and `doc/RELEASE-AUTOMATION-SETUP.md` describe the
managed lockfiles. They also say that the Pi and Kimi distribution
lockfiles stay hand-managed, because they hold attested provider pins.

## Verification

- `node --test .github/scripts/tests/*.test.mjs
scripts/__tests__/build-standalone-concurrency.test.mjs`: 731 tests
pass. New tests cover:
- the policy for provider lockfiles, including a real git history with a
Dependabot commit and a later hand edit
  - the workflow and policy lists match
  - the unexpected-changes check, run with bash against a fixture
- a held refresh round trip, and its invalidation when a provider
lockfile changes on master
  - the release-age gate across lockfile pairs
  - the inline fallback in both install scripts
- `node --test scripts/typecheck-test-programs.test.mjs`: the install
tests pass. Two tests fail locally only because this worktree has no
root `node_modules` (no `tsc`). They also fail without this change.
- I ran the new bot commands on master with pnpm 9.15.4. No package
version changed. pnpm 9.15.4 removes `libc:` fields and adds
`deprecated:` notes, so the first refresh is a metadata-only change. The
release-age gate passes it because it adds no versions.
- I ran the release-age and held-lock steps locally with bash against
this commit. The gate reported `eligible=true`, and `sha256sum --check`
accepted the saved hashes.
- The workflow YAML parses, and `bash -n` accepts every `run` block.
- Not testable before merge: the policy job loads `lockfile-trust.mjs`
from the base branch, so the new rule applies only to pull requests
opened after this merges. The refresh workflow runs only on master.

## Risks

- The release build now resolves a stale Daytona lockfile in place, from
the registry. The root release install already resolves without a frozen
lockfile, so this is the same level of trust.
- The paid runner e2e job still installs Daytona with
`--frozen-lockfile`. After a Daytona manifest change merges, its Daytona
cases fail until the bot's refresh merges. This matches the rule that
paid jobs refuse a new root lockfile until its refresh merges.
- Dependabot pull requests for the provider entries in #19489 change a
provider lockfile. They pass only if each lockfile matches a verified
Dependabot commit, the same as for the root lockfile.
- Low risk otherwise: the bot keeps its existing token, environment, and
merge rules.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with tool use
(shell, file edits, and git).

## 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 10:07:57 -08:00
Nicky LeachandClaude Opus 5.5 98ebeefbc9 feat(environments): let managed config declare plugin environments (#19508)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - A managed instance gets its instance-level environments from the
`PAPERCLIP_MANAGED_CONFIG` document
> - #19490 added the plugin environment rows, their marker index and
write floor, but nothing creates them yet
> - The managed config still accepts only one sandbox entry, so a
managed instance cannot get a plugin-provided environment without manual
setup
> - This pull request lets the managed config declare plugin entries
beside the sandbox entry, and provisions one locked row for each at boot
> - The benefit is that a managed instance gets its plugin environments
with no manual setup, and the rows recover by themselves when their
plugin restarts

## Linked Issues or Issue Description

Refs #19490 (the plugin environment rows this pull request provisions)

**Subsystem affected**
Server environments: the managed-config parser, the managed environment
bootstrap, and the environment routes' write floor.

**Problem or motivation**
A managed instance cannot get a plugin environment from its managed
config. The `environments` section accepts one entry, and that entry
always provisions the managed sandbox. Company settings cannot create a
plugin environment either. So each managed instance that needs one
requires manual setup.

**Proposed solution**
Let an `environments` entry declare `driver: "plugin"`. Boot provisions
one locked row for each plugin entry through the row layer from #19490.
A later pull request adds a one-time instance default for one plugin
entry, and advertises the new managed-config capability.

**Alternatives considered**
Manual setup on each instance, and a new control-plane endpoint. Both
need a step outside the deploy. The managed config already delivers the
sandbox entry.

**Roadmap alignment**
This extends the existing managed-config `environments` section, which
already provisions the managed sandbox. It adds no new product surface.

## What Changed

- `server/src/services/managed-config.ts`: an `environments` entry may
set `driver` to `"sandbox"` or `"plugin"`. An entry without `driver` is
still the sandbox entry, so today's documents parse unchanged.
- A plugin entry has `name`, optional `description`, `pluginKey` (the
plugin's manifest id), `driverKey` and optional `driverConfig`.
- At most one sandbox entry. Names are unique across the section, and
`pluginKey`–`driverKey` pairs are unique. Secret-like keys in
`driverConfig` refuse startup, as for sandbox `config`. An unknown key
or driver still refuses startup, and that includes `instanceDefault`
until the follow-up pull request.
- Plugin entries parse into a new `pluginEnvironments` list. The
`environments` list keeps only the sandbox entry, so its consumers do
not change.
  - `MANAGED_ENVIRONMENT_DRIVERS` lists the accepted drivers.
- `server/src/services/managed-environments.ts`
(`applyManagedEnvironments`):
- Boot refuses to start unless an auto-installed catalog entry installs
each plugin entry's `pluginKey`. `plugins.autoInstall` holds catalog
keys, not manifest ids, so the parser cannot check this. Boot uses the
manifest ids `createApp` already resolves from the bundled and
distribution catalogs (`app.locals.managedBundledPluginKeys`, passed in
by `server/src/index.ts`). Without that list it resolves the catalog
itself.
- Plugin entries run after the sandbox entry and reuse its readiness
handling. Boot awaits `pluginsReady`, then requires the plugin `ready`,
declaring the entry's driver, and running a worker. Otherwise boot
archives the row and re-ensures it on the worker's `ready`.
- Recovery re-ensures on every worker `ready` until one ensure succeeds
or the plugin rejects the config (HTTP 422).
- If the ensure fails because the worker died, boot archives the row and
waits for `ready`. If the worker is still running (for example the call
timed out), boot keeps the row as it is, retries once at once and on the
next `ready`, and otherwise at the next boot. No timer is added.
  - Removing an entry never archives its row.
- A plugin-only document does not conflict with
`PAPERCLIP_EXECUTION_MODE`, because plugin rows do not use the sandbox
slot.
- Plugin entries never change the instance default. The sandbox stamp
still fills only an unset or local default, so it never replaces a
plugin default.
- `server/src/routes/environments.ts`: `isPlatformSlotEnvironment`
treats a marked plugin row as a live slot while the document declares
its entry. So the marker-clear escape hatch is refused then, and allowed
again after the entry leaves the document.
- `doc/DEVELOPING.md`: new "Managed environments" section.

## Verification

- `cd server && npx vitest run src/__tests__/managed-config.test.ts`:
old documents parse unchanged. Sandbox plus plugin parses. Each of these
refuses startup: two sandbox entries, `driver: null`, duplicate names, a
duplicate pair, a secret-like key, an unknown key (including
`instanceDefault`), an unknown driver, a malformed `driverKey` or
`driverConfig`.
- `npx vitest run
src/services/managed-environments-plugin-entries.test.ts` (the
sandbox-entry tests stay in `managed-environments.test.ts`; shared
fixtures are in `managed-environments.test-support.ts`):
- A plugin entry is ensured with the validator's worker manager, after
the sandbox entry.
- Boot refuses a plugin entry whose `pluginKey` no auto-installed
catalog entry installs, both from the passed list and from its own
catalog lookup.
- A plugin that is down archives the row, and worker recovery re-ensures
it. A missing plugin, a plugin without the driver, or a worker manager
without `call` counts as unavailable.
- Recovery stays armed after a failed attempt and stops after one
success or a permanent config rejection (422). A `ready` during an
attempt queues one more.
- A worker that dies during the boot ensure archives the row and arms
recovery. A failure while the worker keeps running leaves the row as it
is and retries.
- Removing an entry does not archive. Plugin entries and the sandbox
stamp never change a plugin default.
  - An ensure failure is counted, not thrown.
- `npx vitest run src/__tests__/managed-plugin-environments.test.ts`
(embedded Postgres, real `applyManagedEnvironments`): the first boot
creates the row and the second changes nothing. A plugin that is down
archives the row, and recovery brings it back. Removing the entry does
not archive the row. The instance default stays unset. The row tests
from #19490 still pass.
- `npx vitest run src/__tests__/environment-routes.test.ts`: the marker
clear is refused while the document declares the entry, and allowed
after it leaves.
- `npx vitest run src/__tests__/instance-settings-service.test.ts
src/__tests__/instance-settings-cloud-defaults.test.ts`: pass with the
new `pluginEnvironments` field.
- `pnpm --filter @paperclipai/server typecheck` passes.
- I did not run the full `pnpm test:run`, `pnpm -r typecheck` or `pnpm
build`. CI covers them.

## Risks

- No schema change.
- A managed-config document with a plugin entry now provisions a row at
boot. A document without one behaves as before.
- Adoption renames an unmarked row for the same plugin and driver to the
declared name and resets its driver config to the declared one. The row
keeps its id, agents and other metadata, and it is then locked like the
managed sandbox.
- Boot now refuses to start when a plugin entry names a plugin that no
auto-installed catalog entry provides. This is the same fail-closed
posture as an unknown sandbox provider.

> 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

- Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, through Claude Code
with tool use (file edits, shell, test runs).

## 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 17:35:13 +00:00
Nicky LeachandClaude Opus 5.5 83c6832ccb fix(build): typecheck package, Playwright, and e2e test files in CI (#18839)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Runner, plugin, and Playwright tests verify how those agents run,
connect, and appear in the board
> - Most package tsconfigs exclude tests, and Vitest strips types, so a
type error in those tests fails nothing
> - The tests drifted to 803 real type errors, and some of those errors
hid assertions that checked nothing
> - paperclipai/paperclip#18739 and paperclipai/paperclip#18738 check
the server test tree and four test projects, but not these files
> - This pull request adds a required check for these test files, fixes
every error, and fails CI if a test file is in no program
> - The benefit is that a type error in any test file outside
`server/src` now fails CI

## Linked Issues or Issue Description

Refs #18739
Refs #18738

**What happened?**

517 test files were in no program that required CI checks. A type error
in those files did not fail CI.

**Expected behavior**

CI fails on a type error in any test file.

**Steps to reproduce**

Add `export const value: number = "text";` to a test file under
`packages/paperclip-runner/src` on master. CI stays green, because
`tsconfig.json` excludes test files and Vitest strips types.

**Measured gap**

Each row is a program with its tests included, on one thread. File and
error counts are for head `7d4b5e907a`. Memory peaks were measured
before the two latest merges of master.

| Group | Test files | Real errors | Peak |
| --- | ---: | ---: | ---: |
| `paperclip-runner` Node source | 290 | 644 | 1.09 GiB |
| `paperclip-runner` surfaces | 9 | 12 | 0.42 GiB |
| `paperclip-runner` devtools and examples | 14 | 0 | 0.68 GiB |
| `sandbox-providers/kubernetes` | 21 | 65 | 0.44 GiB |
| 8 other sandbox providers and `bridge-template` | 32 | 4 | 0.34 GiB |
| `plugins/sdk` | 22 | 15 | 0.41 GiB |
| `plugin-workspace-diff` | 5 | 0 | 0.37 GiB |
| `plugin-orchestration-smoke-example` | 1 | 1 | 0.15 GiB |
| `kv-demo-mcp-server` | 3 | 0 | 0.13 GiB |
| `packages/db` scripts | 1 | 0 | 1.01 GiB |
| 8 Playwright suites under `tests/` | 52 | 25 | 1.72 GiB |
| `tests/runner-acceptance` | 3 | 0 | 0.58 GiB |
| `tests/e2e`, through layer declarations | 63 | 37 | at most 1.59 GiB |
| `ui` `AttentionInteractionResolver.test.tsx` | 1 | 0 | n/a |
| **Total** | **517** | **803** | |

27 of the 803 errors came from master while this pull request was open.
Each merge of master brought new test code that no check had read.

Errors that were config errors, not real errors:

- One TS2688 for each provider, because the root install does not
install provider dependencies.
- 9 in the Runner Node program (TS7016 and TS6059).
- 2 in `tsconfig.browser.json`. TypeScript 7 removed `baseUrl`, so that
config was invalid.
- 213 in the Playwright suites (`@/*` aliases and Vite types).
- About 60 in `tests/e2e` (import extensions and aliases).

`packages/plugins/create-paperclip-plugin` has no gap. Its tsconfig
excludes its test, but `cli/tsconfig.json` reaches that test through an
import. `server/test-baselines` also has no gap, because
`tests/lifecycle-baseline` reads it.

## What Changed

- Added `scripts/typecheck-test-programs.mjs` and its tests. The
`Typecheck + Release Registry` job runs it. It checks each program in
`PROGRAMS` on one thread.
- The script fails if a tracked `*.test.ts(x)` or `*.spec.ts(x)` file
outside `server/src` is in no program. The compiler file list decides
this, because `include` drops `foo.test.tsx` when `foo.test.ts` exists.
- Added a `tsconfig.test.json` to each uncovered package, and
`tests/tsconfig.playwright.json`.
- Added `tests/e2e` to `PROJECTS` in
`scripts/typecheck-test-projects.mjs`, with a `tsconfig.json` and a
`tsconfig.layers.json`.
- Added `scripts/typecheck-sandbox-providers`. It is a small workspace
that installs provider SDKs from one lockfile. I did not add a lockfile
inside each provider, because
`scripts/build-standalone-public-packages.mjs` uses a frozen install
when one exists, and that changes what a release resolves.
- Corrected `packages/paperclip-runner/tsconfig.browser.json` for
TypeScript 7.
- Set `rootDir` to `..` in
`packages/paperclip-runner/tsconfig.test.json`, because one Runner test
imports from `packages/adapter-utils/src`. The program does not emit
files, so this changes no build output.
- Moved the Kubernetes provider from `vitest ^3.2.4` to `^4.1.8`, the
version the other providers use. Vitest 3 requires `tinypool ^1.1.1`,
which has two critical advisories (GHSA-85c8-ppgw-ccpr and
GHSA-5gmw-xhrv-c9v3). The first patched version is 2.1.2. Its tests have
the same result on both versions: 189 passed, and the same 12
`file-sync` tests failed.
- Moved the Kubernetes provider from `zod ^3.24.2` to `^4.6.6`, and gave
its two `z.record` calls a key schema. This is the only production
change, and it stays in this pull request. See "Production change for
review".
- Renamed `AttentionInteractionResolver.test.ts` to
`AttentionInteractionResolver.replace.test.ts`, so TypeScript reads the
`.test.tsx` beside it.
- Fixed all 803 errors, with changes to test files and test support
only. The fix for `contracts/native-execution.test.ts` is the same as
the fix in paperclipai/paperclip#18739, so those two changes merge
cleanly.
- Updated `doc/DEVELOPING.md`.

This pull request does not edit `server/scripts/typecheck-layers.mjs`.
paperclipai/paperclip#18739 and paperclipai/paperclip#18738 have both
merged, and this branch includes them.

### Production change for review

The new lockfile made dependency review flag `zod@3.25.76` as a
high-severity advisory (GHSA-mrhx-c7xc-m3w5). The first patched version
is 4.6.6, so 3.x has no fix. The published Kubernetes plugin uses zod to
validate operator config. The zod 3 source does not compile against zod
4, so a typecheck-only override cannot fix this.

The existing tests do not prove this change, because they also passed
with the invalid one-argument `z.record`. So I parsed 45 inputs with the
same schema on zod 3.25.76 and zod 4.6.7:

| Result | Inputs | Detail |
| --- | ---: | --- |
| Identical | 23 | Includes defaults, valid config, and a `__proto__`
key |
| Same outcome, new error wording | 21 | For example, `Invalid url` is
now `Invalid URL`. `validateConfig` shows this text to operators. |
| Different outcome | 1 | `jobTtlSecondsAfterFinished: 2 ** 60` was
valid and is now rejected. The new limit is `Number.MAX_SAFE_INTEGER`. |

I did not test this against a real cluster.

The decision is to keep this change in this pull request. Since then,
paperclipai/paperclip#17364 has moved the rest of the repository to zod
4.6.x, so the Kubernetes plugin now matches it.

### Behavior change for review

`reducedMotion` under `use` is not a Playwright option. It had no effect
in 11 configs and 2 `test.use` calls, so those suites ran with
`no-preference`. The options are now under `contextOptions`, so reduced
motion now takes effect. `app-shell-design.spec.ts` asserts a real
transition, so it now asks for `no-preference` itself.

The baseline manifest has `snapshotCount: 0`, so this invalidates no
published baseline. A frozen trial reference PNG can differ.

### Findings

These are product questions. I did not change them, and I did not hide
them with casts:

1. **`PrpEvent` and its schema disagree.** The TypeScript type in
`src/protocol/replay-contract.ts` requires `normalizedSessionId`. The
`required` list in `protocol/schemas/event.schema.json` does not include
it. `validatePrpEvent` accepts events that the type forbids.
2. **`requestCheckboxConfirmation` is stricter than its runtime.** It
uses the output type, so plugin authors must pass `continuationPolicy`
and `allowDeclineReason`, although the schema gives them defaults.
`z.input` would fix this.
3. **`RetainedRunnerdMaintenanceInput.backend.kind` is a free string.**
The quarantine domain comes from `descriptor.kind`, but the release uses
`proof.backend.kind`. If they differ,
`completeRetainedNativeSessionCleanup` returns 0 and the quarantine
stays. The production caller passes `"runner"` today, so this is not a
live bug.
4. **`CodexHarnessSession.close(input?)` is optional, but the contract
requires `{ reason }`.**

These are tests that verified nothing. I corrected them, and they pass:

- `backends/native-instruction-measurement.test.ts` filtered on
`placement === "core"`, which is not a valid placement. It measured an
empty tool list. It now measures 14 tools.
- `drivers/acpx/codex-acpx-driver.test.ts` checked for `usage.updated`,
which is not an event type.
- The `hostFixture()` helper in `drivers/acpx/runtime-host.test.ts`
ignored two overrides, so
`expect(prepareSandbox).not.toHaveBeenCalled()` could not fail.
- `live/live-session.test.ts` set `agent: "pi"` before a spread that
overwrote it.
- `native-distribution-integrity.test.ts` passed an AbortSignal where
`openCommand` expects `{ signal }`.

These are gaps that this pull request does not close:

- **The root lockfile still has some old zod versions.**
paperclipai/paperclip#17364 moved the direct zod dependencies to 4.6.x.
`pnpm-lock.yaml` still resolves `zod@3.25.76`, `4.1.11`, and `4.4.3`,
which are below the patched 4.6.6.
`packages/paperclip-runner/scripts/pi-distribution/package.json` pins
`zod` to `3.25.76`, and some agent SDKs resolve `4.4.3`. Dependency
review does not flag them, because this pull request does not add them.
- **Dead GitHub coverage.** `chat-adapters-ui-providers.spec.ts`
returned early for GitHub, so four later `provider === "github"`
branches never ran. I removed them. They included the private key file
and paste match, and the reconnect flow. Nothing asserts those behaviors
in that spec now.
- **Provider tests do not run in CI.** The root `vitest.config.ts` lists
only Daytona. The other 8 providers, `bridge-template` included, are
typechecked now, but CI does not run their tests.
- **One `packages/db` test never runs.**
`scripts/clean-poisoned-claude-sessions.test.ts` is outside the
`include` of `packages/db/vitest.config.ts`.
- **`plugin-orchestration-smoke-example` does not collect.**
`@paperclipai/shared` is not linked in its `node_modules`. It passes 3
of 3 with an alias.

## Verification

Run these commands:

```sh
node scripts/typecheck-test-programs.mjs --low-memory
pnpm --filter @paperclipai/server typecheck
node scripts/typecheck-test-projects.mjs --low-memory --reuse-declarations
node --test scripts/typecheck-test-programs.test.mjs
```

Results on macOS (arm64), Node 26.12. CI uses Node 24, and its
`Typecheck + Release Registry` job also passes. At head `7d4b5e907a`,
the test programs, `tests/e2e`, and the script tests pass again with 0
errors. The times and peaks below come from the run before the two
latest merges of master:

| Check | Result |
| --- | --- |
| Test programs, `--low-memory` | Exit 0, 0 errors, 42 seconds, peak
1.78 GiB |
| Server layers, low memory | Exit 0, 0 errors, 38 seconds, peak 3.41
GiB |
| Test projects, including `tests/e2e` | Exit 0, 0 errors, 13 seconds,
peak 1.59 GiB |
| Script tests | 12 passed |
| Injected type error in each of 23 places | Each one failed its program
with TS2322 |
| Coverage check | 0 unchecked files, 10 seconds |

I did not run this in a 4 GiB container. The peaks above are `maximum
resident set size` for the largest single process.

**Runtime check of the fixes.** Types do not prove that a test still
works, so I ran the suites before the two latest merges of master:

| Suite | Result |
| --- | --- |
| Runner, full suite | 4,885 passed, 3 failed, 13 skipped |
| Sandbox providers, 10 packages | 939 passed, 12 failed, 36 skipped |
| Plugin SDK | 200 passed |
| `kv-demo-mcp-server` | 12 passed |
| Renamed UI test and its sibling | 4 passed |

All 15 failures exist without these fixes or come from the local
machine:

- **3 Cursor Cloud timeouts.** `artifact-delivery.test.ts` has 1 and
`cursor-cloud-driver.test.ts` has 2. They time out in a full local run,
and all 133 tests in those files with `codex-security-config.test.ts`
pass when run alone. They fail in the same way with those two files at
their unedited versions.
- **12 Kubernetes `file-sync.test.ts` failures.** They fail in the same
way before and after the fixes. The first failure is that
`/proc/self/fd` does not exist on macOS.

After each of the two latest merges of master, I ran only the Runner
test files that I changed:

| Merge | Result |
| --- | --- |
| `885c249cb9`, 8 files | 534 passed |
| `7d4b5e907a`, 7 files | 672 passed, 16 failed |

The 16 failures are in the two `source-reconciliation` test files. They
fail in the same way with master's unedited versions of those files. 15
of them fail with `ACPX sidecar exited at initialize`, so I think my
local build of the Rust and sidecar binaries is out of date. I did not
rebuild them to check. CI builds them from scratch, and all Runner jobs
pass in CI at `7d4b5e907a`.

**Not run:**

- `tests/e2e` and the 8 Playwright suites need a server, so most of them
have only compile checks. `playwright test --list` loads 308 tests from
the main e2e config.
- `packages/plugins/sandbox-providers/kubernetes/test/integration` needs
a cluster, so it has only compile checks.
- I did not run the full `pnpm test:run` or root `pnpm build`. Required
CI runs them.

**Reduced motion.** I ran 6 motion-sensitive Storybook specs in system
Chrome with a temporary config, once with `reduce` and once with
`no-preference`. Both runs had 45 passed and the same 5 failed. So
reduced motion did not change those results. The 5 failures do not
depend on motion. At least one comes from the browser, because system
Chrome prints `oklch(55.6% 0 0)` where the test expects `oklch(0.556 0
0)`. I did not run the other Storybook specs. The `storybook-visual`
label runs that workflow.

## Risks

- **A new lockfile to maintain.** A change to a provider `package.json`
now fails the typecheck job until someone refreshes
`scripts/typecheck-sandbox-providers/pnpm-lock.yaml`. The failure
message gives the command.
- **The job has a new install.** The step downloads provider SDKs, so it
depends on the npm registry. It uses `--frozen-lockfile` and
`--ignore-scripts`.
- **The local install replaces provider `node_modules`.** A contributor
with a standalone provider install must reinstall that provider after
running the script.
- **Reduced motion can change Storybook results.** See "Behavior change
for review". That workflow is not part of required CI.
- **Kubernetes plugin validation changed.** A release of this plugin
ships zod 4. Error wording changes, and very large integers are now
rejected. See "Production change for review".
- **Master moves fast.** Each merge of master brought new test code with
type errors, 27 so far. After this merges, the check reports those
errors in the pull request that adds them.

## Model Used

- Provider: Anthropic Claude, through Claude Code
- Model: Claude Opus 5.5 (`claude-opus-5-5`)
- Capabilities: tool use, code execution, and subagents for the type
fixes in separate files

## 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)
- [ ] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived
details. The app generated the branch name.
- [ ] I have run tests locally and they pass. See the failures explained
in Verification.
- [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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
2026-11-06 07:33:59 -08:00
DottaandPaperclip 6cafcaf89b fix(workspaces): recover unpublished archived Git uploads (#19459)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Remote workspace imports preserve existing files before the server
changes workspace authority.
> - Archived Git imports reconstruct saved files and Git state in a
private repository.
> - A failed upload can leave a pending snapshot journal with no object
in storage.
> - A later reconstruction can have different Git administrative bytes
for the same saved logical source.
> - This pull request lets that import record a new unpublished capture
after it proves that prior objects are absent.
> - The benefit is safe retry through the original import journal while
source checks and atomic publication remain in place.

## Linked Issues or Issue Description

Refs #19396. Refs #19409.

A snapshot upload can fail before object persistence. The caller then
removes its private archive. A retry reconstructs the same saved Git
workspace. If its administrative bytes differ, the snapshot owner
rejects the retry with
`remote_workspace_snapshot_operation_content_changed`. The pending
journal remains blocked even though no snapshot object or remote
authority was published.

## What Changed

- Add an optional unpublished recapture capability to snapshot storage.
Bind it to the original source operation. Existing callers keep the
exact manifest check.
- Enable this capability only for archived Git reconstruction. The
migration owner keeps the source recipe, task binding, ownership, and
publication checks.
- Verify every prior object before new capture admission. Unknown or
corrupt objects stop the retry. Reuse an available prior object,
including an object that appears while the replacement upload runs.
- Compare the observed upload journal under the snapshot row lock before
appending an attempt. Keep network I/O outside that lock. Preserve all
prior attempt metadata.
- Keep the first atomic publication as the winner. A losing uploader
verifies and returns that saved reference.
- Add real PostgreSQL, filesystem, and Git regression tests. Document
the retry behavior.

## Verification

- Baseline `70d23612dd9176cae8ee6b2b6dcf2f6eade9a42a`: the new real Git
fixture fails with
`remote_workspace_snapshot_operation_content_changed`. It fails the
first upload before persistence, removes the old source cache, and
advances unrelated remote refs. The saved task commit and restore point
stay fixed.
- Final frozen source: 20 tests pass in a fresh process. This includes
the real Git regression and all snapshot storage cases. Tests cover
prior object recovery, corrupt and unknown objects, normal caller
mismatch rejection, operation binding, stale journal admission, and late
upload publication in both orders.
- Reproduce the final focused check from `server/`:

  ```sh
node ../node_modules/vitest/vitest.mjs run --config vitest.config.ts
src/services/remote-workspace-snapshot-storage.test.ts
src/services/remote-workspace-migration.test.ts -t
'failed-upload-retry|snapshot storage' --reporter=dot
  ```

- An earlier six-suite run had 201 passing cases and one failing
late-object case. That run started before the final prior-object recheck
was added. The failing case passes in the fresh final run above. This
earlier run is not a clean full-family result for the final source.
- That run skipped 16 lifecycle cases because
`PAPERCLIP_REMOTE_WORKSPACE_LIFECYCLE_TEST_DATABASE_URL` was unset.
Migration, storage, reservation, and concurrency tests used real
disposable embedded PostgreSQL.
- `git diff --check` passes. Full repository typecheck passed before
rebasing. Full test, build, and current-head CI results are pending.

## Risks

- The optional capability permits different physical captures. The
migration owner must prove that the logical source and current ownership
are unchanged. Ordinary mutable workspace uploads keep the previous
mismatch guard.
- An old upload can complete after the last object check. The first
authenticated atomic publication wins. A late upload cannot replace its
object or snapshot reference. Every candidate remains in the retention
journal.
- Unknown storage results and journal changes fail closed. They can
require another canonical retry. This change adds no retry loop and
changes no database schema.

## Model Used

OpenAI Codex, GPT-6 family. The worker used reasoning, tool use, code
editing, and local test execution. The worker runtime did not expose an
exact model ID or context window.

## 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

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-06 08:04:35 -06:00
DottaandPaperclip 2f35eb1080 feat(dev): add incremental local verification and pass reuse (#19345)
## Thinking Path

> - Paperclip coordinates agents that make and verify repository
changes.
> - Local verification currently defaults to the complete Vitest suite.
> - Contributor instructions also require broad local checks at each PR
handoff.
> - CI already owns conservative affected-test selection and broad
final-revision checks.
> - This pull request adds local selection and pass reuse from those
existing contracts.
> - Agents can get focused feedback and use CI to close the remaining
coverage gaps.

## Linked Issues or Issue Description

**Subsystem affected**

Developer verification scripts and contributor guidance. Related
selection work: #18398 and #18464.

**Problem or motivation**

An agent that repeats an unchanged local verification step starts the
complete suite again. The handoff guidance also duplicates broad CI
coverage locally.

**Proposed solution**

Add `pnpm verify` for the actual working tree. Select affected Vitest
specifications with the CI task policy and dependency graph. Reuse
successful checks whose inputs are modeled. Run opaque checks fresh.
Report exit 2 when broader verification is required. Update the
contributor contract to accept applicable final-revision CI coverage.

**Alternatives considered**

Plain `vitest related` omits filesystem and opaque dependencies.
Commit-only cache keys miss dirty files. Running full local suites at
every handoff repeats CI work.

**Roadmap alignment**

This is repository development tooling. It does not change the product
roadmap.

## What Changed

- Add `pnpm verify`, `--explain`, `--base`, `--full`, and `--no-cache`.
- Reuse CI selection and exact runner ownership for dirty, staged,
committed, deleted, renamed, and untracked inputs.
- Keep native server suites and serialized suites in their local owners.
Keep six sequential chat shards.
- Cache selected passes within one worktree. Hash source, fixtures,
installed package contents, dependency bindings and installation
metadata, dotenv files, child environment, toolchains, platform, and
selection.
- Run opaque consumers fresh. Preserve failed, interrupted,
mutated-input, and partial-coverage outcomes.
- Update AGENTS.md, CONTRIBUTING.md, and DEVELOPING.md guidance. Record
the shared `verify` command as the sole exception to the package-script
rule. Register the new tests in the existing CI contract-test command.
- Add optional root/environment inputs to shared graph helpers. Existing
CI defaults stay the same.

## Verification

- Fourteen new integration tests pass locally across focused runs with
real Vitest selection and execution; CI colors are covered.
- 51 existing targeted selector/input, project-isolation, and
stable-runner checks passed. Four relevant runner contracts also pass
after the workspace change.
- Repeated unchanged execution skips reusable tests. Source,
environment, installed code, dependency bindings, and new untracked
tests invalidate results.
- Installed-code mutation with a restored modification time still
invalidates a cached pass. Internal skill-directory links preserve
reuse.
- Workspace B/C tests prove discovery, reusable/fresh partition
execution, pass reuse, and external-input failure. Chat selection
produces exactly six single-worker partitions.
- A deliberate unrelated failing test is omitted by narrow selection and
caught by `--full`.
- Red/green regressions prove fingerprints preserve file boundaries and
reject edits made between diff discovery and snapshotting.
- Opaque external-file changes still fail on a subsequent run. Source
mutation and process interruption cannot publish reusable passes.
- `pnpm verify --explain` works in the checkout and requests broad CI
coverage for this tooling change. No duplicate full local suite was
started.
- [Final-revision
CI](https://github.com/paperclipai/paperclip/actions/runs/42117291789)
passed on `ed85d96ddff82c05c325948680b593b0f48c473d` (attempt 2). The
scoped Canary retry preserved all passing test/build results.
- [Greptile
review](https://github.com/paperclipai/paperclip/pull/19345#issuecomment-6670050175)
is 5/5; all four review threads are resolved.
- The additional Paperclip review concluded neutral because its
execution stopped; it produced no assessment.

## Risks

- Pass reuse depends on conservative dependency classification. Opaque
consumers, external database/live settings, and non-isolated projects
retain fresh or broad coverage.
- Local passes cover selected Vitest checks. Required CI,
build/typecheck, release, browser, and platform acceptance remain
separate obligations.
- Cross-worktree caching and cross-agent scheduling are outside this
change.
- The initial installation scan reads dependency contents;
stat-validated, worktree-local digest memoization avoids rereading
unchanged contents. Subsequent scans still inspect file identity and
nanosecond change/modification times.
- No dependency lockfile or workflow changes.

## Model Used

OpenAI Codex, `gpt-6.1-sol`, max reasoning, with local shell and file
tools. Context window size is not exposed by this host.

## 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>
2026-11-06 07:29:10 -06:00
DottaandPaperclip 70d23612dd fix: offer Interrupt when queued-message steering is unavailable (#19450)
## Thinking Path

> - Paperclip lets people manage work performed by AI agents.
> - Task chat saves follow-up messages while an agent runs.
> - A native runner can accept Steer only after an active provider turn
exists.
> - During preparation, or with an unsupported provider, the queue
showed a disabled Steer button and no delivery action.
> - The server also rejected Interrupt for ordinary native queues.
> - This change offers an explicit Interrupt fallback and uses the
existing cancellation and admission path.
> - People can send their saved messages while Stop confirmation,
cleanup, and execution gates remain enforced.

## Linked Issues or Issue Description

Related: #15865 covers mixed legacy queues. #15030 covers steering
acknowledgements. This change covers native queues without available
steering.

**What happened?**

A queued message had a disabled Steer button while the native runner was
still preparing. Clicking it did nothing. The server returned HTTP 409
for an explicit Interrupt request against the same native queue.

**Expected behavior**

Offer Steer when the provider can accept same-turn input. Otherwise
offer Interrupt, labeled with its actual effect. Preserve saved messages
until the previous execution stops and normal admission accepts the
successor.

**Steps to reproduce**

1. Start a task with the Paperclip Runner adapter.
2. Submit a follow-up while the run is preparing, before its provider
turn opens.
3. Observe the disabled Steer button above the composer.
4. With this change, click Interrupt. The existing Stop path cancels the
previous execution and submits the saved queue through normal admission.

**Paperclip version or commit**

Reproduced locally on master at 523818ea9b. The branch is rebased on
2f9d3d43c3.

## What Changed

- Offer Interrupt for unavailable or unsupported native steering when
the parent supplies an interrupt callback.
- Keep Steer for an available provider turn.
- Accept explicit Interrupt for a deferred native queue and record its
run target.
- Bind native continuation to the exact Interrupt queue, run, actor, and
cancellation receipt. This lets one click send the messages after Stop
completes.
- Add component, task-thread, real PostgreSQL route, and continuation
authorization regressions.
- Close the route fixture database pool before disposing its PostgreSQL
instance.
- Document the fallback and its Stop and admission requirements.

## Verification

- Red: two component cases failed because Interrupt was absent. Two
route cases returned HTTP 409, `This queue does not support
interruption`, before the repair.
- Red: stronger delivery assertions also caught `send_predates_stop`
after the first repair. The admission fix covers both the freshness
exception and later eligibility check.
- Green: both route regressions now wait for preparation settlement,
then deliver both saved messages exactly once without a second click.
The complete route suite passes 119 tests. The complete continuation
suite passes 376 tests, including wrong actor, queue, target, and
missing-receipt cases.
- UI: task-thread and queued-message suites pass 394 tests, with one
existing skip. The issue-page suite also passes (the earlier three-suite
run passed 644 tests before the final three UI cases).
- Token gates and `git diff --check` pass.
- Full workspace build and low-memory typecheck pass. The initial
typecheck caught a missing `membershipRole` in an unrelated fixture; the
rebase picked up the correction already on master, and the complete
typecheck then passed.
- The full local `pnpm test:run` passed all six chat shards (1,931
tests). It was stopped during general-server validation after the final
commit passed all PR CI gates. The complete local suite is not claimed
as a pass.
- Earlier route-suite teardown timed out with an open database pool.
Closing that pool fixed teardown; the complete route suite then passed.
- All final-head CI gates pass: 52 successful checks and two intentional
skips. Greptile is 5/5 on the same head with no unresolved review
threads.

## Risks

Interrupt stops the previous execution and starts a successor; it is a
different action from same-turn steering. The UI labels that action
explicitly. Cleanup or execution gates can keep the messages queued.
Existing company access, board permissions, queue revision, run target,
cancellation proof, and admission checks remain in place. No schema
migration is needed.

## Model Used

OpenAI Codex (GPT-6), with reasoning, tool use, and code execution. The
exact model ID and context window are not exposed by this client.

## 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>
2026-11-06 07:11:38 -06:00
DottaandPaperclip 275b334fc5 fix(workspaces): skip redundant repository admission snapshots (#19444)
## Thinking Path

> - Paperclip manages AI agents and their execution state.
> - Remote workspace admission must preserve files before execution
starts.
> - Admission saved the entire workspace once per registered repository
on every run.
> - Existing snapshot receipts can prove that validated repositories are
already saved.
> - This change uses those receipts and saves new repositories once per
admission batch.
> - It also preserves fresh configuration metadata and reports actual
workspace reuse.

## Linked Issues or Issue Description

**What happened**
Remote follow-up runs uploaded an unchanged workspace for each
registered repository before starting the provider. Configuration
persistence also overwrote new evaluation metadata, and freshness logs
could claim replacement when the same workspace was reused.

**Expected behavior**
Validate existing repositories without uploads when a committed snapshot
covers their descriptors. Save acquired repositories before publishing
ready receipts. Retain current evaluation metadata and report the actual
workspace outcome.

**Steps to reproduce**
Use a remote workspace with two registered repositories. Prepare it,
then admit a follow-up run. Observe repository snapshot operations
despite unchanged repositories. The regression tests exercise this with
real Postgres, Git, and separate sandbox directories.

**Environment**
Server remote workspace admission at commit
c0214826b3. Related work: #19374 handles
interrupted clone staging; this change handles snapshot admission cost.

## What Changed

- Skip repository saves when the committed snapshot covers the validated
descriptor.
- Save all repositories in one admission snapshot before publishing
ready receipts.
- Retain descriptor coverage only when the new archive contains the
checkout. Drop deleted checkout coverage so admission can acquire it
again.
- Restore `needs_repair` status for failed batch saves and retry failed
uploads.
- Let fresh preparation metadata override stale reserved metadata while
preserving storage authority.
- Report actual reuse when freshness policy requested replacement.
- Add regression coverage and fix an existing routine user fixture
missing its membership role.

## Verification

- Red: original code fails unnecessary-snapshot, evaluation-metadata,
and reuse-message regressions.
- Green: 517 affected tests across six suites before the final coverage
correction. After that correction, all 102 remote workspace/concurrency
tests and 96 archive tests pass. Imported-repository, deleted-checkout,
and upload-retry cases pass.
- Additional red/green: deleted checkout coverage fails before the fix
and passes after it. All 96 archive tests pass, including manifest
digest and size bounds.
- `pnpm -r typecheck`, `pnpm build`, and `pnpm check:token-gates` pass
locally.
- All final-head CI verification jobs pass, including the aggregate `ci
/ verify` check. Greptile gives the final head 5/5.
- The monolithic local `pnpm test:run` passed all six chat shards and
continued through general server tests. It was stopped after final-head
CI passed; it did not complete locally. The targeted local regressions,
affected suites, typecheck, and build completed successfully.

## Risks

Snapshot receipts must refer to committed bytes. Legacy receipts require
one conservative save. Failed uploads must not publish repository
readiness. Replacement-class drift still retains the original
configuration for an explicitly reused workspace.

Existing directories with damaged or missing Git metadata still require
repair. Master and this PR both validate those directories without
cloning over them, preserving any surviving user files. Clearing a
snapshot descriptor would not change that path. Complete directory
deletion is different: this PR clears coverage so normal acquisition can
clone it again.

## Model Used

OpenAI gpt-6.1-sol through Codex. Used reasoning, repository inspection,
code editing, and local execution. The host does not expose the 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>
2026-11-06 07:08:59 -06:00
DottaandPaperclip c1d567ff6a fix(workspaces): isolate archived nested Git reconstruction (#19409)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Durable workspace import must preserve archived task files and Git
history.
> - A saved nested checkout can be a linked worktree whose branch
belongs to its old absolute path.
> - Archived import reconstructs that checkout in a new scratch
directory.
> - Ordinary linked recovery rejects the old branch at that new path. It
can also write into a cache used by other import workers.
> - This pull request reconstructs archived nested checkouts as private
standalone repositories.
> - Each import preserves saved files and extra history without changing
shared worktree registrations or branches.

## Linked Issues or Issue Description

**What happened?**
Archived workspace import fails when a saved nested linked checkout has
a branch owned by the old path. The new scratch path fails the
linked-worktree ownership check. The existing cache lock is
process-local, so separate import processes also share mutable Git state
without a common lock.

**Expected behavior**
Archived import must create an independent portable copy of the saved
checkout. It must retain the saved commit, branch name, staged edits,
working files, ignored recovery files, settings, and extra saved
commits. It must keep the source cache unchanged and enforce source
authorization.

**Steps to reproduce**
1. Create a managed nested linked checkout with an unpushed commit and
staged and unstaged edits.
2. Save an encrypted restore point, including ignored files and an extra
history tip.
3. Restore its saved contents under a different absolute workspace path.
4. Before this repair, the new path cannot adopt the branch owned by the
old path.

**Paperclip version or commit**
The real Git regression fails before the repair at `fc1f5f3052`. The
final branch includes the merged interrupted-upload and nested-source
authorization fix from #19396.

**Deployment mode**
Archived remote workspace migration with real Git repositories,
disposable PostgreSQL, and encrypted object storage. Local integration
tests use the filesystem storage provider.

Builds on merged #19402 and #19396. Related #19374 concerns interrupted
clone staging; it does not implement private archived reconstruction. No
duplicate open repair was found.

## What Changed

- Enable private repository reconstruction only for archived migration.
Ordinary linked recovery keeps its path ownership guard.
- Add an object-only source to the managed checkout owner. A verified
cache supplies only the saved commit and authenticated bundle
prerequisites through scoped fetches. The private copy includes no
unrelated task refs or objects, hard links, object alternates, or
current cache files.
- Fetch missing authenticated bundle prerequisites before importing a
saved bundle in both private reconstruction and ordinary linked
recovery. A pruned cache can use the approved remote; unavailable
history still blocks restore.
- Keep every authenticated restore point's extra commit under a private
ref in root and nested private copies so portable archive capture and
garbage collection retain it. Ordinary recovery keeps its existing
history and expiration rules.
- Share the verified, bounded ignore-file copy between root and nested
reconstruction. Sources remain unchanged.
- Retain source authorization before and after reconstruction and the
final source-row locks from #19396.
- Test concurrent private copies, source rejection, foreign task refs
and objects, ordinary linked prerequisite recovery, a real migration,
and cold restore after removing all original repositories. Test hard
links, oversized excludes, unsafe info paths, and replacement during a
descriptor read.

## Verification

- Final affected run: 292 tests pass across ten suites. These cover real
Git repositories, encrypted restore points, disposable PostgreSQL
migration, portable archives, the restore-point ledger, source
rejection, and concurrent copies.
- Full repository typecheck and build pass after the scoped-object
repair. Final server typecheck and full build also pass after
restricting preserved refs to archive mode.
- RED then GREEN: a linked checkout at a different path; a pruned bundle
prerequisite still available from the approved remote; foreign task refs
and objects entering the archive; root extra history disappearing after
cold restore; and archive-only refs blocking ordinary standalone
expiration.
- Two concurrent private copies retain the saved head, branch, staged
and unstaged edits, ignored recovery bytes, settings, and modes. Source
refs, index, worktree registrations, and working files remain unchanged.
- Delete the original checkout, cache, remote, and private copies after
portable capture. Cold restore retains the saved files and extra history
after garbage collection. No alternates or unrelated task objects
remain.
- Ordinary linked recovery retains its path ownership check and recovers
pruned prerequisites. New and existing ordinary standalone destinations
have no archive-only refs and remain eligible for expiration after
normal object cleanup.
- Unsafe exclude tests reject hard links, oversized files, nonregular
paths, info-directory substitution, and replacement during the
descriptor read. They preserve the target and replacement source bytes.
- Preserve the failed attempts: an initial migration fixture changed its
home after constructing the source path. Later expiration fixture
attempts used a filtered current-head tip, omitted the local-source
callback, or used cleanup that generated Git server-info files or left
packed unreachable objects. Correct those setup assumptions before the
actual regressions fail. Final affected suites pass.
- Two earlier local full-suite attempts were interrupted before editing
valid review findings. Neither is reported as a full-suite PASS.
Final-head full CI passes; review is 5/5 with no open findings.

## Risks

Archived imports use additional private disk space for independent Git
objects. Missing, changed, or unsafe sources still block import. The
repair does not weaken the default linked-worktree ownership check,
change stored formats, or update live provider state. The shared
checkout addition is optional and has no effect for existing callers
that do not supply an object source.

## Model Used

OpenAI GPT-6 in Codex, with code editing, tool use, and test execution.
The exact runtime model identifier and context-window size are not
exposed in this session.

## 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>
2026-11-06 00:56:06 -06:00
DottaandPaperclip 66d3fa97a9 fix(workspaces): preserve ignored files in archived Git imports (#19402)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Durable workspace migration must preserve archived files and saved
recovery data.
> - An archived Git workspace can contain ignored recovery receipts and
bundles in its encrypted restore point.
> - The importer reconstructs a private repository from a verified
source before it applies that restore point.
> - Reconstruction omitted the source repository's local ignore rules.
The restored files then changed classification, and the exact
restore-point check failed.
> - This pull request copies the verified local ignore rules into the
private repository before restoration.
> - The source stays unchanged, and the original restore-point integrity
checks still apply.

## Linked Issues or Issue Description

**What happened?**
An archived workspace with saved files under an ignored recovery
directory failed migration with `restored_contents_mismatch`. The task
commit and staged index matched. The ignored files were restored, but
the private repository treated them as untracked work because its
`info/exclude` rules were missing.

**Expected behavior**
Reconstruction from an existing verified source must preserve its local
ignore policy. Saved ignored files must survive migration and a cold
object-store restore with their original classification. Import must not
follow a symlink to an unrelated ignore file or edit the source
repository.

**Steps to reproduce**
1. Exclude a recovery directory in the managed source repository's
`info/exclude` file.
2. Save staged edits, unstaged edits, an ignored recovery receipt, and
an ignored binary bundle in an encrypted restore point.
3. Archive and remove the task worktree.
4. Import the archived workspace. Before this change, restore-point
validation fails because the reconstructed repository lacks the local
exclusion rule.

**Paperclip version or commit**
Reproduced on master at `879140cbbd`.

**Deployment mode**
Cloud workspace migration with a retained verified Git source,
PostgreSQL, and encrypted durable object storage. The tests use real
disposable PostgreSQL, Git repositories, and encrypted filesystem-backed
object storage.

Related migration work: #18826, #19138, and #19396. No duplicate open
fix was found.

## What Changed

- Copy the verified source's `info/exclude` file into the private
reconstructed repository before applying its restore point.
- Bound the read to one MiB. Reject symlinked, non-regular, hard-linked,
or changing source files.
- Keep the original source bytes unchanged.
- Add regressions that check staged and unstaged edits, ignored recovery
files, cold restore, and rejection of a symlinked ignore file.
- Document the reconstruction behavior.

## Verification

- Before the repair, the saved-ignored-files regression fails with
`restored_contents_mismatch`.
- After the repair, both focused cases pass.
- At rebased head `81a0b1c041`, all 206 tests across migration, snapshot
storage, archive, and migration concurrency suites pass. The merged
interrupted-upload and nested-source approval regressions remain intact.
- Server package typecheck passes.
- Full repository typecheck and build pass at the rebased head. The full
local test suite is running. The prior local full-test run was
interrupted for rebase, and is not a passing result.
- Initial CI hit a 15-second timeout in unchanged
`activity-routes.test.ts`; the exact case passed in a focused local run.
The browser shard lost its self-hosted runner, as confirmed by its check
annotation; GitHub did not retain its full log. Those failures remain
recorded. An unchanged retry was superseded by the required conflict
rebase. At exact head `81a0b1c041`, all 53 CI checks and both required
aggregate gates pass; Greptile is 5/5. The full local suite remains in
progress, so no local full-suite PASS is claimed.

A second automated review noted the existing nested-checkout
counterpart. This PR fixes root reconstruction. The nested
linked-checkout repair and its saved-ignored-files/cold-restore
regression are implemented in #19409, which is required before the
migration rollout uses nested imports. This PR leaves that sibling
recovery path unchanged. The two identical scope warnings are addressed
through that linked repair.

## Risks

The copy applies only when an archived Git restore-point source is still
present and verified. It changes only the private reconstruction
directory. Missing sources retain the existing restoration path. Unsafe
or unstable local ignore files block import and retain the original
migration obligation. No database migration or saved format changes are
included.

## Model Used

OpenAI GPT-6 in Codex, with code editing, tool use, and test execution.
The exact runtime model identifier and context-window size are not
exposed in this session.

## 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>
2026-11-05 23:11:28 -06:00
DottaandPaperclip da34bcd48d fix(workspaces): resume archived imports from their saved upload (#19396)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Durable workspaces let a replacement web server restore saved task
files.
> - Legacy workspace imports keep a journal and an encrypted upload
receipt across interruption.
> - An archived Git import can rebuild a missing source from its saved
task commit and edits.
> - A fresh clone can also contain newer remote refs. Those refs change
the archive manifest even when the task files are unchanged.
> - This pull request recovers the exact authenticated upload for an
interrupted archived Git import.
> - The original journal, source binding, task binding, and execution
checks still control publication.

## Linked Issues or Issue Description

**What happened?**
An archived Git workspace import stopped after its upload persisted. A
retry rebuilt the source from the remote repository. New remote refs
changed the archive manifest, so the original upload receipt rejected
the retry with `remote_workspace_snapshot_operation_content_changed`.

**Expected behavior**
The retry must recover its original saved upload and complete the same
import. It must keep the saved task commit, staged edits, unstaged
edits, lifecycle state, and task binding. A changed source or task
binding must still block publication.

**Steps to reproduce**
1. Archive a Git task with staged and unstaged edits, save its
restoration recipe, and remove its local repository.
2. Start the workspace import and lose the upload reply after object
persistence, or interrupt its independent restore after the upload is
acknowledged.
3. Advance the remote default branch and add an unrelated branch.
4. Retry the original import. Before this change, both interruption
cases fail with the same content-change error.

**Paperclip version or commit**
Reproduced on master at `d8b0eae68772a3bd2bb4a8163b5ce95764b97cff`.

**Deployment mode**
Cloud workspace migration with external PostgreSQL and durable encrypted
object storage. The regression tests use real disposable PostgreSQL, an
HTTP Git remote, and encrypted filesystem-backed object storage.

Related merged work: #18826 and #19138. No duplicate open fix was found.

## What Changed

- Add scoped recovery of an acknowledged snapshot or a pending upload
whose object persisted. Authenticate the archive before returning it.
Recovery alone does not publish the snapshot.
- Resume archived Git imports from those exact saved bytes. Keep the
original operation and all publication checks.
- Lock and recheck each saved nested source’s company, project, and
repository identity in the final publication transaction.
- Keep mutable local sources on the existing capture and
content-comparison path.
- Add regressions for both interruption points, unrelated remote
changes, source revocation during recovery, and local edits after
interruption.
- Document the retry behavior.

## Verification

- Before the repair: both new archived retry regressions fail with
`remote_workspace_snapshot_operation_content_changed`; the
mutable-source control passes.
- After the repair: all 204 tests in the migration, snapshot storage,
archive, and archive environment suites pass. The suites use real
PostgreSQL and encrypted storage.
- Server package typecheck and full repository typecheck pass on
`bffebbab60edbdf50b42fc37a9e58beb01ceb94d`.
- An added source-revocation test initially expected a later expiry
error. The existing publication fingerprint rejected the change first.
The test now requires that earlier
`remote_workspace_migration_publication_changed` error and still checks
that authority was not published.
- The review finding was reproduced before the safety repair: changing a
saved nested repository URL after upload still allowed publication. The
new regression requires rejection, and unchanged approved nested sources
still restore.
- Full repository typecheck and build pass on the final head. The full
local test command stopped at one Slack manager authorization fixture
with `socket hang up`; the exact case then passed in isolation on the
same head, and all three CI chat shards passed. The original local
failure is retained.
- The first CI server shard run had 4,724 passes and one runtime-process
readiness failure in an unchanged fixture. The exact fixture passed in
isolation. One unchanged rerun of that shard passed. The first failure
remains recorded in the workflow history.
- The earlier candidate’s full local test run was stopped after the
confirmed review finding; that interrupted run is not reported as a
pass.
- All CI gates, including `ci / verify` and `ci / e2e`, pass on
`bffebbab60edbdf50b42fc37a9e58beb01ceb94d`. Greptile is 5/5 on that
head, with no remaining findings or unresolved review threads.

## Risks

Recovery applies to archived Git sources, whose saved recipe and
lifecycle checks still run before publication. A source change during
recovery must keep the snapshot unpublished. Missing or corrupt saved
objects still fail authentication or retain the existing import
obligation. Mutable local sources still reject changed contents. This
change adds no database migration and changes no saved archive format.

## Model Used

OpenAI GPT-6 in Codex, with code editing, tool use, and test execution.
The exact runtime model identifier and context-window size are not
exposed in this session.

## 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>
2026-11-05 22:19:20 -06:00
f2593b7905 feat: make Coordinator and Agent Chat standard and speed up navigation (#19360)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - People enter that work through the workspace, agent conversations,
and tasks.
> - Coordinator and Agent Chat still require experimental enrollment.
> - Task link prefetches do not warm the compact queries used by the
default task view. Chat also waits for a request when its navigation
list already holds the conversation.
> - This pull request makes Coordinator and Agent Chat standard and
reuses the reads needed for navigation.
> - People can choose Classic workspace in Experimental settings. Cached
work can appear while fresh data loads.

## Linked Issues or Issue Description

**What existing behavior does this improve?**

Workspace selection, Agent Chat availability, and navigation between
Chat, Tasks, and task details.

**Subsystem affected**

Cross-cutting: UI, workspace preferences, instance settings, and the
database migration.

**Current behavior**

People must enable Coordinator and Agent Chat in Experimental settings.
Opening a task can repeat requests because prefetch warms the full
detail and comment queries, while the default view reads compact task
data and a recent comment window. Opening Chat waits for a detail
request even when the current person's conversation list contains it.

**Proposed behavior**

Coordinator is the standard workspace for everyone. Experimental
settings offer Classic workspace, off by default. Old Coordinator
experiment values do not select Classic. Agent Chat is available to
everyone, including instances with an old saved or managed off value.
Task link intent warms the queries used by the mounted view. Chat can
use the current person's company-scoped conversation list during
refresh.

**Reason and benefit**

People can use the standard workspace without setup. Repeat navigation
can show cached content while the server refreshes it.

**Breaking changes**

Existing Coordinator experiment and Agent Chat off values no longer
disable these surfaces. Classic requires an explicit new opt-in. The
workspace API keeps its existing response shape and audit checks. The
migration retains legacy values and adds a separate Classic preference.
Execution permissions, company access, and chat privacy checks still
apply.

**Additional context**

Roadmap check: this graduates existing surfaces and improves their
navigation. It does not add a new agent execution capability. Duplicate
searches found no open Coordinator workspace PR. Related server cache
work, Refs: #17828, addresses compact issue-list invalidation; this PR
addresses client navigation queries.

## What Changed

- Add a default-off Classic workspace preference. Derive the existing
workspace API response from that choice. Keep personal persistence,
account isolation, and audited writes in the workspace preference
service.
- Replace the Coordinator experiment control with Classic workspace. Use
Coordinator while preferences load. Update the existing settings
examples and navigation recipe.
- Retire the Agent Chat experiment control. Ignore old stored and
managed off values. Retain the compatibility key and the existing
execution and access checks.
- Reuse account- and company-scoped chat list data with its original
freshness timestamp.
- Share compact task and recent-comment query options between prefetch
and the task view. Keep full-history prefetch for Classic tasks and
expanded history.
- Add upgrade, replay, cache, account isolation, and browser switching
regressions. Update product, database, development, and roadmap
documentation.

## Verification

- Targeted preference, settings, migration, cache, and UI regression
tests passed during implementation. The cache tests hold refresh
requests pending and check that content still renders. They also check
account isolation and stale refresh behavior.
- A real browser test verified fresh Coordinator defaults, Classic
opt-in persistence, and return to Coordinator. It used an isolated
source checkout with fresh data on macOS.
- Token, migration numbering and safety, map, and Storybook catalog
checks pass after the rebase.
- Repository typecheck and build pass. Typecheck and token gates also
pass after review repairs. The broad local run passed all six chat
integration shards (1,931 tests). It then found the host-CLI-dependent
recovery fixture described below. Its remaining duplicate work was
stopped after the full current-head CI matrix passed; this is not a
claim that the broad local command completed green.
- Review repairs passed 419 UI/migration fixture tests, 19 Coordinator
navigation tests, and all 214 tests in the five affected server suites.
The 24 Chat/workspace browser tests pass, including standard Coordinator
switching and explicit Classic persistence.
- The broader browser repair run passed 85 tests. It retained two failed
assertions and skipped five later serial cases. The affected files then
passed all 11 tests after the fixes: reopen the desktop panel after
reload and open More for Audit and Connectors. This includes the five
serial cases that had not run.
- The broad local suite exposed a recovery fixture that executed the
host Codex CLI during a simulated remote probe. On a host with Codex
0.154.0, model fallback broke its fixed-model assertion. The fake
sandbox now reports Codex 0.160.0. All 20 selected recovery/provider
compatibility cases pass after the repair.
- A CLI company import/export suite timed out during server startup in
the second CI run. The port fallback is intentional in that fixture. No
root cause was established. That suite passes on the final commit in CI.
This records recovery, not a claimed product fix for the earlier
timeout.
- The first CI run exposed remaining assumptions about the retired flags
and Classic UI. The repair commit updates those fixtures and navigation
steps. It also restores the missing enabled Cases destination in
Coordinator. Earlier local recovery attempts used the wrong fixture
notification and advanced fake time during live execution; the corrected
tests use the subscribed recovery queue and wall time during execution.
- Greptile reviewed commit `98972b030d4505d838427a2fca6b196b8cad6d47` at
**5/5** with no new comments. The original finding is resolved.
- Current-head CI is green: **56 successful checks**, with three checks
skipped by workflow filters. This includes typecheck, build, the
complete Vitest matrix, all eight browser shards, Runner verification,
release checks, and security checks. [Final CI
run](https://github.com/paperclipai/paperclip/actions/runs/42132651414).
- Typecheck caught missing `pid` and `startedAt` fields in the simulated
command result. The fixture now returns the complete process contract,
and the server test-layer typecheck passes.
- Storybook catalog alignment was checked. Storybook play tests were not
run. Hosted latency and cold bundle loading were not measured.

## Risks

- The new default changes the workspace for people who previously left
the Coordinator experiment off. They can opt into Classic in
Experimental settings.
- The additive migration must run before the new server code. It is safe
to replay and preserves explicit Classic choices.
- Cached content can be stale during background refresh. Existing query
invalidation and source timestamps still control freshness.
- These changes reduce avoidable loading waits. They do not establish a
measured improvement in hosted request latency or initial bundle
download time.

## Model Used

OpenAI Codex, based on GPT-6, with reasoning, repository tools, code
execution, and browser automation. The exact serving revision and
context-window size are not exposed in this session.

## 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: Scott Tong <scott@scottsmbpm5max.lan>
Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-11-05 16:28:25 -08:00
DottaandPaperclip 62a5aa7705 fix(runner): forward configured bindings into OpenCode (#19319)
Forward controller-selected task bindings into OpenCode shell commands. Keep OpenCode runtime configuration isolated. Redact raw and JSON-escaped binding values while preserving the non-secret environment manifest.

Fixes #19257

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-11-05 14:01:12 -06:00