Commit Graph
5309 Commits
Author SHA1 Message Date
DottaandPaperclip d75b3fc33f perf(daytona): observe command exit before log-follow closure (#16561)
Return completed Daytona session commands after recorded exit and a final log snapshot. Keep bounded early status reads, command deadlines, late callback fences and stream recovery.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
canary/v2026.1016.0-canary.10
2026-10-16 07:09:30 -05:00
DottaandPaperclip 43ffe8ce95 perf: skip conditions for unselected tool profile entries (#16556)
Check exact tool profile selectors before evaluating conditions. Matched entries retain fresh policy condition checks and existing approval, deny, binding, and decision-phase behavior.

Validation: 70 affected cases pass with zero skips. Full repository typecheck and build pass. A balanced same-database comparison over 47,931 entries preserves all decision JSON and reduces 200 decisions from about 1.05 seconds to 0.40 seconds. Fresh exact-head full CI, E2E, Superagent, legacy security, and Apex 5/5 passed with no unresolved findings.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-10-16 05:59:23 -05:00
DottaandPaperclip 8556539364 perf(adapter-utils): batch remote GitHub launcher staging (#16552)
Stage the nine managed GitHub launcher files through one bounded control command. Preserve per-file locks, content verification, atomic replacement and control-channel dispatch.

Real Daytona staging decreased from about one second to 0.24–0.34 seconds. Full CI, E2E, Superagent and Apex 5/5 passed on the reviewed head.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-10-16 04:59:21 -05:00
8f1cb11a03 fix(workspaces): name the owner action when a shared source is restricted (#16545)
A reused task workspace in a shared project checkout keeps its source
denial when another task's restricted worktree shares that checkout
(#16095 deliberately does not clone over existing workspaces). The run
then failed as an opaque `setup_failed` 403 and the task was blocked
with a generic "no live execution path" notice.

Convert that exact denial into a `configuration_incomplete` failure
with reason `workspace_source_restricted`, give the task notice and the
recovery action the owner step, and keep this pre-dispatch owner action
out of the unexpected Sentry run-failure stream. The reason and
predicate live in a dependency-free module. Access checks are unchanged.

Co-Authored-By: Paperclip <Paperclip-Paperclip@users.noreply.github.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
canary/v2026.1016.0-canary.8
2026-10-16 01:33:53 -07:00
DottaandPaperclip f1d4bc1617 perf(slack): resolve only signing secret during webhook checks (#16548)
Resolve only the current Slack signing secret during workspace checks and authenticated setup evidence. Preserve full runtime credential resolution, company bounds, rotation, and auditing.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
nightly/v2026.1016.0-nightly.0 canary/v2026.1016.0-canary.7
2026-10-16 03:05:05 -05:00
Devin FoleyandPaperclip 78b833c495 Dispatch routine and monitor work at saved deadlines (#16514)
## Thinking Path

> - Paperclip manages work that agents run for a company.
> - Routines and issue monitors store their next run time in the
database.
> - The app currently waits for the heartbeat interval to find that
work.
> - This can delay work after a workspace wakes before its saved
deadline.
> - This pull request uses the existing work coordinator to schedule
each known deadline.
> - It also parses each cron expression once, so sparse schedules do
less work on the event loop.
> - Agents can start due work sooner while the existing execution checks
stay in place.

## Linked Issues or Issue Description

**What happened?**

Routine and issue-monitor dispatch depends on the heartbeat scan
interval. A workspace can wake early and still wait for the next scan. A
sparse cron search also parses the same expression for every minute it
checks. In a local annual-schedule test, the deadline callback ran on
time but schedule calculation delayed the routine record by 13.6
seconds.

**Expected behavior**

Use a saved future deadline to request the existing dispatch scan.
Restore deadlines at startup and update them after a producer
transaction settles. Do not let future timers keep an idle workspace
active. Parse a cron expression once for each search.

**Steps to reproduce**

1. Set an active routine and an assigned issue monitor to the same
future deadline.
2. Choose a deadline between heartbeat scans. Use an annual routine
expression to exercise a sparse search.
3. Compare the saved deadline with the routine firing and agent start
times.

**Paperclip version or commit**

Source checkout based on c7ea5c0216.

Related public changes: #16215 reports routine deadlines for external
wake. #8034 caches time-zone formatters in the cron search. This change
reuses those contracts.

## What Changed

- Register separate routine and issue-monitor workers with the existing
delivery coordinator after startup housekeeping.
- Restore the earliest eligible future deadline from the database after
each scan.
- Notify the matching worker when routine or monitor writes settle,
including the native `set_task_monitor` tool. Keep the heartbeat
interval as a recovery scan for blocked or externally written work.
- Retain the scan-start cutoff so a deadline crossed during a slow scan
receives an immediate follow-up scan.
- Retain the coordinator gates for standby, idle drain, and shutdown.
Future timers do not count as active work. Bound expired deadline
retries during idle reconciliation so a paused worker cannot spin.
- Parse a cron expression once during a next-run search. Skip impossible
UTC dates before time-zone formatting. Preserve the existing calendar
and time-zone matching.
- Add clock, transaction, failure, SQL eligibility, and producer
notification tests. Document the scheduler behavior.

## Verification

- `pnpm -r typecheck`: passed.
- `pnpm build`: passed.
- Full CI, browser tests, and security scan: passed on final head
9fc857dcec. Greptile Apex is 5/5 with no
unresolved comments.
- Final focused startup, deadline, routine, SQL eligibility, native
monitor, cron, and coordinator tests: 159 passed across seven suites.
The crossed-deadline and native-notification regressions failed before
their fixes.
- CI caught the existing startup suppression assertion. It failed
locally before restoring the outer timer-dispatch guard; all 38 startup
tests now pass.
- A canceled-drain regression also failed before the fix. Future timers
keep their saved time; only expired deadlines use the bounded idle
retry. Server typecheck and build passed again.
- The idle-drain regression reproduced 22 checks in 20 ms before its
fix. After the fix, 43 coordinator and related worker tests passed.
Server typecheck and build passed again after the review fixes.
- The broad local `pnpm test:run` attempt reported existing
host-sensitive failures. Two Git fixture tests fail identically on
unchanged c7ea5c0 because the host default `main` leaves an extra branch
in an intended master-only remote. Both pass with a command-scoped
`init.defaultBranch=master` setting. No Git settings were changed on
disk.
- A diagnostics test also fails on both unchanged master and this branch
because its broad `private` substring assertion matches the canonical
macOS temporary source path in an error stack. A local Anthropic hire
assertion failed only in the broad run; all 70 tests in that file pass
on both source revisions when run separately. Its broad-run cause is not
determined. These failures remain recorded. The full exact-head CI
matrix passed; the broad local development attempt was then stopped.
- An earlier full run was interrupted after PostgreSQL reported host
shared-memory exhaustion. One retry was stopped when timing required the
UTC optimization. Acceptance then used an owned database on the existing
local PostgreSQL service. No shared services were stopped or reset.
- Local dispatch: routine record at +0.102 s, routine agent start at
+0.171 s, monitor agent start at +0.159 s. Both scripted agents
succeeded using real run-scoped API authentication. No model provider
was called. No duplicate runs occurred during the 70-second follow-up.
Platform: macOS, Node 25.6.1, isolated database on local PostgreSQL 16,
source checkout. The final run used a fresh database and a clean
checkout of 9fc857dcec.
- The first timing run exposed the repeated cron parsing described
above. A diagnostic run showed the timer fired 1 ms after the deadline
while the annual search blocked the event loop. Parsing once reduced
local dispatch to 5.9 seconds, which still missed the five-second test
target. The next change skips impossible UTC dates before formatting. A
second regression failed before that fix. The final timing result and
duplicate check passed.
- A separate acceptance setup failed because the direct local server had
no agent signing key. That owned fixture was removed. The retry uses an
ephemeral key in its isolated process environment.
- Owned fixtures were deleted, the local runtime exited normally, and
the disposable databases were dropped. Shared services remain running.
- No production deployment or npm publication is part of this PR.

## Risks

- Known deadlines now trigger a scan between heartbeat ticks. Existing
atomic claims, suppression checks, budgets, and execution rules still
decide whether work runs.
- Direct database writers rely on the heartbeat recovery scan. Overdue
blocked work also retains that recovery interval to avoid a tight retry
loop.
- This is not a hard real-time guarantee. Provider startup, queue load,
and other synchronous work can still delay agent execution.
- No database migration or API schema change. Revert this commit to
restore interval-only dispatch.

## Model Used

OpenAI GPT-6 (Codex), with reasoning, repository tools, terminal
execution, and automated tests. The session does not expose a more
specific model version 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 and contains no internal
Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass for the changed areas;
full-suite CI and local exceptions are documented 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>
canary/v2026.1016.0-canary.6
2026-10-15 22:44:17 -07:00
DottaandPaperclip 82a12f1a8b perf(skills): batch project source authorization reads (#16536)
Batch project-source read authorization through the existing decideReads path. Keep company scope, source union rules and fresh permission decisions.

The local80-project fixture reduces select builders from322 to4 and complete legacy preparation from689ms to128ms. All88 affected cases and both fresh-database cases pass. Full current-head CI/E2E, security and Apex5/5 pass with no unresolved findings. This is component proof; hosted latency still needs verification.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
canary/v2026.1016.0-canary.5
2026-10-16 00:42:37 -05:00
DottaandPaperclip 185483e090 perf(slack): keep authorization revision rows inside PostgreSQL (#16527)
Compute Slack authorization revisions in one PostgreSQL statement while retaining all existing scope and invalidation inputs. Return one ordered digest instead of materializing retained profile rows in Node.

Validated with 19 affected cases, full typecheck/build, final-head CI/E2E/Superagent, and Apex 5/5.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
canary/v2026.1016.0-canary.4
2026-10-15 22:31:46 -05:00
github-actions[bot]andlockfile-bot 560d895306 chore(lockfile): refresh pnpm-lock.yaml (#16516)
Auto-generated lockfile refresh after dependencies changed on master.
This PR only updates pnpm-lock.yaml.

Co-authored-by: lockfile-bot <lockfile-bot@users.noreply.github.com>
2026-10-16 02:57:47 +00:00
DottaandPaperclip 90924d61b3 fix(tools): batch profile selector validation (#16521)
Batch company-scoped profile selector validation while preserving both existing write boundaries and exact selectors.

Verified with 81 affected local cases, full repository typecheck/build, current-head CI/E2E, Superagent and Apex 5/5; no unresolved findings.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
canary/v2026.1016.0-canary.3
2026-10-15 21:12:10 -05:00
DottaandPaperclip 0e58f29eb7 fix(observability): trace pre-dispatch controller waits (#16515)
Measure usage startup, MCP handoff, dispatch admission, and budget reservation with the existing endpoint-gated tracer. Preserve outer attempt context across asynchronous provider dispatch.

Validated with 135 focused tests, full typecheck/build, fresh full CI/E2E, Superagent, and Apex 5/5 on 9b28865bb3.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
canary/v2026.1016.0-canary.2
2026-10-15 20:30:05 -05:00
Nicky LeachandPaperclip fa9f3f8a08 feat(runner): support preconfigured user homes for Codex and ACPX (#16486)
## Thinking Path

> - Paperclip manages AI agents and their work.
> - Runner launches the selected provider and keeps durable session
state.
> - Runner currently prepares private provider homes for each session.
> - Operators can already have working login, skills, and MCP
configuration on the execution machine.
> - This PR adds an explicit mode that uses that existing setup.
> - Runner keeps its task bridge and session ownership while leaving the
user's configuration in place.

## Linked Issues or Issue Description

**Problem or motivation:** Rebuilding a provider home is unnecessary
when the execution account is already configured.

**Proposed solution:** Add `homeMode: "preconfigured"` to Runner adapter
config and runnerd transport options. Keep `"isolated"` as the default.
Initially support native Codex and ACPX Claude.

**Alternatives considered:** Continue copying user configuration into a
private home, or add an approval workflow. Both add work outside this
feature's scope.

**Roadmap alignment:** This extends the existing cross-provider Runner.
It does not add another runtime.

Related work: #14056 covers managed Codex credentials. #14474 covers
command environment delivery. This mode uses user-owned credentials and
retains the existing launch boundaries.

## What Changed

- Add a closed v7 launch contract for the selected home mode. Existing
contracts retain their behavior.
- Keep homeMode under operator control. Reject task overrides and
agent-authenticated changes, including removal through replacements,
adapter changes, or rollback. Ignore stored task values and exclude it
from automatic hire inheritance.
- Skip managed AI login, assigned-skill materialization, and external
MCP setup in preconfigured mode. Preserve the Runner task/completion
bridge.
- Keep protocol state and provider lifetime fences scoped to the Runner
session. Different sessions can share a home.
- Fail preconfigured ACPX planning/read-only launches before provider
admission until a read-only user-home launch is qualified. Use isolated
mode or native Codex for planning.
- Reject ACPX approval requests. Keep native Codex on `never`. Local
permission rules and hooks remain effective. Initially require the
default Runner ACPX `approve-all` setting; other Runner policies are
unqualified in this mode and fail before launch.
- Keep the internal ACPX bridge in a stable session namespace,
preserving an existing user MCP server named `paperclip`.
- Reject preconfigured ACPX Codex before launch until a session
permission profile can enforce Runner-state denial. Remove the
unprotected full-access mode switch; use native Codex or isolated mode
for that model family.
- Bump Pi to profile 23 because its attestation covers shared Runner
source changed here. Preserve profile 22 for historical recovery, and
update Docker/package verification inputs.
- Fence recovery on mode and home bindings. Fail missing
provider-history recovery without starting a replacement session.
Exclude the external Codex home from backups and credential cleanup.
- Discover remote HOME on the execution machine. Do not project
controller HOME or XDG paths onto it.
- Separate task instructions from Codex ACP isolation and update the
generated provider digest.
- Keep remote configured-environment manifests consistent when dropping
controller paths. Preserve exact Claude model IDs through per-launch
environment settings, without editing the user home or patching the
provider.

## Verification

- Targeted local checks cover native contracts and launch allowlists,
user-config preservation, provider admission, permissions, session
recovery, remote environment projection, heartbeat preparation, and
operator-only configuration. Runner, shared, and server TypeScript
checks and the Rust binary build pass; generated ACPX profiles are
current.
- Following the latest master integration, all 757 server
configuration/executor tests and 115 Runner admission/recovery tests
passed. Additional review-fix checks passed: 103 planning contract/host
tests, 78 provider-backend tests, 95 route/preparation/inheritance
tests, 43 task-validator tests, and 43 workspace-policy tests. Counts
describe separate runs and can overlap.
- The real pinned Claude ACP/SDK regression reproduces exact-model
aliasing without the fix (`claude-sonnet-5-5` becomes `sonnet`) and
passes with the fix. All 89 adapter tests pass. User settings remain
byte-for-byte unchanged.
- Localhost-only Claude SDK probes with synthetic credentials verify the
private bridge runs, local `ask` reaches the existing reject callback,
local `deny` blocks without a callback, and a user MCP server named
`paperclip` remains available. No user model allowlist is required.
- Review regressions cover fail-closed provider admission, saved-mode
recovery before routing, controller-home path removal without
configured-environment manifest drift, pre-launch rejection of
unqualified read-only ACPX launches, and denial of task/agent changes to
the operator-owned home mode.
- Before rebase, `d4d4ee2aebe4cb88c4f4d9ef8e22fed4b36b87be` received
standard Greptile 5/5 with no unresolved threads. Prior Apex findings
are fixed and covered by regressions. No manual Greptile retrigger is
requested for this rebase, per reviewer direction.
- The prior PR head and master hit the same GitHub runner encoding crash
in workspace-b on three PR attempts, including diagnostic logging
([prior PR
CI](https://github.com/paperclipai/paperclip/actions/runs/38818474563/job/116714538405),
[prior master
CI](https://github.com/paperclipai/paperclip/actions/runs/38819528748/job/116712423193)).
Rebased onto `origin/master` at `c3ffa3f0dd` to pull in its bridge-test
index correction. The rebased head
`edd153db410bea063b645e0000aa68649f287b00` passes all CI checks ([CI
run](https://github.com/paperclipai/paperclip/actions/runs/38824676914)),
including workspace-b. Greptile's automatic standard review is 5/5 on
this exact head, with no unresolved threads; no manual review was
requested.
- Local workspace-b investigation passed 911 shared tests and 3,868
tests across the remaining 15 workspace projects. The catalog run
separately hit an existing ignored
`.agents/skills/design-guide/SKILL.md` description-budget violation in
this checkout; that file is untracked, outside the PR, and left
untouched. Repeating shared tests with CI reporting enabled also passed.
- Rebase verification: the final Git tree exactly matches the previously
reviewed branch combined with current master. All 192 Runner
admission/contract tests, 61 server preparation/provider tests, and 68
bridge tests pass, as do Runner/server TypeScript and generated-profile
checks. The real Claude adapter fixture hit an `ENOTEMPTY` cleanup race
on its initial run; all 89 adapter tests passed on retry.
- Apex on rebased head `edd153db` returned 2/5: ACPX Codex selected full
access without enforcing Runner-state denial, and agent configuration
replacement could remove the operator mode. Both are fixed in
`26e14dbbf`. Preconfigured ACPX Codex is temporarily unqualified;
re-enabling it requires session permission enforcement on thread/turn
operations and a real filesystem-denial probe. The config guard covers
effective replacements, adapter changes, and rollback while allowing
ordinary agent merges and operator removal. All 190 focused Runner
tests, 103 server tests, both typechecks, and generated-profile checks
pass. Standard review and CI passed before the next Apex request.
- CI on `26e14dbbf` passed 1,967 Runner-shard tests but hit the
previously observed `ENOTEMPTY` fixture cleanup race after successful
Claude model admission. `eb83284fb` adds bounded filesystem retries to
that fixture's teardown; all 87 adapter tests pass. Assertions and
production cleanup behavior are unchanged. Head
`eb83284fb42ee19a15d9a93b106c1bbb07e1695e` passes all 59 CI checks ([CI
run](https://github.com/paperclipai/paperclip/actions/runs/38829500857))
and standard Greptile at 5/5 with no unresolved threads. Apex also
completed at **5/5** on that exact head ([Apex
result](https://github.com/paperclipai/paperclip/pull/16486#issuecomment-6201559527)).
All review threads are resolved, the branch has no merge conflicts, and
the PR remains unmerged.
- No live paid-provider or remote-machine smoke was performed. The
lockfile remains unchanged under the repository's refresh-bot policy;
local dependency installation resolved the changed patch hash.

## Risks

This explicit opt-in grants Codex tools access to the execution home
(read-only in planning), including credentials. Native Codex separately
denies Runner-owned protocol state. ACPX Claude retains its existing
provider trust boundary, and the isolated default is unchanged.
Providers may refresh credentials and update their own metadata.

User configuration can block tools or the completion reporter. Existing
blocked results and failure diagnostics remain the recovery path. Edit
the local settings and retry; no new approval workflow is added.

External provider history remains on the execution machine and is not
backed up by Runner. Remote HOME discovery requires `getent` and fails
explicitly when unavailable. Other harnesses need separate
qualification.

The Codex ACP bundle digest changes. Existing sessions tied to the old
bundle may need a fresh session. No database migration is required.

## Model Used

OpenAI Codex, GPT-6, with reasoning and code execution. The exact
runtime model ID was 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 described the issue in-PR following the feature issue
template
- [x] I have not referenced internal/instance-local Paperclip issues or
links
- [x] My branch name describes the change and contains no internal
ticket id
- [x] I have run targeted 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 risks above

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
canary/v2026.1016.0-canary.1
2026-10-15 17:57:58 -07:00
Devin FoleyandPaperclip c7ea5c0216 perf(server): skip settled committed finalizations in unscoped passes (#16485)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - On restart, `/api/health` reports `starting` until startup recovery
finishes, and deploys wait for it
> - Native recovery and the orphan reap each run an unscoped native
finalization reconciliation pass, and readiness waits for both
> - The pass selects every committed finalization with a result,
including runs that ended long ago, and spends dozens of sequential
queries on each one
> - On a busy instance this is about one minute per pass, so about two
minutes of every restart, and the periodic recovery repeats it on every
tick
> - This pull request skips settled committed finalizations in unscoped
passes, and keeps a small rotating upkeep page so their upkeep still
runs
> - The benefit is faster restarts and less steady database load, with
no change for unsettled work

## Linked Issues or Issue Description

Related: #16330 and #16329 (startup and reconciliation timing).

**What existing behavior does this improve?**
Startup recovery time and steady-state recovery load.

**Current behavior**
- The unscoped candidate scan in `reconcileNativeFinalizations` returns
every native finalization with a result and phase other than
`terminal_failure`. Nothing excludes rows that are already settled.
- Each committed row then takes the full per-row path: pending-effect,
assessment, evidence and decision reads, presentation repair (twice),
the workspace barrier read, a `finalizeNativeRun` re-read of the
committed coordinator, and workspace settlement (lease release check and
agent status update). That's about 40–60 sequential round trips per row.
- Startup runs the unscoped pass twice (native recovery, then the orphan
reap), and readiness waits for both. The periodic orphan reap runs it
again on every tick.
- On one instance, all 268 candidates were committed finalizations whose
runs had ended. Native recovery took 50–80 s and the orphan reap 47–80 s
on every restart, with database round trips of about 3.4 ms.

**Proposed behavior**
An unscoped pass skips a committed finalization when:
- its run is `succeeded`, `failed`, `cancelled` or `timed_out`, and
- the run finished more than an hour ago, and
- its decision has no `pending` or `failed` status-decision effect.

Each unscoped pass also includes up to 10 such settled rows in a
rotating order, so the presentation and evidence upkeep still reaches
every row over time. Scoped passes (explicit run IDs) are unchanged.

**Reason and benefit**
These settled rows have nothing left to finish. Recent rows, unfinished
runs and rows with undelivered effects stay in every pass, so
crash-window repairs and effect delivery behave as before. Startup and
periodic passes no longer scale with the full history of committed runs.

**Breaking changes**
None. A late repair on a settled row can be delayed until its turn in
the upkeep rotation instead of the next pass.

## What Changed

-
`server/src/services/native-runtime/native-finalization-reconciler.ts`:
- `settledCommittedFinalization(now)`: the settled predicate above,
including a `NOT EXISTS` on undelivered `status_decision_effects` for
the same company, issue and decision.
- The unscoped candidate scan adds `NOT settled OR run in the upkeep
page`.
- `nextSettledCommittedUpkeep`: up to
`NATIVE_SETTLED_COMMITTED_UPKEEP_PER_PASS` (10) settled run IDs after an
in-process cursor, ordered by run ID, wrapping at the end.
- New constants `NATIVE_SETTLED_COMMITTED_GRACE_MS` (1 hour) and
`NATIVE_SETTLED_COMMITTED_UPKEEP_PER_PASS`, plus
`resetSettledCommittedUpkeepForTests`.
- New
`server/src/__tests__/native-finalization-settled-candidates.test.ts`.
- `doc/execution-semantics.md`: describes the settled rule and the
upkeep rotation.

## Verification

- `pnpm exec vitest run
src/__tests__/native-finalization-settled-candidates.test.ts` (in
`server/`): 4 passed. The test mocks the timing hook to capture the
candidate count and stop the pass after the scan:
- 25 settled rows give 10, 10, 5, then 10 again over four passes
(rotation and wrap).
- A row finished 10 minutes ago, a running row, and a terminal row
without `finished_at` are all candidates.
  - A settled row whose decision has a `failed` effect is a candidate.
  - A scoped pass with an explicit run ID still selects a settled row.
- `pnpm exec vitest run` for `native-finalization-recovery`,
`legacy-finalization-regression`, `native-run-finalizer-telemetry`,
`native-workspace-finalizer`, `native-finalization-reconciler-timing`,
`external-chat-wait.integration` and `native-status-arbiter-corpus`: 316
passed.
- `heartbeat/recovery.test.ts`: the 8 tests that do not need a database
passed. The 20 database tests were skipped locally because embedded
PostgreSQL could not start (the host's shared-memory segments were
exhausted by other processes). CI runs them.
- `pnpm typecheck` in `server/`: passed.

## Risks

- A settled row that needs a late repair (for example a missing chat
presentation) waits for its turn in the upkeep rotation, up to
`ceil(settled rows / 10)` passes, instead of the next pass.
- The upkeep cursor is in memory. After a restart the rotation starts
from the beginning; the work is idempotent.
- A run left `running` with a committed finalization is never considered
settled, so it is still projected before the reaper's active-run loop.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), 1M context, through Claude Code
with tool use (shell, file edits, test runs, database and log analysis).
A separate Claude agent mapped the recovery call tree.

## 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
- [ ] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
canary/v2026.1016.0-canary.0
2026-10-15 16:42:15 -07:00
Nicky LeachandPaperclip c3ffa3f0dd test(adapter-utils): fix feedback request index in bridge round trip (#16507)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Sandbox agents use the callback bridge to call the Paperclip API.
> - The bridge round-trip test checks request delivery and credential
removal.
> - #12785 added an accepted API-key request before the feedback
request.
> - The feedback assertions still read request 2, which is now the
GitHub credentials request.
> - This PR checks request 3 and verifies that all four accepted
requests reached the host.
> - This restores the shared test gate while retaining the Unicode
payload and token checks.

## Linked Issues or Issue Description

Related PR: #12785 introduced the stale feedback index. The reported
failure appears on #16486 and master. Searches for `workspaces-b`,
`sandbox-callback-bridge`, `surrogate`, and `EncoderFallbackException`
found no duplicate fix.

**What happened?**

The `General tests (workspaces-b)` job fails on PRs and master. The
hosted PR job and AWS master job both report
`System.Text.EncoderFallbackException` for an unpaired `\uD83D`. The
runner exits during the test step and does not upload that step's log.

The unchanged master test reproduces a deterministic assertion failure
at the feedback request. It compares `/runtime-tools/github/credentials`
with `/api/companies/company-1/agent-commentary` and prints a diff
containing 5,000 crying emoji. The assertion output is the likely
trigger for the runner's Unicode logging crash.

- [Reported PR
job](https://github.com/paperclipai/paperclip/actions/runs/38818474563/job/116719880033)
- [Master job with the same runner
exception](https://github.com/paperclipai/paperclip/actions/runs/38821128038/job/116717690951)

**Expected behavior**

The test checks the actual feedback request, verifies its full payload,
and confirms that its authorization header is removed. Both shared CI
lanes complete normally.

**Steps to reproduce**

1. Check out master at `c4a16cbe981f96e2756c7014103c88da67e5514f`.
2. Install dependencies with pnpm 9.15.4.
3. Run `node_modules/.bin/vitest run
packages/adapter-utils/src/sandbox-callback-bridge.test.ts -t
'round-trips localhost bridge requests'`.
4. Observe the feedback assertion reading the preceding GitHub
credentials request.

**Paperclip version or commit**

Master at `c4a16cbe981f96e2756c7014103c88da67e5514f`.

**Deployment mode**

Built from source. GitHub-hosted PR CI and AWS post-merge CI.

## What Changed

- Assert that four accepted requests reached the host.
- Check feedback delivery and authorization stripping on request 3.
- Retain the large Unicode payload and all existing authentication
checks.

## Verification

- Unchanged master: the focused round-trip test fails at the stale
feedback index.
- Fixed branch: all 68 tests in `sandbox-callback-bridge.test.ts` pass
with real localhost gateways.
- `pnpm --filter @paperclipai/adapter-utils typecheck` passes.
- `git diff --check` passes.
- Exact CI group: `node scripts/run-vitest-stable.mjs --mode general
--group general-workspaces-b` passes (4,800 tests passed, 28 skipped
across 17 projects).
- `pnpm --filter @paperclipai/adapter-utils build` passes.
- Greptile reviewed current head
`3de15d3374354809ea84ca4df5f93c2473715f02`: 5/5, success, no comments or
actionable findings.
- All GitHub checks pass on current head
`3de15d3374354809ea84ca4df5f93c2473715f02`: 55 successful checks and 2
intentional skips, including `workspaces-b`, build, typecheck, Runner
verification, and e2e.
- Full local `pnpm test:run` was started and stopped after the CI test
lanes passed; it did not complete locally. No worktree-owned test
processes remained afterward.
- Full local typecheck and build were attempted. Both stop at the Runner
Rust commands because `cargo` is absent from the shell PATH. The changed
package typecheck passes. The complete repository typecheck and build
pass in CI.
- The first sandboxed local reproduction could not bind localhost
(`EPERM`). It was repeated with listener permission and reached the
deterministic assertion failure described above.

## Risks

Low risk. This changes three test lines. Runtime behavior, credentials,
workflow settings, and payload coverage stay the same. The GitHub runner
Unicode logging defect remains upstream; this fix removes the incorrect
assertion that triggers it in this test.

## Model Used

OpenAI GPT-6 in Codex, with reasoning, repository inspection, and
command 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
#` 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>
canary/v2026.1015.0-canary.24
2026-10-15 16:32:20 -07:00
8aaef59339 fix(pi-local): add stdout compaction to stop quadratic run-log growth (#10249)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The `pi_local` adapter runs the `pi` CLI in `--mode json` and
records its NDJSON stream as a run-log per turn
> - In JSON mode `pi` emits one `message_update` event per streaming
token, each carrying the **full cumulative assistant message**, so a
single turn's run-log grows quadratically with output length (measured
~77 MB for one thinking-model turn)
> - The root cause is in `pi`, but the Pi project declined to add a
compact mode (earendil-works/pi#3905, closed the same day), so Paperclip
has to filter on the consumer side
> - This PR adds a dedicated, config-gated compactor at the `pi_local`
stdout boundary (`stdoutLogMode`: `raw` | `compact`, default `compact`)
that strips the cumulative snapshots while preserving streaming deltas,
terminal events, and parser/UI output
> - The benefit is linear run-log growth (~150× smaller in practice)
with **no change** to `parsePiJsonl` results, token usage, or live
typing — keeping storage and replay bounded

## Linked Issues or Issue Description

- **Refs #5699** — same root cause ("full accumulated partial state" →
46 MB log, per that PR). This PR takes a **different, single-concern
approach**: a dedicated `stdout-compaction.ts` module with an explicit
`stdoutLogMode` config (default `compact`, fail-safe fallback to `raw`),
scoped to `pi_local` only. #5699 instead filters inline in
`buffered-on-log.ts`, bundles an unrelated `claude-local` change, and is
currently **conflicting** + stale (last updated 2026-05-14). Happy to
coordinate with @ukint-vs on a merged direction.
- **Refs earendil-works/pi#3905** — proposed adding a compact JSON mode
upstream in `pi`; closed by the maintainer, which is why this filters on
the Paperclip side rather than the producer.
- **Related #1846** (run-log/retention TTL) — complementary: this PR
reduces what's stored per run; #1846 addresses how long rows live.
- No public GitHub issue exists that is an exact duplicate of the
`pi_local` quadratic-growth symptom; the problem is tracked via #5699
above. (No internal/instance-local references used.)

## What Changed

- **`packages/adapters/pi-local/src/server/stdout-compaction.ts`** (new,
123 lines) — `createPiStdoutLogCompactor(mode)`. `raw` passes lines
through unchanged; `compact` strips the cumulative
`message`/`assistantMessageEvent.partial` from `message_update` events
while preserving streaming deltas, terminal events, and passthrough of
unknown event types. Default mode `compact`; an invalid explicit mode
fails safely to `raw`.
- **`packages/adapters/pi-local/src/server/execute.ts`** — read the mode
via `resolvePiStdoutLogMode(config)` and apply the compactor at the
stdout → `onLog` (run-log) boundary.
- **`packages/adapters/pi-local/src/index.ts`** — expose the
`stdoutLogMode` config option (documented inline: `string`, optional,
default `"compact"`).
- **`packages/adapters/pi-local/src/ui/parse-stdout.ts`** — confirm the
stdout parser consumes compacted output unchanged.
- **Tests** — new `stdout-compaction.test.ts` (359 lines) covering
modes, edge cases, and `parsePiJsonl` replay equivalence; updated
`execute.remote.test.ts`.

## Verification

- **Unit:** `pnpm --filter @paperclipai/adapter-pi-local exec vitest
run` → **121/121 passing (12 files)**.
- **Typecheck:** `pnpm --filter @paperclipai/adapter-pi-local exec tsc
--noEmit` → **clean, 0 errors**.
- **Real-data replay:** a real `pi --mode json` stream (`zai/glm-5.2`,
thinking=high) compacted line-by-line through this compactor:
- Raw **76.96 MB** → Compact **525.5 KB** = **99.33% reduction
(≈150×)**.
- 4503 lines in, 4503 out (**0 dropped**); **0** `message_update` with a
cumulative `.message` remaining; **4489** streaming deltas preserved.
- **Parser equivalence:** `parsePiJsonl(raw) ≡ parsePiJsonl(compact)` —
**0 errors** on both; identical `finalMessage` (13,369 chars); identical
`usage` (`inputTokens 2896, outputTokens 4491, cachedInputTokens 6848`).
Result, token accounting, and live-typing are unchanged.

## Risks

- **Behavioral shift:** default `compact` changes what is stored in
run-logs vs today. Operators who need the verbatim stream can set
`stdoutLogMode: "raw"`. Flagging for reviewer preference — happy to flip
the default to `raw` for upstream if that's preferred.
- **Ordering with secret redaction (#8027 / #9856):** compaction is
structural and runs at the stdout boundary **before** redaction; it only
removes cumulative duplicates and never alters token content, so it does
not change what redaction sees.
- **Unknown event types** pass through unchanged (forward-compatible
with future `pi` events).
- Low risk otherwise — the change is contained to the `pi_local`
adapter.

## Model Used

OpenAI `gpt-5.6-luna` — via pi's `openai-codex` provider (272K context
window). Used for implementation and for the real-data measurement in
Verification.

Reasoning/thinking: extended thinking enabled at level `high` (pi
`--thinking high`; maps to OpenAI reasoning effort). `gpt-5.6-luna` is a
reasoning-capable model.

## 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>
Co-authored-by: commitperclip[bot] <284812584+commitperclip[bot]@users.noreply.github.com>
2026-10-15 16:24:06 -07:00
Huanyi Xie c4a16cbe98 fix(plugins): follow local package path changes in dev watcher (#15247)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Local plugin development uses file changes to restart the plugin
worker.
> - A plugin can move to a different local package directory.
> - The watcher rejected every later registration for the same plugin
ID.
> - This pull request replaces the watcher when the resolved package
path changes.
> - The benefit is that current plugin files trigger reloads and
previous files stop doing so.

## Linked Issues or Issue Description

Refs: #14955. This change addresses its second observation: the watcher
keeps the previous local directory after its package path changes. The
issue also tracks stored configuration replay as a separate problem.

Related PRs: #11336 shares the lifecycle manager across routes and the
dispatcher. #14381 controls when production file watching is enabled.
#10100 orders configuration delivery. Those changes address other parts
of plugin reload behavior.

## What Changed

- Store the resolved package path with each watcher. Keep repeated
registrations of the same path as a no-op. Replace the watcher for a
different path.
- Cancel pending changes from the previous directory. Ignore late
change, error, and timer callbacks from a replaced watcher.
- Apply only the latest pending directory lookup. Manual registration,
unwatching, and shutdown invalidate earlier lookups.
- Stop a failed watcher without cancelling its pending replacement
lookup. Explicit unwatching, disable, unload, and shutdown still cancel
pending registrations.
- Stop the old watcher when the new directory is unavailable or the
plugin no longer has a local package path.
- Document the path-change behavior and add twelve regression cases.

## Verification

- `pnpm exec vitest run server/src/__tests__/plugin-dev-watcher.test.ts
server/src/__tests__/plugin-lifecycle-restart.test.ts`: 18 tests passed.
Regressions cover path changes, stale callbacks, lookup order, explicit
cancellation, and watcher errors during a pending replacement. The
current-watcher error case fails before the stop-versus-cancel fix; the
stale-watcher error control passes.
- A local smoke check used real Chokidar watchers and two real temporary
plugin directories. It confirmed that a pending old change is cancelled,
later old-directory changes are ignored, and a new-directory change
triggers one restart.
- `pnpm -r typecheck` passed on the path and lookup guards. The final
watcher-error fix passed `pnpm --filter @paperclipai/server exec tsc
--noEmit`.
- `pnpm build` passed on the initial path-change fix. The final source
passed `pnpm --filter @paperclipai/server build`.
- `git diff --check`: passed.
- Greptile reviewed `bef3182` at 5/5 with no new findings. The
watcher-error review thread is resolved. CI is still running.
- The full `pnpm test:run` suite was not repeated for this watcher-only
change. The affected suites ran locally. The broad test shards will run
in CI.

## Risks

- Low risk. The watcher follows the current registered path. An
unavailable replacement stops watching until another valid registration
arrives.
- Closing a filesystem watcher is asynchronous. Callback identity checks
prevent an old watcher from acting on its replacement.
- No database migration, API shape, or dependency change is required.

## Model Used

- OpenAI Codex based on GPT-6, with reasoning, tool use, and code
execution. The runtime does not expose the exact serving 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
- [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
2026-10-15 16:13:35 -07:00
Aashish Mahato 457d3209b1 fix: name the real reason a connection request expires on reassignment (#14067)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - When an agent's selected AI account is unavailable, the issue thread
shows a `connection_intent` card. A person must reconnect the account or
pick another connection.
> - If the issue assignment changes while that card is still pending,
the server expires it. This is the ownership-change path in
`expireConnectionIntentsForOwnershipChange`.
> - The expired card showed the reason "The task assignment changed".
That text is wrong in two ways. It does not say that the connection
request was never answered, and it does not say the connection is still
missing.
> - Worse, the reason never reached the screen at all: the expired
branch of the card hard-codes "This request is no longer active.", so
any guidance the server stores is discarded. My first round of this PR
claimed the opposite, which was incorrect — the UI change is required
for the fix to be visible.
> - Issue #14040 reported the symptom: users saw a run fail with
"assignment" blame and no hint that a connection needed attention. It
happened on both `claude_local` and `codex_local` agents, so the message
— not one adapter — is the defect.
> - This pull request therefore fixes both ends: the server stores a
sentence that names what happened and what to do next, per kind of
request, and the card prints the stored reason instead of a generic
string.
> - The issue asks for a larger behavior change (hold reassignment until
the card resolves). That needs a product discussion, so this PR keeps
the scope to the message and where it is displayed.
> - The benefit is that the card tells the truth: the blocker is the
connection, not the assignment, and it says so on screen.

## Linked Issues or Issue Description

- Fixes: #14040

## What Changed

- `server/src/services/issue-thread-interactions.ts`:
`expireConnectionIntentsForOwnershipChange` now selects each pending
row's payload before expiring it and writes a per-request reason: "The
task was reassigned before the connection request was answered, so the
AI account is still not connected. Reconnect it or choose an available
connection." for AI-account intents, and the same sentence naming "the
`<serviceName>` connection" for tool intents. The subject is chosen from
`payload.purpose === "ai"`, falling back to "the requested connection"
for a payload that carries neither, because this one path expires both
kinds and the recovery step differs.
- `ui/src/features/connections/ConnectionIntentInteractionBody.tsx`: the
expired branch now renders `interaction.result?.reason` and keeps "This
request is no longer active." only as the fallback for results stored
before this change. The `superseded` outcome keeps its own wording. This
component is the shared body for both the compact task card and the full
thread card, so both views get the reason.
- `server/src/__tests__/issues-service.test.ts`: the expiry test now
expires a tool (`Notion`) and an AI (`claude_local`) intent in the same
run and asserts both stored reasons, so neither wording can regress into
the other.
-
`ui/src/features/connections/ConnectionIntentInteractionBody.test.tsx`:
new test renders an expired card whose result carries a reason and
asserts the reason is on screen and the generic fallback string is not.

## Verification

- `npx vitest run server/src/__tests__/issues-service.test.ts
ui/src/features/connections/ConnectionIntentInteractionBody.test.tsx` —
151/151 passed (127 server, 24 UI; 33.4s, Node 22.22.2, local). My first
revision of this body cited 168 for the same set; that count came from a
run on the wrong branch, and 151 is what this command prints on
`fix/connection-intent-expiry-reason`.
- The pinned server test drives the real path: it inserts pending
`connection_intent` rows plus a live `toolOauthStates` row, reassigns
the issue through `svc.update(...)`, then asserts both expired reasons
and the deleted OAuth state row.
- Mutation checks: forcing the AI subject for every row makes the expiry
test fail on the tool-row assertion (`1 failed | 126 skipped`, `expected
[ { …29 fields } ] to deeply equal [ ObjectContaining{…} ]`), and
deleting the `result.reason` branch in the card fails exactly `shows the
stored reason on an expired request` (`1 failed | 23 passed`). Both
revert clean. The reverse wording mutation (tool subject forced onto AI
rows) was not run, so that half of the test is pinned by its assertion
rather than by a demonstrated mutation.
- No schema, wire-format, or payload change. Only the free-text
`result.reason` value differs and the card now reads the field it was
already given.

## Risks

- Low risk. The value is display text on a terminal interaction outcome.
No code parses the old string, and no stored data is migrated; cards
that expired before this change keep their old text and now render it as
the stored reason they carry.
- The deeper request in #14040 (do not expire a pending
`connection_intent` on reassignment) is intentionally out of scope here
and needs a maintainer decision.

## Model Used

- Anthropic Claude (Opus 4.x, agentic CLI coding assistant with file
edit and shell tool use) assisted with the code change, the test
updates, and this PR text. A human reviewed the diff and the issue
context before submission.

## 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
2026-10-15 16:11:35 -07:00
Phorel e15435b651 fix(cli): accept npm 12 array output when resolving published version (#14000)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The CLI `install` and `update` commands resolve the published
version with `npm view paperclipai@<spec> version --json`
> - npm 12 changed the output of this command. It wraps a single value
in an array: `["2026.916.1"]` instead of `"2026.916.1"`
> - `parseResolvedVersion()` accepts only a bare JSON string, so it
throws "npm returned an unexpected version response"
> - Node 26 ships with npm 12, so a new install with the official
`install.sh` fails for these users
> - This pull request makes the parser accept a one-element string array
> - The benefit is that install and update work with npm 12 and with
older npm versions

## Linked Issues or Issue Description

Fixes #12226

## What Changed

- `cli/src/commands/install.ts`: `parseResolvedVersion()` returns the
value when npm returns a one-element array of strings. Other shapes
still throw the same error.
- `cli/src/__tests__/install-command.test.ts`: add a test for npm 11
output, npm 12 output, and plain-text output. The test also checks that
a multi-element array still throws.

## Verification

- Before the fix: on Node 26.8.2 with npm 12.0.2, `bash install.sh`
fails with `npm returned an unexpected version response: [ "2026.916.1"
]`.
- `npm view paperclipai@latest version --json` gives `["2026.916.1"]`
with npm 12.0.2 and `"2026.916.1"` with npm 11.20.0.
- `cd cli && npx vitest run src/__tests__/install-command.test.ts
src/__tests__/update-command.test.ts src/__tests__/channels.test.ts`: 40
tests pass.
- Without the source change, the new test fails with the same error as
the bug report.

## Risks

- Low risk. The change adds one accepted input shape. Existing accepted
shapes do not change.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with tool use
(shell and file editing). It helped to find the cause, write the change
and the test, and run the tests.

## 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
- [ ] 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)
2026-10-15 16:08:11 -07:00
Prompt-SurferandClaude Opus 5.5 fa062b202d fix(ui): ignore MDXEditor initial markdown normalization in MarkdownEditor (#13915)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Operators edit agent instructions, routine descriptions, and other
Markdown fields in the web UI
> - All of these fields use the shared `MarkdownEditor`, which wraps
MDXEditor
> - MDXEditor re-serializes the initial Markdown when it loads, and it
sends the result through `onChange`
> - MDXEditor marks that event with the second `onChange` argument,
`initialMarkdownNormalize`, but `MarkdownEditor` ignores the flag
> - Thus each parent with dirty tracking shows unsaved changes before
the user types, and each parent must add its own interaction gate
(#12502, #13485)
> - This pull request drops the flagged event inside `MarkdownEditor`
> - The benefit is that no consumer reports unchanged content as
modified on load, and new consumers do not need their own gate

## Linked Issues or Issue Description

Refs #13472

Related:
- #12502 (merged) adds an interaction gate for agent instructions in
`AgentDetail.tsx`.
- #13485 (open) adds the same gate to the two routine description
editors. Its description names "a shared fix inside `MarkdownEditor`" as
a follow-up. This PR is that follow-up. It does not conflict with
#13485. The two changes can merge in any order.

## What Changed

- `MarkdownEditor.tsx`: read the second `onChange` argument
(`initialMarkdownNormalize`). When it is `true`, do not call the parent
`onChange`.
- The check runs after the empty-document mount guard. That guard still
restores content when the first event is empty.
- `latestValueRef` keeps the parent value. Thus the prop-sync effect
does not push the original Markdown back into the editor.
- `MarkdownEditor.test.tsx`: the MDXEditor mock can now send a flagged
normalization event on mount. A new test makes sure that the parent
`onChange` does not run and that the editor keeps its content.

## Verification

- `pnpm --filter @paperclipai/ui exec vitest run
src/components/MarkdownEditor.test.tsx`: 48 tests pass.
- The new test fails without the change ("expected vi.fn() to not be
called at all, but actually been called 1 times"). It passes with the
change.
- `pnpm --filter @paperclipai/ui exec vitest run` (full UI suite): 634
test files and 6653 tests pass.
- `pnpm --filter @paperclipai/ui typecheck`: passes with 0 errors.
- I read the MDXEditor 4.2.3 source (`dist/plugins/core/index.js`). The
flag is `true` only for the first export after the initial Markdown is
set. The editor sets it to `false` after that export. User edits and
`setMarkdown` echoes get `false`.
- Manual check: we tested the same guard in a real browser on an older
Paperclip base (MDXEditor 3.55), together with two changes that `master`
already has from #12502. We opened an agent Instructions tab with `-`
bullets. The Save bar and the unsaved-changes prompt did not show until
we typed. After an edit, one prompt showed for each navigation, and Save
still stored the edit.

Manual steps for a reviewer:
1. Put an instruction file with `-` bullets on an agent, for example `-
first` and `- second`.
2. Open the agent Instructions tab. Do not type.
3. Make sure that the Save bar does not show.
4. Go to another tab. Make sure that no unsaved-changes prompt shows.
5. Do the same steps with a routine description that has `-` bullets.

## Risks

- Low risk. The change affects only the first `onChange` event after the
editor loads.
- A consumer that uses the first event to learn the normalized Markdown
no longer gets it. We found no such consumer in the 24 files that render
`MarkdownEditor`, and the full UI suite passes.
- There are no API, database, migration, or visual changes.

> 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`), 1M-token context
window, run as a Claude Code agent with tool use (shell, file edits,
test runs). The model wrote the code, the test, and this description. A
human operator approved them before submission.

## 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
- [ ] I have updated relevant documentation to reflect my changes (no
docs describe this behavior)
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green (pending: CI runs after push)
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
(pending: runs after push)
- [x] I will address all Greptile and reviewer comments before
requesting merge

Co-authored-by: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
2026-10-15 16:06:53 -07:00
馨冉and馨冉 7c6d977929 fix(wake-queue): skip malformed queued comment ids so one bad id cannot block an issue's wakes (#13912)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The wake queue decides whether a finishing run's `@`-mention
actually wakes the mentioned agent, by checking the liveness of the
comment ids queued in the wake payload
> - `getQueuedCommentLiveness` passes every queued comment id straight
into an SQL `inArray`. Postgres rejects the whole statement on the first
malformed uuid, so one bad id (for example an 8-char short form written
into a wake payload) silently blocks every queued wake for that issue
> - The run that triggers the check still records `succeeded`, so from
the board the agent finished its work and the mentioned agent simply
never responds; the reporter hit this twice on the same long-lived issue
> - This pull request filters the queued ids with the existing
`isUuidLike` helper before the query, and skips the query entirely when
nothing valid remains
> - The benefit is that a malformed id is skipped instead of poisoning
the batch — it can never match a comment row anyway, so the downstream
liveness semantics do not change

Fixes: #13908

Related issue class (malformed ids reaching database queries): #887,
#7639, #8093, #11018, #13504 — this is the first report for the
wake-queue site.

## What Changed

- `server/src/modules/wake-queue/adapters/postgres.ts`: in
`getQueuedCommentLiveness`, filter `queuedCommentIds` through
`isUuidLike` before building the `inArray` predicate; when no valid uuid
remains, skip the query and return an empty row set.
- The post-processing loops now iterate the filtered id list, which is
equivalent because a malformed id can never match a comment row.

## Verification

- New embedded-Postgres regression tests in
`server/src/modules/wake-queue/adapters/postgres.test.ts`:
- a batch mixing one live comment id, one malformed short-form id, and
one valid-but-missing uuid returns only the live comment instead of
throwing;
- an all-malformed batch returns nothing live instead of generating
`inArray ()`.
- `./node_modules/.bin/vitest run
server/src/modules/wake-queue/adapters/postgres.test.ts` — 58/58 pass.

## Risks

Low risk. The only behavioral change is that a wake batch that would
previously fail the whole statement now dispatches the valid entries. A
malformed id previously matched no rows (the statement errored before
any filtering), so treating it as not-live is exactly what the old
downstream filters would have concluded had the query run.

## Model Used

Codex (OpenAI GPT-5, coding agent, tool use, repo-level context) —
assisted with locating the call site, authoring the guard, and the
regression tests; human review before submission.

## 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: 馨冉 <xinxincui239@gmail.com>
2026-10-15 16:04:57 -07:00
lorenzozane 1b2632facc fix: serialize concurrent issue reference syncs (#13898)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The server keeps issue references synchronized with issue title and
description changes.
> - Concurrent updates can rebuild the same source issue's reference
mentions at the same time.
> - The replacement writes can then collide on the unique mention key
and return a 500 error.
> - This pull request serializes each source issue's reference rebuild
and adds concurrent regression coverage.
> - The benefit is that repeated unchanged descriptions complete without
duplicate-key failures.

## Linked Issues or Issue Description

Fixes #13731

## What Changed

- Lock the source issue row before replacing title and description
reference mentions.
- Add a 20-way concurrent regression test with repeated `COM-2`
references.

## Verification

- `pnpm exec vitest run
server/src/__tests__/issue-references-service.test.ts
packages/shared/src/issue-references.test.ts` passed with 10 tests.
- `pnpm --filter @paperclipai/server typecheck` passed under Node
22.22.1; the repository declares Node >=24.11 and emitted engine
warnings.
- `git diff --check` passed.

## Risks

- The row lock serializes rebuilds for one source issue and may reduce
concurrency for simultaneous updates to that issue.
- A theoretical lock-order risk remains for concurrent syncs of
different mutually referencing source issues. That path is outside this
fix and is not covered by the focused regression.
- Remote CI and Greptile review have not run yet.

## Model Used

OpenCode runtime, model `supercodes5/gpt-5.6-luna`; context window size
is not exposed. Repository tool use and reasoning were enabled.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` /
`Closes: #` / `Refs: #` OR (b) described the issue in-PR following the
relevant issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] 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
2026-10-15 16:02:45 -07:00
cc549691a1 fix(claude-local): stop sealing max-turns failures as model_not_found (#13885)
<!-- Written in Simplified Technical English -->

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The `claude_local` adapter runs the Claude Code CLI and maps each
finished process to a terminal result. The `errorCode` in that result
decides which recovery path the issue takes.
> - `execute.ts` resolves the error code with one long ternary chain.
The order of the branches is the precedence rule.
> - The model-not-found branch sits before the max-turns branch, and it
is driven by `isClaudeModelNotFoundError()`, which regex-scans the run's
full stdout for the phrase `model_not_found` (also `model not found`,
`unknown model`, `model does not exist`).
> - The agent's own tool output is part of that stdout. A run that greps
adapter source, tails a log, or echoes an issue body about this defect
matches the detector on text the agent printed, not on text the provider
returned.
> - A real `subtype=error_max_turns` failure therefore never reaches
`max_turns_exhausted`. Downstream, `model_not_found` counts as a
configuration-incomplete failure, so the issue goes to `blocked` with a
wrong "configuration incomplete" notice instead of the normal max-turns
continuation.
> - This pull request gates the model-not-found branch behind the two
structured signals that the `providerQuota` and `transientUpstream`
branches above already apply.
> - The benefit is that a structured CLI signal outranks a regex scan of
untrusted output, so exhausted runs continue instead of blocking the
issue.

## Linked Issues or Issue Description

No public issue exists for this defect. I searched the open pull request
list for `packages/adapters/claude-local` and for the `model_not_found`
and `max_turns_exhausted` error codes, and found no duplicate or related
pull request. The description follows the bug template.

**What happened**

A run that fails with `subtype=error_max_turns` is recorded with
`error_code=model_not_found`.

In `packages/adapters/claude-local/src/server/execute.ts`, the
resolved-error-code ternary evaluates the model-not-found branch before
the max-turns branch:

```ts
: failed && isClaudeModelNotFoundError({ parsed, stdout: proc.stdout, ... })
? "model_not_found"
: failed && clearSessionForMaxTurns
? "max_turns_exhausted"
```

`isClaudeModelNotFoundError()` in `parse.ts` pushes `input.stdout` into
its candidate list and tests it against `CLAUDE_MODEL_NOT_FOUND_RE`. The
run's stdout holds the agent's own tool output, so any run that prints
the phrase poisons its own classification. Because the branch is first,
a genuine max-turns failure never reaches `max_turns_exhausted`.

This is not cosmetic. Downstream, `model_not_found` is treated as a
configuration-incomplete failure. The issue moves to `blocked` with a
misleading "configuration incomplete" recovery notice instead of the
normal max-turns continuation path.

**Steps to reproduce**

1. Run a `claude_local` agent on a task whose tool output contains the
literal string `model_not_found`. Grepping the adapter source or reading
a bug report about this defect is enough.
2. Let the run exhaust its turn budget, so the CLI emits
`subtype=error_max_turns`.
3. Observe that the recorded `error_code` is `model_not_found` and not
`max_turns_exhausted`.

**Expected behavior**

A run whose parsed result carries `subtype=error_max_turns` is
classified `max_turns_exhausted`, whatever phrases appear in its stdout.
A structured CLI signal outranks a regex scan of untrusted output.

**Paperclip version or commit**

`ghcr.io/paperclipai/paperclip@sha256:23090eb6`. The branch is rebased
onto current `master` (`b41ccf0`). The adapter is
`@paperclipai/adapter-claude-local` on the `engine=cli` lane.

**Deployment mode**

Self-hosted, Docker Compose.

## What Changed

- `packages/adapters/claude-local/src/server/execute.ts`
- Gate the model-not-found branch with `!clearSessionForMaxTurns &&
!poisonedPreviousMessageId`, the same guard the `providerQuota` and
`transientUpstream` branches ~30 lines above already apply. One line, no
new state.
- Add a comment that records why the order matters, so a later reorder
is a deliberate decision.
-
`packages/adapters/claude-local/src/server/execute.max-turns-classification.test.ts`
(new)
- A parsed `error_max_turns` result whose stdout carries the literal
`model_not_found` phrase still classifies as `max_turns_exhausted`.
- A real provider 404 (`API Error: 404 model not found`) still
classifies as `model_not_found`, so the guard does not hide the genuine
case.

Only the parsed-result path changes. The unparsed fallback path (`if
(!parsed)`) is left alone: neither guard variable is in scope there, and
a run with no parsed result has no structured max-turns signal to
honour.

## Verification

- `pnpm exec vitest run
src/server/execute.max-turns-classification.test.ts` in
`packages/adapters/claude-local`: 2/2 pass.
- Negative control: with the one-line guard reverted, the first test
fails with `expected "max_turns_exhausted", received "model_not_found"`.
The test pins the defect and not the surrounding code.
- `pnpm exec vitest run` for the whole adapter: 313 pass, 1 skipped, 3
fail. The 3 failures are in `acp.test.ts` and `acp.auth.test.ts`, all
with `claude_acp_node_unsupported` because the local machine runs Node
v22.23.1 and the repository requires Node >= 24.11.0. They fail the same
way on `master` without this branch, and they do not touch the CLI
classification path.
- `tsc --noEmit -p tsconfig.json` for the adapter: no errors.

## Risks

- Low risk. The change is one added condition on one branch of an
existing ternary.
- A real model-not-found failure still classifies correctly, because
neither `clearSessionForMaxTurns` nor `poisonedPreviousMessageId` is set
on that path. The second test covers this.
- The narrow case that changes behaviour is a run that is both out of
turns and pointed at a missing model. That run now reports
`max_turns_exhausted` first. The next run reports the model error
against a clean session, which is the same outcome the quota and
transient-upstream branches already accept.

## Model Used

- Provider: Anthropic Claude.
- Exact model ID: `claude-opus-5` (Claude Opus 5).
- Reasoning mode: extended thinking.
- Capability details: tool use for shell, file editing and test
execution.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] I have updated relevant documentation to reflect my changes (no
user-facing documentation covers adapter error-code precedence)
- [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: Builder <builder@nublo.net>
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
2026-10-15 16:01:40 -07:00
Ash Simons 550e959934 fix(task-watchdogs): deliver board instructions and stopped leaves in the wake payload (#13771)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Task watchdogs wake an agent when a watched issue subtree stops
moving.
> - An operator can write `instructions` on the watchdog record. The
wake prompt has a slot for this text in the "Task Watchdog Mandate"
block.
> - The producer writes `customInstructions` and `stoppedLeaves` at the
top level of the wake payload. The normalizer reads them only from the
nested `taskWatchdog` object. Thus the normalizer drops both fields on
every watchdog wake.
> - The agent then sees "No board-supplied watchdog instructions"
although the record holds an instruction. The operator cannot see this
failure, and the agent cannot see it either.
> - This pull request puts both fields in the nested `taskWatchdog`
object.
> - The benefit is that operator instructions and the stopped-leaf list
reach the agent again.

## Linked Issues or Issue Description

No public issue exists. This is the bug description (bug_report
template).

**What happened?**
`watchdogWakeContext()` in `server/src/services/task-watchdogs.ts`
writes `customInstructions` and `stoppedLeaves` at the top level of the
wake payload. `normalizePaperclipWakePayload()` in
`packages/adapter-utils/src/server-utils.ts` reads
`payload.taskWatchdog` only. The two fields are lost. The "Task Watchdog
Mandate" block always shows "No board-supplied watchdog instructions.
Apply the mandate above." The "Terminal / stopped leaves to verify"
section never shows.

**Expected behavior**
When the watchdog record has non-empty `instructions`, the wake prompt
shows that text. When the subtree has stopped leaves, the prompt lists
them.

**Steps to reproduce**
1. Create a task watchdog on an issue. Set a non-empty `instructions`
value.
2. Let the watched subtree stop, so that the watchdog triggers.
3. Read the wake prompt of the watchdog agent. It shows the "No
board-supplied watchdog instructions" line.
4. `GET /api/issues/{id}/watchdog` still returns the non-empty
`instructions` value.

**Paperclip version or commit**
Reproduced on `master` before this change. The new test in this PR fails
on `master`.

**Agent adapter(s) involved**
Not adapter-specific (core bug). The drop occurs in the shared
wake-payload normalizer.

## What Changed

- `server/src/services/task-watchdogs.ts`: add `customInstructions` and
`stoppedLeaves` to the nested `taskWatchdog` object. Map each stopped
leaf to the shape the normalizer expects (`issueId` becomes `id`). Keep
the top-level copies, so that other consumers do not change.
- Add a test for the full path: real service, real wake payload,
`normalizePaperclipWakePayload`, then `renderPaperclipWakePrompt`. The
test also asserts that the "No board-supplied watchdog instructions"
line is absent.

## Verification

- Run from the repo root:
  ```
  npx vitest run server/src/__tests__/task-watchdogs-scheduler.test.ts \
server/src/__tests__/task-watchdogs-classifier.test.ts \
server/src/__tests__/task-watchdogs-incident-fixture.test.ts \
                 server/src/__tests__/issue-watchdogs-routes.test.ts
  npx vitest run packages/adapter-utils/src/server-utils.test.ts
  ```
- Local result: watchdog suites 52 of 52 pass. `server-utils.test.ts`
117 of 117 pass.
- The new test fails on `master` because
`taskWatchdog.customInstructions` is absent. It passes on this branch.
- All Paperclip CI gates on this PR are green. Greptile gives 5/5.

## Risks

- Low risk. The change adds fields to a nested object. It does not
remove fields.
- No schema change, no migration, no data write.
- Behavior change: agents now receive operator instructions that they
did not receive before. This is the intended result.
- Rollback: revert the single commit.
- Note: the normalizer field name is `terminalLeafSummaries`, but the
classifier fills `stoppedLeaves` with non-terminal stopped leaves. The
renderer heading ("Terminal / stopped leaves to verify") covers both.
This PR does not rename a public payload field. Maintainers can align
the names in a separate 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

- Provider: Anthropic Claude, Opus family, used through Claude Code as
an agent with tool use and shell execution.
- This PR description revision: `claude-opus-5-5`, 1M context window.
- The model found the cause, wrote the fix and the test, and ran the
test suites. A human owns the account that opened the PR.

## 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
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] I have updated relevant documentation to reflect my changes (not
applicable: no documented behavior changed)
- [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

Duplicate search: I searched open and closed PRs and issues for
"watchdog instructions" and "watchdog customInstructions". I found no
related PR or issue.

Branch name: the branch name has an internal prefix. If the maintainers
want it, I can open the same commit again from a `fix/...` branch.
2026-10-15 15:47:54 -07:00
SkilLab HR and TechandPaperclip 92bedaac4a fix(server): treat a scheme-less public base URL as absent instead of crashing startup (#13727)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - At boot the server selects the origin that agents must dial for the
control plane. It exports that origin to every run as
`PAPERCLIP_API_URL`
> - The selection starts from `auth.publicBaseUrl`. An operator writes
this value by hand
> - If the operator writes `host:port` and omits the scheme, the server
does not reject the value. The value is a valid URL with an opaque
scheme. The `origin` of such a URL serializes to the *string* `"null"`
> - The string `"null"` is truthy. Thus it gets through the `if (value)`
guard. The enclosing `try/catch` does not help, because the parse did
not fail. A later `new URL("null")` then throws `TypeError: Invalid URL`
on the startup path
> - The result is that the server does not start. The error message
names neither the configuration key nor the bad value
> - This pull request parses the public base URL in one helper. The
helper treats an unusable origin as absent configuration. This is the
same treatment that input which fails to parse gets today
> - The benefit is that a missing `https://` falls back to the existing
derived candidates. It no longer stops the boot

## Linked Issues or Issue Description

Fixes: #13576 — that issue reports this defect and includes a standalone
reproduction.

**Related PRs found by the duplicate search (none fix this defect).** I
searched the open PR list
for `runtime-api`, `publicBaseUrl`, `public base url`,
`PAPERCLIP_API_URL` and `Invalid URL`. I then
read the diff of every close neighbour. Refs #10517, Refs #9916, Refs
#7342, Refs #12886,
Refs #11564, Refs #9228. No one of them contains a test for an opaque
origin, and no one of them
compares an origin against `"null"`. They change *which reachable origin
wins*. This pull request
changes *how one unusable value is rejected*. The two subjects do not
overlap.

Refs #10517 and Refs #9916 are duplicates of each other. Neither touches
`server/src/runtime-api.ts`.

**One neighbour needs attention.** Refs #11564 adds a new function
`resolveRuntimeApiUrl`. That
function contains this code:

```ts
try {
  const origin = new URL(explicitPublicBaseUrl).origin;
  return { url: origin, reason: "explicit-public-base-url", ... };
} catch {
  // Fall through to derived candidates if config parsing drifted.
}
```

This is the same defect in a third location. A scheme-less value parses
correctly. Thus the `catch`
does not run, and the function returns the literal string `"null"` as
the URL. The lines are pure
additions, so there is no text conflict with this pull request. But if
#11564 merges after this one,
it puts the defect back in a new function. The helper in this pull
request is module-private and
available to that function. I can add the one-line change to this branch
if the maintainers prefer
that.

## What Changed

`server/src/runtime-api.ts` — one new module-private helper, used at the
two existing call sites:

```ts
function parsePublicOrigin(rawUrl: string | null | undefined): string | null {
  const trimmed = rawUrl?.trim();
  if (!trimmed) return null;
  let origin: string;
  try {
    origin = new URL(trimmed).origin;
  } catch {
    return null;
  }
  return origin === "null" ? null : origin;
}
```

- `choosePrimaryRuntimeApiUrl` now calls the helper. Its inline
`try/catch` is removed.
- `buildRuntimeApiCandidateUrls` now calls the helper. Its inline IIFE
is removed.
- `server/src/__tests__/runtime-api.test.ts` gets two new cases. One
case covers the wrong `"null"`
  result. The other case covers the startup exception.

Counts: **+20 / −17** in `runtime-api.ts`. Five of the added lines are
the comment that explains the
opaque scheme. The test file is **+23 / −0**. There is no new
dependency. There is no `any` type. No
exported signature changes. The duplicated parse logic at the two call
sites becomes one function.

## Verification

I ran every step below against `master` at commit
`c65fc9e3c81c41aafe421aa90a00514b84343285`. That
commit is the merge base of this branch.

- **Unit tests**, with the repository runner (`vitest`), on the two
added cases:
- Before the fix: `Tests 2 failed | 6 passed (8)`. The two failures are
exactly the two new cases.
    The assertion error is
`AssertionError: expected 'null' to be
'http://runtime-host.example.test:3102'`.
  - After the fix: `Tests  8 passed (8)`.
- Both new cases are pure additions. No existing expectation changes,
because no existing test
    uses a scheme-less `authPublicBaseUrl`.
- **Standalone reproduction with 8 arms** (attached to #13576): **6/8**
on unpatched `c65fc9e3`, and
**8/8** with the patch. The 5 regression arms and the 1 control arm give
the same result on both
sides. The control arm uses input that truly fails to parse. Thus the
reproduction discriminates
  between the two builds. It does not pass by accident.
- **Typecheck**: `tsc --noEmit --strict --noEmitOnError --target ES2023
--module NodeNext` exits 0 on
  the patched file. It also exits 0 on the unmodified file.

## Risks

**Low risk.** Reasons:

- The change only affects input that makes the server crash today. No
operator can depend on the
  present behaviour, because the present behaviour stops the boot.
- The new path is not new code. The helper returns `null`, and `null`
goes to the fallback that
  already exists for input that fails to parse.
- The second call site previously put the string `"null"` into the
candidate list. It now omits that
entry. A `"null"` origin is not reachable, so no caller can lose a
usable candidate.

**The one behaviour change a reviewer must agree with.** A bad value now
degrades quietly instead of
failing loudly. An operator who writes `host:port` gets a server that
starts on a derived origin. The
operator does not get an error.

I did not add a warning log, for one reason: the existing parse-failure
path is also silent. A log
would change behaviour that this pull request does not target, and it
would enlarge the diff. If the
maintainers want the warning, the correct fix is one log line inside
`parsePublicOrigin`, which
covers both input classes at once. This is now possible only because the
two call sites share one
function. Tell me if you want that, and I will add it.

**Migration:** none. No schema change, no data change, no configuration
change.

## Model Used

- Provider and model: Anthropic Claude, Opus 5
- Exact model ID: `claude-opus-5[1m]`
- Context window: 1M tokens
- Mode: extended thinking
- Capabilities used: tool use, shell execution, file editing, and GitHub
API access
- The human operator reviewed and authorized this submission. A human
approved the publication of
  this pull request before I opened 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 — I read
the file. It has no item for the runtime API URL, for startup URL
validation, or for
      configuration parsing.
- [x] I have searched GitHub for duplicate or related PRs and linked
them above — 5 queries, and I
read the diff of each close neighbour. See the linked-issues section.
- [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 — the branch is
      `fix/scheme-less-public-base-url`
- [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 — no
user-facing document
      describes this internal fallback, so no document change applies.
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green — not yet true, and I do not
check a box that is not true. On
commit `13ffb649`: 43 checks pass, 7 checks still run, 2 checks fail.
Both failures are the
PR-description gate that this update repairs. I will check this box when
the gates are green.
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups —
not yet true. Greptile gave
4/5 with one P2. That P2 is "Required PR sections missing", which this
update repairs.
- [x] I will address all Greptile and reviewer comments before
requesting merge — this update is
      that work for the first review round.

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 15:46:11 -07:00
514d8738cf fix: keep the JWT run-mismatch audit when the claimed run is missing (#13183)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Rejected agent JWTs whose run header disagrees with the signed claim
are audited into `activity_log` so operators can see spoof attempts
> - The audit insert writes the claimed run id into `run_id`, which is a
real foreign key to `heartbeat_runs`; a bogus claim violates the FK and
the catch swallows it, so the audit row is silently lost exactly when it
matters most
> - This pull request verifies the claimed run exists before trusting it
into the FK column; the claim itself stays in `entityId` and `details`
> - The benefit is a reliable audit trail for rejected credentials

## Linked Issues or Issue Description

Refs #10498 — the anonymous fall-through half was fixed on master
already (every failed-credential branch now returns an explicit
401/403/422); this closes the residual FK-swallowed audit defect.

## What Changed

- `server/src/middleware/auth.ts`: `auditAgentJwtRunHeaderMismatch`
looks up the claimed run id and populates `runId` only when the row
exists; `entityId` and `details.claimRunId` carry the claim either way.
- `server/src/__tests__/agent-auth-middleware.test.ts`: a mismatch whose
claimed run does not exist still produces the audit row with `runId`
omitted.

## Verification

- `pnpm --filter @paperclipai/server vitest run
src/__tests__/agent-auth-middleware.test.ts` — 17 tests pass.
- Before: a run-header mismatch whose claimed run id was absent from
`heartbeat_runs` violated the `activity_log.run_id` FK, and the catch
swallowed it — no audit row. After: the row lands with `runId` null and
the claim preserved in `entityId`/`details`.

## Risks

- Low risk. One extra indexed select on a rare rejection path; the audit
payload is unchanged apart from `runId` now being conditional on
existence.

## Model Used

- Anthropic Claude — SWE-2 Max agent via Devin CLI, tool use 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
- [ ] 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: Waseem Ilyas <1478353+Waseemilyas@users.noreply.github.com>
Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 15:43:56 -07:00
880d4ae60f fix: reject done when an executionPolicy replace discards a live review cycle (#13178)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The issue PATCH route applies executionPolicy edits and status
changes through one transition function, so both can arrive in a single
request
> - A replacement executionPolicy regenerates stage ids, which orphans
the stored currentStageId; the orphaned-stage path clears executionState
> - When a review cycle is live (pending or changes_requested), that
clear lets a caller-supplied `status: "done"` stand although the review
never ran
> - This pull request rejects `done` on that combined write and leaves
every other requested status — including board cancellation — on the
established abandon-and-clear path
> - The benefit is that a review gate cannot be bypassed by attaching a
fresh policy object to a completion request

## Linked Issues or Issue Description

Fixes #13176

Refs #13001 (same transition function, distinct defect)

Supersedes #13164 — same fix, resubmitted on a correctly named branch
with the review findings addressed: the guard no longer rejects board
cancellation, and the internal ticket reference is gone.

## What Changed

- `server/src/services/issue-execution-policy.ts`: in the orphaned-stage
branch, reject the transition with 422 `unexecuted_review_stage` only
when a live review cycle (pending or changes_requested) meets a
requested status of `done`. All other requested statuses — including
`cancelled`, where abandoning the cycle is the intent — fall through to
`clearExecutionStatePatch` exactly as a bare policy edit does.
- `server/src/__tests__/issue-execution-policy.test.ts`: regression
coverage for the rejected `done`, the preserved board cancellation, a
routine non-`done` status change on the same path, the unchanged-policy
`done` route to the stored reviewer, and the bare policy edit.

## Verification

- `pnpm --filter @paperclipai/server vitest run
src/__tests__/issue-execution-policy.test.ts` — 75 tests pass locally.
- `pnpm --filter @paperclipai/server typecheck` passes.
- Manual reasoning check: PATCH `{executionPolicy: <new object>, status:
"done"}` on an issue whose `executionState.status` is `pending` or
`changes_requested` now returns 422; the same request with `status:
"cancelled"` or with no status clears the orphaned stage as before.

## Risks

- Low risk. The only newly rejected request is one that previously
discarded a live review while claiming completion — a silent-bypass bug,
not a supported workflow. Callers intending to cancel or repurpose an
issue mid-review are unaffected.

## Model Used

- Anthropic Claude — SWE-2 Max agent via Devin CLI, tool use and code
execution; the original fix commit was authored by an earlier agent pass
on the same task.

## 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
- [ ] 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: Waseem Ilyas <1478353+Waseemilyas@users.noreply.github.com>
Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 15:38:28 -07:00
DottaandPaperclip becdc3b08e perf(slack): remove delays before mention acknowledgements (#16491)
Slack mentions now start eyes reactions after the authorized task/comment commits, independently of attachments, subscription and scheduler acceptance. Omit unused optional URL-preview polling while retaining message text, links and files. Keep receipt failures and missing-file warnings independent, including terminal cleanup of older multi-line diagnostics.

Verified with full current-head CI and E2E, Superagent and legacy security checks, Apex 5/5 with no unresolved findings, 19 selected real-PostgreSQL receipt/authorization/cleanup cases, and full frozen-source typecheck/build. The first CI attempt's unchanged Cursor probe timeout is retained in the PR; the one failed-only retry passed under unchanged deadlines. Live Slack latency still requires deployed acceptance.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-10-15 17:36:50 -05:00
81cea89d6b fix(cli): require confirmation for instructions file deletes (#11504)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The CLI exposes board/operator controls for managing agent
configuration and instructions.
> - Agent instructions files influence future agent behavior, so
deleting one is a destructive configuration mutation.
> - Nearby destructive CLI commands already require explicit `--yes`
confirmation before sending DELETE requests.
> - `agent instructions-file:delete` skipped that local confirmation
guard and could delete a bundle file from a scripted or mistyped
command.
> - This pull request aligns that command with the existing
destructive-command safety convention.
> - The benefit is a small, predictable operator-safety guard with
focused regression coverage.

## Linked Issues or Issue Description

Bug report:

### Pre-submission checklist

- [x] I have searched existing open and closed issues and this is not a
duplicate.
- [x] I am on the latest released version of Paperclip (or can reproduce
on `master`).
- [x] I have confirmed the error originates in Paperclip itself — not in
my agent adapter, API provider, or local configuration.

### What happened?

`paperclipai agent instructions-file:delete` deleted an agent
instructions bundle file without requiring explicit CLI confirmation.

### Expected behavior

Destructive CLI delete operations should require `--yes` before sending
a DELETE request.

### Steps to reproduce

1. Run `npx paperclipai agent instructions-file:delete <agent-id> --path
AGENTS.md`.
2. Observe that the CLI immediately issues `DELETE
/api/agents/:agentId/instructions-bundle/file?path=AGENTS.md`.
3. No local confirmation guard blocks the destructive request.

### Paperclip version or commit

`fd472d02ba950519ca5eff75ed9fd55cf976f4c2`

### Deployment mode

Local dev (`pnpm dev`)

### Installation method

Built from source (`pnpm dev` / `pnpm build`)

### Agent adapter(s) involved

- [x] Not adapter-specific (core bug)

### Database mode

Not database-related

### Access context

Board (human operator)

### Node.js version

`v20.x`

### Operating system

macOS

### Relevant logs or output

```text
Current behavior is local CLI behavior: the command proceeds to the DELETE call without requiring `--yes`.
```

### Relevant config (if applicable)

None.

### Additional context

This command already sits next to other destructive CLI actions such as
`agent delete`, which require explicit confirmation. Aligning the guard
makes the CLI safety model consistent.

### Privacy checklist

- [x] I have reviewed all pasted output for PII (usernames, file paths,
API keys, tokens, company names) and redacted where necessary.

## What Changed

- Added a `--yes` confirmation option to `agent
instructions-file:delete`.
- Refuse the command locally before resolving API context or sending a
DELETE request when confirmation is missing.
- Updated CLI parity coverage for confirmed and refused
instructions-file deletion.
- Updated the CLI documentation example to include `--yes`.

## Verification

-
`/Users/xinran/Downloads/dev/paperclip-pr-work/node_modules/.bin/vitest
run cli/src/__tests__/agent-lifecycle.test.ts --config
cli/vitest.config.ts` equivalent executed from the PR worktree using
temporary dependency symlinks: 3 tests passed.
- `git diff --check`

## Risks

- Low risk: this only changes one destructive CLI command and matches
existing `agent delete`, `issue delete`, and other delete-command
confirmation behavior.
- Scripts that intentionally delete instructions files must add `--yes`,
which is the intended explicit confirmation path.
- No database, API contract, or lockfile changes.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5-based coding agent in Codex desktop with
shell/tool use and local 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

---------

Co-authored-by: 馨冉 <xinxincui239@gmail.com>
Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 15:36:23 -07:00
Michel Tomas 5b15de9568 fix(adapter-utils): accept the bridge token in X-API-Key (#12785)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - An agent can run inside a sandbox. The sandbox callback bridge is
the loopback gateway that lets the agent call the Paperclip API from
inside that sandbox
> - The gateway authenticates each local call with a per-run bridge
token. It read that token from the `Authorization: Bearer <token>`
header only
> - The run hands the agent that token in `PAPERCLIP_API_KEY`, next to
`PAPERCLIP_API_URL` (`execution-target.ts`). The token is named an API
key, and the public Paperclip API documents that an API key goes in the
`X-API-Key` header
> - An agent that follows the documentation therefore sends `X-API-Key`
first, and its first call fails with 401 `Invalid bridge token.`
> - The agent then retries with a bearer header and the same token. The
run still succeeds, but it wastes a turn and it can leave a confused
agent trying unrelated repairs
> - This pull request makes both generated gateways read the bridge
token from `X-API-Key` when the request carries no bearer token
> - The benefit is that a documented header convention stops producing a
needless failure, at no cost to the token check

## Linked Issues or Issue Description

No existing issue found. I searched the repository for open pull
requests matching `x-api-key` and `bridge token`. Nothing addresses the
in-sandbox gateway header convention. The closest neighbours are
unrelated: #12632 (Composio `mcp.headers.x-api-key`) and #12120 (the
HTTP/2 transport for this bridge, already merged). The problem follows
`bug_report.yml`:

**What happened?**

An agent running in a sandbox calls the Paperclip API through the
loopback callback bridge. When it sends the credential as `X-API-Key:
<bridge token>`, the gateway answers `401` with `{"error":"Invalid
bridge token."}`. The token in that header is the correct per-run bridge
token.

**Expected behavior**

The gateway accepts the correct per-run bridge token in either header
convention. The public API documents `X-API-Key`, so an agent that
follows the documentation succeeds on its first call.

**Steps to reproduce**

1. Start a run whose agent executes in a sandbox execution target, so
the callback bridge is active.
2. The run exports `PAPERCLIP_API_URL` (the loopback bridge origin) and
`PAPERCLIP_API_KEY` (the bridge token) into the sandbox environment.
3. From inside the sandbox, call the bridge with that key in the
documented header:
   ```bash
curl -i -H "X-API-Key: $PAPERCLIP_API_KEY"
"$PAPERCLIP_API_URL/api/agents/me"
   ```
4. The response is `401 {"error":"Invalid bridge token."}`.
5. Repeat the same call with `-H "Authorization: Bearer
$PAPERCLIP_API_KEY"`. The response is `200`.

**Paperclip version or commit**

Branched from `master` at `06c0e883f`.

**Deployment mode**

Self-hosted Kubernetes, with the agent in a sandbox execution target and
a local model behind an OpenAI-compatible endpoint.

**Agent adapter(s) involved**

Not adapter-specific (core bug). Observed with a local-model adapter on
a sandboxed lane. Any agent that follows the public API documentation
sends this header.

**Additional context**

The variable name is the trigger. The run calls the credential
`PAPERCLIP_API_KEY`, and an agent that has read the public API
documentation knows an API key goes in `X-API-Key`. Paperclip's own
in-prompt guidance uses `Authorization: Bearer $PAPERCLIP_API_KEY`, so
the two conventions sit side by side.

Across 12 observed runs on that lane, the agent's first bridge call used
`X-API-Key` in 6 runs. Every one of those runs recovered by retrying
with a bearer header and the same token. In some runs the agent first
tried unrelated repairs, such as writing a test comment, before it
changed the header.

## What Changed

- Add one `readBridgeToken(req)` helper to the generated in-sandbox
gateway source. The helper returns the bearer token from `Authorization`
when the header carries one. It otherwise returns the `x-api-key` header
value, or an empty string.
- Use that helper in both generated gateway request handlers: the
file-mode queue gateway and the HTTP/2 gateway. Both previously repeated
the same two lines of bearer parsing.
- The token still goes to the same `timingSafeEqual` comparison. The
change does not alter the comparison, the token, or its lifetime.
- Extend the file-mode round-trip test to cover an `X-API-Key` request
with the right token, an `X-API-Key` request with a wrong token, and the
fact that the header never reaches the host.
- Add one HTTP/2-path test that covers the same three cases, and that
proves a bearer token still wins when a request carries both headers.

## Verification

Commands run on this branch:

```
node_modules/.bin/vitest run packages/adapter-utils/src/sandbox-callback-bridge.test.ts
  Test Files  1 passed (1)
       Tests  52 passed (52)

cd packages/adapter-utils && ../../node_modules/.bin/tsc --noEmit
  0 errors in the two files this pull request touches
```

Both new tests are real regression guards. With the test file in place
and the source change reverted, each one fails with `expected 401 to be
200`: the file-mode round-trip test and the HTTP/2 test. Both pass with
the source change applied.

A reviewer can confirm the security properties by reading two things.
First, `tokensMatch` in the generated source is unchanged, so the
constant-time comparison against the same per-run token is unchanged.
Second, `allowedHeaders` in the same source is a closed allowlist of
`accept`, `content-type`, `if-match`, and `if-none-match`.
`normalizeHeaders` drops every other header, so neither `authorization`
nor `x-api-key` leaves the sandbox on either transport. The independent
host-side check in `http2-bridge-server.ts` is untouched, because each
gateway sets `authorization: Bearer <token>` on the request it forwards.

**ROADMAP.md check:** I grepped `ROADMAP.md` for `bridge`, `x-api-key`,
`redaction`, and `sandbox callback`. There were no matches. This is a
small bug fix in an existing subsystem, so it does not overlap planned
core work.

**Duplicate search:** I searched pull requests in this repository for
`x-api-key` and `bridge token`. No open or merged pull request changes
how the in-sandbox gateway reads the token.

## Risks

Low risk.

- The change widens which header the gateway reads. It does not widen
what the gateway accepts. A request still needs the exact per-run bridge
token, and it still passes the same constant-time comparison.
- A bearer token keeps priority. A request that carries both headers
behaves exactly as it did before, which a test now pins.
- A caller that presents a non-bearer `Authorization` header and a valid
`X-API-Key` header now succeeds instead of failing. This is intentional:
the bridge only ever issues bearer tokens, so no bridge caller relied on
that failure.
- The header allowlist already excluded `x-api-key`, so no forwarded
request changes shape.
- No migration, no configuration change, and no behavior change for a
caller that already sends a bearer token.

## Model Used

Claude Opus 5 (`claude-opus-5`), extended thinking at high effort —
verify before merge.

## 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 — no
documentation describes the bridge's header convention, so there is
nothing to update
- [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

---
<sub><em>**[@superbiche](https://github.com/superbiche)** · contributor
· drafted with Claude Opus 5, reviewed before posting; the voice and
decisions are mine.</em></sub>
2026-10-15 15:31:31 -07:00
DottaandPaperclip 67a9d5cc37 perf(runner): bypass skill cache waits for empty selections (#16498)
Native runs with no skill files no longer queue behind company skill-cache work. Preserve saved empty selections and the existing exclusion for selected and legacy operational skills.

Verified with real PostgreSQL held-lock regressions, 20 distinct affected cases, full repository typecheck/build, fresh full CI/E2E/security and exact-head Apex 5/5. Hosted latency remains to be verified.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
canary/v2026.1015.0-canary.23
2026-10-15 17:01:57 -05:00
Nicky LeachandPaperclip ec3eb1968b feat(runner): expose credential updates through PRP (#16463)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The Runner uses PRP to send harness events to the host.
> - A harness can replace its stored OAuth tokens during a run.
> - The host has no PRP signal that tells it to read the updated
credential.
> - This pull request adds a durable credential update event and
observers for supported stores.
> - The host can react before it acknowledges the event. Token values
stay outside PRP.

## Linked Issues or Issue Description

**Subsystem affected**

`packages/paperclip-runner`: native provider execution, PRP schemas, and
host event delivery.

**Problem or motivation**

A Paperclip host that consumes PRP needs to react when a harness changes
its refresh-token credential. Existing credential copy-back paths do not
provide a common event during a warm session.

**Proposed solution**

Add `auth.credentials.updated` as a P0 runner event. Include only the
provider, binding ID, revision, and detection method. Observe native
Codex and Codex/Grok ACPX credential files. Retain each pending event
across runner restart until the durable outbox accepts it. Raw PRP
consumers opt in with `observeCredentials: true` before session open.
The bundled transport opts in for fresh sessions.

**Alternatives considered**

`harness.diagnostic` would mix a runner observation with harness
diagnostics. Sending token values through PRP would expose credentials
to event logs. Both approaches are unnecessary.

**Roadmap alignment**

I checked `ROADMAP.md`. This change extends the existing Runner protocol
and does not duplicate a planned core feature.

**Additional context**

Refs: #11094, #14056, #12696. These describe credential copy-back and
staging work. This PR adds the notification contract. It does not
replace those private credential channels or claim to fix their full
scope.

## What Changed

- Add strict credential update payload validation to PRP v1, v2, and v3.
Regenerate validators, the manifest, and the event catalog.
- Watch supported credential directories with `notify`. Add a periodic
read as a fallback and check at terminal and close boundaries.
- Persist a private baseline and pending event together. Notify on
account identity changes and retain the new baseline for later
refreshes. Ignore incomplete files, unsafe files, and metadata changes.
- Forward the event through the host transport. Test commit-before-ACK
delivery and replay.
- Commit pending runner observations before suspend and shutdown
commands complete. Preserve the provider event backlog.
- Create the private ACPX runtime directory before configuring
observation. Cover fresh session startup with observation enabled.
- Fence asynchronous PRP commits to the current authenticated connection
and run authority. Ignore replaced callbacks while preserving the
maintenance drain of admitted work.
- Deliver observations found during final provider cleanup before
clearing terminal recovery state. Retain the outbox and recovery state
when the host ACK is lost.
- Advance the pending Copilot candidate profile to v19 for the changed
shared PRP source hashes. Preserve its v18 history and pending
qualification status. Include the current fixture in the Docker build
context.
- Commit credential updates through an awaited host callback before PRP
ACK, including during idle and close. Persist them in a separate run-log
source namespace with company, agent, session, and runner checks.
- Preserve public event metadata through server redaction. Register the
event in task run details.
- Document opt-in behavior, supported stores, event semantics, and the
local run-log path.

## Verification

- All 45 durable runner control tests and 24 native executor integration
tests pass.
- Ten Rust credential observer tests pass. They cover atomic
replacement, polling, recovery, account-only changes and later refreshes
for Codex and Grok, unsafe files, fresh runtime creation, and the Grok
close handoff. Account identity stays private.
- The full Runner TypeScript suite passes: 3,565 tests in 221 files. An
additional 12 tests are skipped by the suite.
- All 214 focused tests pass for the contract, Codex event routing,
catalog, and durable host delivery.
- All 13 Node protocol contract tests pass.
- The exact Docker context integrity command passes: `docker buildx
build --file .github/docker-context-checks.Dockerfile .`.
- Rust formatting and generated protocol checks pass.
- `pnpm -r typecheck` and `pnpm build` pass. The full local `pnpm
test:run` was attempted with CI-compatible `init.defaultBranch=master`,
then stopped after a reproducible failure outside this change:
`git-workspace-expiration.test.ts` expects one re-expired workspace but
gets zero. The same case fails in isolation on this macOS checkout. Full
repository validation is provided by CI; the focused Runner and host
tests pass locally.
- All 253 native transport and restart tests pass against the final
release binary.
- All 3 durable recovery tests and 139 candidate profile and native
admission tests pass.
- All 41 host redaction and task protocol surface tests pass. `pnpm
check:token-gates` passes.
- All 467 CI policy tests pass, including the 15 CI profiling tests. The
upstream secret-reference test fix is retained from master. No workflow
changes are included.

- The Apex host-delivery fix passes 381 targeted Runner tests, six host
database tests, repository typecheck, and the production build. The
Runner tests cover commit-before-ACK, retry after a rejected host
commit, warm attachment, and close after the turn queue ends.
- Prior head `2f125cfcb` passed CI, standard Greptile 5/5, and Apex 5/5.
One CI shard was interrupted by GitHub runner shutdown; its single rerun
passed. Both Apex findings are addressed: idle/cleanup host delivery and
late callback reconnect fencing. Current head `5db78f082` passes CI (56
successful statuses and four optional skips) and standard Greptile 5/5.
Apex review of the account-change update is 5/5 on this exact head, with
no actionable issues.
- All 121 durable control-plane and credential callback tests pass,
including account-only change delivery, subsequent refresh on the new
account during close, host commit retry, late success/failure races,
forward cursor delivery on a replacement connection, and the existing
maintenance retirement contract. All 27 native provider and durable
recovery integration tests pass after the account-change update.

## Risks

- File changes signal a stored credential update. They do not prove that
an OAuth refresh succeeded. Changes between reads can be combined.
- Unix Codex and Codex/Grok ACPX stores are supported. Other harnesses
and credentials held only in memory need their own integration.
- Hosts must update their event schemas before opting in. Older hosts
omit the flag and receive no new event. Older runners ignore the flag.
- The host must use its existing private credential channel and account
checks to read or copy the token. Account switches trigger notification
but do not authorize accepting the new account. The event grants no
credential access.
- Tests use synthetic credentials. No live OAuth refresh has been
forced.

## Model Used

OpenAI Codex, exact model ID `gpt-6.1-sol`, with high reasoning effort,
repository inspection, tool use, and code execution. The session does
not expose its context window size.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 14:49:00 -07:00
23e7ee9a2d fix(issues): exclude terminal children from helper cap (#11542)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The issue service lets agents create bounded child work through a
helper.
> - The helper counted completed and cancelled children against its
safety limit.
> - A recurring coordinator could reach the limit even when almost all
historical children were terminal.
> - The safety limit must still bound current delegated work.
> - This pull request counts only non-terminal children when it applies
the limit.
> - The benefit is that recurring parents can keep their lineage without
losing the active-work guardrail.

## Linked Issues or Issue Description

**What happened?**

The child-creation helper rejected a new child after a parent had 25
historical children. It counted children with `done` and `cancelled`
status.

**Expected behavior**

The helper must apply its limit to non-terminal children. Terminal
children must remain attached to the parent for lineage and audit
history.

**Steps to reproduce**

1. Create one parent issue.
2. Create 25 child issues and move them to `done` or `cancelled`.
3. Use the issue-service child helper to create another child.
4. Observe that the current code rejects the new child.

**Paperclip version or commit**

`1a17cbf23`

## What Changed

- Exclude `done` and `cancelled` children from the helper cap query.
- Keep the limit at 25 non-terminal children.
- Add a regression test with terminal history and the active limit
boundary.
- Clarify the limit error so it says `active child issues`.

## Verification

- `pnpm exec vitest run server/src/__tests__/issues-service.test.ts -t
"counts only non-terminal children toward the helper child limit"`
passed: 1 test passed and 118 skipped.
- `pnpm -r typecheck` passed.
- `pnpm build` passed.
- `pnpm test:run` completed the general server and UI groups
successfully. The CLI group then reported one unrelated environment
failure because port 3199 was already in use. The failing test was
`doctor > re-runs repairable checks so repaired failures do not remain
blocking`.

```test-evidence:
sha: 071edbf019
command: pnpm exec vitest run server/src/__tests__/issues-service.test.ts -t "counts only non-terminal children toward the helper child limit"
exit: 0
totals: 1 test passed; 118 skipped; 1 test file passed
worktree: clean before and after; local == remote == PR head
finished_at: 2026-08-17T14:03:53Z
```

## Risks

- Low risk. The change affects only the helper-specific count query.
- The helper still rejects creation when 25 non-terminal children exist.
- No schema or migration changes are present.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI GPT-5 Codex with reasoning, repository tools, code execution,
and test execution.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [ ] 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: Codex Engineer <agent+codex-engineer@agents.techwright.io>
Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: commitperclip-bot <305974387+commitperclip-bot@users.noreply.github.com>
canary/v2026.1015.0-canary.22
2026-10-15 14:36:48 -07:00
Dylan RoyandClaude Fable 5 7b09e3da73 fix: count writes from unscoped heartbeat runs against the cross-issue cap instead of rejecting them (#12621)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Agents act inside heartbeat runs, and the server attributes every
issue comment and task update to a run so the per-run cross-issue
influence cap can be counted
> - A timer heartbeat that wakes an agent with no checked-out issue
stores no `issueId` in the run context snapshot
> - The influence gate treats that missing source issue as "no valid
run" and rejects every comment and PATCH from the run with
`cross_issue_influence_run_context_required`, even though the run row
exists and fully attributes the write
> - Issue creation is not gated, so an unscoped run can open an issue it
then cannot describe, update, or comment on
> - This pull request counts writes from unscoped runs against the
cross-issue cap instead of rejecting them
> - The benefit is that unscoped heartbeat runs keep their write
channels while the anti-spray cap and the audit trail stay fully intact

## Linked Issues or Issue Description

No public issue exists. Description follows the bug report template.

**What happened?**

An agent woken by a plain heartbeat timer (no assigned issue) received a
403 with code `cross_issue_influence_run_context_required` on every
`POST /api/issues/{id}/comments` and `PATCH /api/issues/{id}` request.
The agent JWT was fresh and its `run_id` matched a live `heartbeat_runs`
row. The error text said the request "arrived without a valid run", but
the run was valid. `POST /api/companies/{companyId}/issues` succeeded
with the same token, so the run created an issue it could not then
update.

**Expected behavior**

A live, authenticated run must be able to comment and update issues. A
run with no source issue has no same-issue exemption, so each of its
writes must spend the per-run cross-issue cap. The
`cross_issue_influence_run_context_required` error must fire only for
malformed, unknown, or mismatched run ids.

**Steps to reproduce**

1. Let an agent wake from the heartbeat timer with no checked-out issue.
2. From that run, call `PATCH /api/issues/{id}` or `POST
/api/issues/{id}/comments` with the agent JWT.
3. The server returns 403 `cross_issue_influence_run_context_required`,
because `observeCrossIssueInfluence` throws when `readRunSourceIssueId`
returns null.

**Paperclip version or commit**

master (c7ebc089c); also reproduced on the current published npm
package.

**Deployment mode**

Local single instance (embedded Postgres).

**Installation method**

npx paperclipai

## What Changed

- `observeCrossIssueInfluence` no longer throws when the persisted run
has no source issue. It counts the write as cross-issue influence and
records `sourceIssueId: null` in the activity log entry.
- The same-issue exemption applies only when the run has a source issue.
- Replaced the test that pinned the old rejection with two tests: an
unscoped run's write is counted and allowed, and an unscoped run is
still capped once its budget is spent.

## Verification

- `cd server && pnpm vitest run
src/__tests__/cross-issue-influence-limit.test.ts` — 11 tests pass.
- `cd server && pnpm vitest run
src/__tests__/cross-issue-influence-limit-postgres.test.ts
src/__tests__/interaction-resolution-cross-issue-cap-postgres.test.ts` —
8 tests pass.
- Manual: wake an agent from a plain heartbeat timer, then PATCH any
issue with the run's JWT. Before the fix the server returns 403
`cross_issue_influence_run_context_required`; after the fix the write
succeeds and an `issue.cross_issue_influence_observed` activity row
appears with `sourceIssueId: null`.

## Risks

- Behavioral shift: writes from unscoped runs were rejected and are now
allowed up to the existing per-run cap of 20. This is the conservative
direction — with no source issue there is no same-issue exemption to
abuse, and every write is still attributed to a locked run row and
logged.
- No schema or migration changes. The activity log
`details.sourceIssueId` field can now be null; it was previously always
set on these rows.

## Model Used

- Claude Fable 5 (Anthropic, model id `claude-fable-5`, 1M context,
extended thinking, tool use enabled) authored the change and tests,
driven through 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 Fable 5 <noreply@anthropic.com>
2026-10-15 14:34:23 -07:00
DottaandPaperclip 89ef37d7e0 fix(slack): accept linear DM receipt destinations (#16494)
Accept the pinned Slack SDK linear DM address for receipt add/remove while preserving channel, source message, credential and timeout checks.

SDK regressions, 106 affected tests, repository typecheck/build, full CI/E2E, Superagent, legacy Snyk and exact-head Apex 5/5 passed.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-10-15 16:28:19 -05:00
DottaandPaperclip 8843887c24 fix(runner): preserve managed GitHub access in OpenCode (#16488)
## Thinking Path

> - Paperclip manages AI agents and their authorized connections.
> - Native OpenCode agents use managed Git and GitHub launchers for
shell work.
> - Each operation must obtain credentials from the active run's broker.
> - Two OpenCode environment filters dropped that broker binding before
the shell started.
> - The shell therefore ran anonymously even when connector tools had
authorized access.
> - This pull request preserves the explicit broker environment through
both filters.
> - The benefit is working GitHub shell access with current identity and
revocation checks.

## Linked Issues or Issue Description

**What happened?**

Native OpenCode shell commands reported `GitHub capability_missing`
despite an authorized GitHub connection. Both runner startup and
provider startup dropped the controller's broker settings. Connector MCP
calls used a separate path and could still succeed.

**Expected behavior**

A managed shell operation obtains credentials for the current run. A
later operation uses the new identity after rotation and loses access
after revocation. Ambient host credentials do not supply authority.

**Steps to reproduce**

1. Start the native GitHub broker with an active run binding.
2. Pass its environment through native OpenCode startup.
3. Run `gh api user` from the provider shell.
4. Observe anonymous access before this fix.

**Paperclip version or commit**

Reproduced on master `6943904bad` before this change.

**Deployment mode**

Native Paperclip Runner with OpenCode, including remote execution.

Related: #16401 fixes the separate oversized OpenCode SSE failure and is
already merged. The same live-driver regression was verified locally
against its exact pre-fix source and current source. This PR does not
duplicate that fix. Searches found no open PR for this native broker
propagation defect; #15309 concerns the legacy OpenCode adapter.

## What Changed

- Use the existing GitHub credential environment projection at both
OpenCode launch boundaries.
- Preserve explicit controller authority while excluding an ambient host
broker.
- Exercise the real launcher and broker from an OpenCode child process,
directly and through runner projection.
- Check operation-time identity rotation, revocation, and exclusion of
controller API credentials and persistent GitHub tokens.
- Document the managed OpenCode shell contract.

## Verification

- Red: both new `native-github-access.test.ts` cases returned
`anonymous` instead of `fixture-a` before production changes.
- Green: both cases pass after the fix, including `fixture-a` to
`fixture-b` rotation and anonymous operation after revocation.
- Full native GitHub broker suite: 18 tests pass.
- OpenCode, provider-event, and configured-environment suites: 141 tests
pass across eight files.
- Separate SSE red/green verification: the existing live-driver
regression times out on `fd057f6ac4^` and passes with merged #16401. The
full OpenCode group also passes after restoration.
- Full repository build and typecheck pass locally. All CI jobs pass for
`23d734293f6a5c6d6128cae0c8773661816daf9a`. Final GitHub rollup: 55
successful checks/statuses, two skipped checks, and one neutral check;
none pending or failing. Greptile gave that commit 5/5 with no findings
or unresolved threads.
- Paperclip Review spent over 23 minutes preparing its runtime without a
provider assessment. Its run was cancelled for recovery and ended
neutral (review execution did not complete). This neutral result is not
a code assessment. No check policy or branch protection was changed.
- The full local Vitest attempt first hit embedded PostgreSQL startup
failures. Running the unchanged `initdb --version` and `postgres
--version` independently showed missing native library symlinks. The
dependency had been installed with scripts disabled. Running its bundled
`hydrate-symlinks.js` restored startup; all 15 affected native-session
cases and all 112 AI connection tests then passed without application
code changes. The original full-suite attempt was stopped after the
setup failure and its log is retained. A complete local suite pass is
not claimed.
- The broker and executable are local fixtures. No live GitHub account,
credential change, or test PR is required by these regressions.

## Risks

The change affects credential delivery into OpenCode processes. It
reuses the existing bounded GitHub projection and accepts broker
authority only from explicit input. Each shell operation still uses the
normal broker, scope, identity, and revocation rules. Unrelated
controller secrets remain excluded. There are no database or
permission-policy changes.

## Model Used

OpenAI `gpt-6.1-sol`, through Codex, with xhigh reasoning and repository
tools/code execution. The session does not report its 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 the focused regression and affected suites locally and
they pass; the full local attempt and setup failure are disclosed 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 (Paperclip Review is
neutral/incomplete, as disclosed above)
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 16:15:38 -05:00
Devin FoleyandPaperclip 0b62c736a0 feat(connections): add generic Daytona API and Toolbox access (#16483)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Apps connections give agents controlled access to external services.
> - Daytona provides sandbox, file, command, Git, and account APIs.
> - Operators need to assign this access without exposing a server
credential.
> - A small task-specific tool list cannot serve general Daytona work.
> - This pull request adds the published HTTP actions through the
existing connection gateway.
> - Operators keep control of identity, agent access, and each action.

## Linked Issues or Issue Description

**Problem or motivation**

Paperclip has a Daytona sandbox provider for its own execution
infrastructure. It lacks a normal Apps connection for agents to manage
an operator's Daytona account. Reusing the server's provider credential
would bypass normal connection ownership and action permissions.

**Proposed solution**

Add a Daytona connection with personal or shared vault credentials.
Generate its action catalog from the official platform and Toolbox API
specifications. Use the existing run-bound gateway, grants, action
policies, approvals, revocation, and audit paths. Sandbox IDs come from
Daytona; tools need no Paperclip task or lease ID.

**Alternatives considered**

A four-action diagnostic subset cannot support general provider work.
Launching the provider CLI would expose host filesystem behavior. Native
OAuth is not included because a supported third-party registration path
was not verified. The native method uses an organization API key.
Existing Composio setup is a separate possible OAuth route and is not
qualified by this change.

**Roadmap alignment**

This extends the existing Apps and Connections provider coverage in
`ROADMAP.md`. It uses that system's credential and permission model.
GitHub searches found no existing Daytona Apps connector PR or issue.

## What Changed

- Add the Daytona catalog entry, provider source override, official
theme logos, permission review, and setup documentation.
- Generate 274 HTTP actions: 169 platform and 105 Toolbox operations.
Record two WebSocket upgrades separately; do not advertise them as HTTP
tools. Record source URLs and hashes.
- Add provider-focused execution for sandboxes, snapshots, volumes,
files, Git, commands, computer use, and account resources. Provider
authority still limits which endpoints accept an organization key.
- Validate action arguments. Resolve Toolbox targets through the fixed
platform API. Check sandbox identity and organization before using an
approved Daytona proxy. Keep normal guarded network requests and vault
resolution.
- Transfer file bytes without reading or writing host files. Share one
caller deadline across prerequisite reads, dispatch, and response
reading. Bound requests and responses. Do not automatically retry writes
with unknown outcomes. Redact the selected credential from results and
errors.
- Classify credential access, access changes, interactive input, command
execution, file permissions, and deletion (including TTL and
auto-delete) as destructive actions. Keep new and changed actions under
catalog review.
- Upgrade saved catalogs and retire the earlier diagnostic names. Hide
retired actions from the UI and agent discovery even when provider
refresh fails. Preserve existing action choices and historical records.
Reject stale same-name contracts during agent discovery and dispatch
before a board refresh.
- Add database-backed gateway and catalog-upgrade regressions, schema
generator tests, a browser setup check, and both capability map updates.

## Verification

- Passed on the review-fix head: 57 focused Vitest cases (18 Daytona
database/client cases, five HTTP boundary cases, and 34 shared catalog
cases), four generator tests, `pnpm -r typecheck`, and `pnpm build`. The
five HTTP cases use a real local server through the pinned production
transport. The normal browser setup check and 17 generator/artwork cases
passed on the initial PR head; those UI and artwork paths are unchanged.
- Passed on this branch: brand asset validation, token gates, map
structure checks, and `git diff --check`. All latest-head GitHub checks
pass on `ea979ccb3a64dc9508807823540f935c4316ea35`. Apex is 5/5, with
all five findings addressed and zero unresolved threads. The branch has
no merge conflicts.
- The initial catalog-generation command could not find the external
research corpus. The supported `--definitions-only` mode regenerated the
definitions successfully. Unrelated generated drift was excluded.
- An earlier full local Vitest attempt on the preview branch failed when
bundled PostgreSQL could not start on macOS. After replay onto current
master, all three unchanged event-sequencing cases pass with bundled
PostgreSQL; the earlier startup cause remains uncertain.
- The first full-suite command on this branch used my external test
database override. Chat fixtures require a current migrated schema and
failed because `agents.lifecycle_state` was absent in that disposable
database. A focused comparison reproduces failure with the override and
passes with normal setup. That attempt was stopped, and the full suite
restarted without the override. Focused Daytona cases use their own
migrated PostgreSQL 16 databases.
- The clean local full-suite attempt recorded embedded PostgreSQL
startup failures in two unchanged native-runtime cases and two failures
in unchanged Git fixtures. It was stopped after these failures were
isolated; no full local suite pass is claimed. The 15 matching
native-runtime cases pass separately. The Git cases fail with the local
`init.defaultBranch=main` setting and pass with `GIT_CONFIG_COUNT=1
GIT_CONFIG_KEY_0=init.defaultBranch GIT_CONFIG_VALUE_0=master` limited
to the test command. No global Git setting was changed. Full Linux CI is
green.
- Fixtures use real database persistence and run-bound gateway sessions
with provider responses replaced by fixtures. They cover personal/shared
vault ownership, reads and writes, file bytes, Off policies, revocation,
organization mismatch, untrusted proxy rejection, output bounds, saved
catalog upgrades, failed refresh, and permission preservation.
- The first Apex review found five valid issues: multipart transport
compatibility, destructive classification, caller deadlines, audit
filters, and stale saved contracts. All five were fixed with regressions
before the second review. A typecheck then found the nullable saved
schema hash; admission now accepts that stored type and rejects null as
stale.
- The browser check covers setup controls without submitting a provider
key. No real Daytona account, provider write, native OAuth flow, or
agent model run is qualified. Live provider read/write proof remains
pending a test account.

## Risks

- Daytona keys have broad Toolbox authority, including keys with no
selected resource scopes. Only assign this connection to trusted agents
and review its action permissions.
- Remote writes or commands can continue after a timeout. Calls do not
automatically retry an uncertain outcome.
- The bridge targets Daytona Cloud. Proxy hosts are restricted; an
unrecognized future regional host fails closed.
- Files and responses have an 8 MiB bound. Each action has one caller
deadline, capped at 30 seconds across all provider requests and response
reading. Interactive WebSocket sessions are not exposed as HTTP actions.
- The generated JSON snapshot exceeds 1,000 lines because it holds the
provider input contracts. Generator logic and execution code remain in
separate small modules. Updates require explicit regeneration and
catalog review.
- No database migration or lockfile change is required.

## Model Used

OpenAI Codex, GPT-6. The runtime identifies the model family but does
not expose the exact backend model ID or context window. Used reasoning,
repository inspection, code editing, shell tools, database verification,
and browser tests.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 14:05:26 -07:00
DottaandPaperclip 61831ba7b8 refactor: defer adapter launcher imports during workspace snapshots (#16492)
Defer adapter launcher imports until a directory merge resolves its lock root. Snapshot-only workers retain the same hashes, modes, exclusions, and ownership checks.

Verification: 63 focused cases; full typecheck/build; exact-head full CI/E2E/security; Apex 5/5. Local native Daytona replies: 66.939s cold and 26.485s warm. Hosted staging and the cold latency target remain unverified.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-10-15 16:03:47 -05:00
Dotta f1d925b726 fix(issues): keep workspace restoration failures retryable (#16489)
## Thinking Path

> - Paperclip manages agent work and its saved files.
> - Finished Git workspaces can expire and restore from a saved commit.
> - A task comment must restore a closed workspace before the comment is
saved.
> - Failed restoration returned HTTP 503 and hid the restoration
message.
> - The composer treats 5xx writes as uncertain, so it blocked the draft
instead of offering a clear retry.
> - This change returns a definite rejection before the write and
preserves the restoration message.
> - Users can restore repository access and retry the same draft.

## Linked Issues or Issue Description

Refs #16457 and #16476.

Live acceptance found this gap with a disposable expired workspace and
an unavailable upstream. The saved commit and unique-file control stayed
intact. No fallback workspace or comment was created. The UI still
showed an uncertain comment result because the route returned 503.

## What Changed

- Return HTTP 409 for a rejected workspace rebuild before the consuming
write.
- Preserve the service's safe restoration message in the response.
- Cover rejected comment, comment-update, and checkout paths.
- Document the response and draft retry behavior.

## Verification

- `pnpm exec vitest run
server/src/__tests__/issue-closed-workspace-routes.test.ts
ui/src/api/issues.test.ts`: 38 passed in 26.80s.
- Route tests assert that failed restoration does not save a comment or
update the task.
- Existing client controls preserve 409 rejections and still treat
network failures and 5xx writes as uncertain.
- `pnpm -r typecheck` and `pnpm build` passed. Full PR CI passed on
attempt 2: [run
38804449401](https://github.com/paperclipai/paperclip/actions/runs/38804449401).
The first attempt timed out in the unrelated fresh personal-AI
connection browser case while waiting for its first reply. Logs and
browser evidence were inspected and retained; only failed jobs were
rerun once, and that shard passed.
- Retained live fixture will verify the error, retry, exact saved
commit, and subsequent persisted work after deployment.

## Risks

Clients now receive 409 instead of 503 for this known pre-write
rejection. They must retry after repository access is restored. The
route uses the service's fixed messages, not raw Git errors. This change
does not alter restoration, authorization, cleanup, or genuine
uncertain-write handling.

## Model Used

OpenAI Codex, GPT-6 family, with code execution and browser tools. The
exact deployment model ID 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 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
2026-10-15 15:59:31 -05:00
DottaandPaperclip 6943904bad perf: stage independent remote GitHub launchers concurrently (#16484)
Stage at most three independent remote GitHub launcher files at once only when the existing effective concurrent-sync capability permits it. Preserve serial fallback, per-file locks and integrity checks, and settle every started upload before failure returns.

Verification: 119 affected tests pass (one existing Linux-only oracle skipped on macOS); full repository typecheck/build pass; same-sandbox real-Daytona component comparison preserves all bytes/modes; current-head full CI/E2E/Superagent/Snyk and Apex 5/5 pass. The full native timing target remains separate and is not claimed by this change.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
canary/v2026.1015.0-canary.21
2026-10-15 15:36:43 -05:00
DottaandPaperclip 676d3ec8d4 perf(ci): reuse package downloads and overlap runtime checks (#16474)
## Thinking Path

> - Paperclip contributors wait for CI before delivering changes.
> - Build still finishes last after #16460.
> - CI already downloads the public npm graph while the build runs.
> - Bundled-package preparation ignores that cache and downloads the
same archives again.
> - Reuse the existing cache and overlap independent runtime checks
while preserving fresh installs, integrity, offline lifecycle and
admission verification.
> - Measure staging and the full workflow separately.

## Linked Issues or Issue Description

Refs #16460 and #16434. This is a focused follow-up to merged #16460,
now based directly on master.

**Current behavior:**
The Build workflow warms `PAPERCLIP_PUBLIC_INSTALL_NPM_CACHE`, but
`startBundledInstalls` inherits the host's default npm cache. Server
staging took 31.17 seconds in the latest passing run, before packing and
the clean consumer install.

**Proposed behavior:**
Pass the verifier environment, including the explicitly configured warm
cache, to the three existing staging children. Without an explicit
shared cache, keep the usual producer npm configuration.

**Alternatives considered:**
Copying an installed dependency tree would bypass normal fresh
installation. Adding jobs would add setup cost. This change reuses only
npm's integrity-checked download cache. It does not remove coverage or
change product behavior and does not overlap a roadmap feature. Open PR
title search found no equivalent cache wiring change.

## What Changed

- Initialize the existing consumer cache before package staging and
expose it to producer npm only when explicitly configured.
- Pass that environment to the existing bundled-install children.
- Extend the child orchestration check to verify cache propagation and
document the cache boundary.
- Start Pi setup after the offline lifecycle, in its own download
sandbox, while Codex and Grok probes run in separate offline sandboxes.
Join successful Pi setup before lock verification and Pi admission. Name
and clean up only the verifier-owned setup container.

## Verification

- 33 focused public-install, closure and child-orchestration tests pass
on Node 24.21.0.
- A real server dependency staging experiment used
`prepare-bundled-package.mjs`, its actual manifests, provider overrides
and release patches. Built application payloads were omitted from this
dependency-only measurement.
- Cold cache: **16.139s**. After the actual CI warm-up script:
**6.980s**. A fully warm producer cache took **6.127s**. These are local
sequential measurements, not a CI wall-clock claim; filesystem warmth
and registry timing vary.
- All **28,329 files/links**, including both lockfiles, were
byte-identical between the cold output and the actual-workflow-warm
output.
- The warm-up itself took 49.631s; CI already runs it during Rust
restore/build. This change adds no warm-up operation.
- First follow-up run [passed all 48
jobs](https://github.com/paperclipai/paperclip/actions/runs/38791277425),
and Greptile gave the cache-only head 5/5. Server staging fell **31.172s
→ 17.565s** and total staging **70.169s → 54.869s**. But complete CI was
**8m20s**, slower than the parent's 8m04s; longer Codex/Pi probe times
outweighed that saving. This is not a full-run speed improvement claim.
- The next revision overlaps the independent probes instead of
serializing Pi setup behind them. All 46 focused sandbox, staging,
closure and process-supervision tests pass, including failed background
children, parent exit and cancellation. Pre-retarget head `590873a44`
passes all 48 jobs and Greptile 5/5 with no review findings. After
#16460 merged, head `fe4f8d38e` incorporates master and retargets this
PR directly to master. Its diff remains only four
optimization/documentation/test files; 46 focused checks pass again.
Fresh full CI and review are pending. The unchanged parent
conflict-resolution run passed all 48 jobs in 8m04s:
https://github.com/paperclipai/paperclip/actions/runs/38789785045.

Final paired runs against the same updated master, both on
`m7i-flex.xlarge`:

| Measurement | Parent #16460 | This PR |
| --- | ---: | ---: |
| Bundled server staging | 22.220s | 14.202s |
| All package staging | 61.277s | 48.304s |
| Clean consumer install | 67.617s | 73.490s |
| Pi setup remaining wait | 25.428s (serial setup) | 20.719s |
| Build job | 385s | 368s |
| Build start after workflow creation | 23s | 136s |
| Entire workflow, including admission and aggregates | 452s (7m32s) |
552s (9m12s) |

[Parent
run](https://github.com/paperclipai/paperclip/actions/runs/38792983313),
[final
run](https://github.com/paperclipai/paperclip/actions/runs/38792986392).

Build execution improved by **17s (4.4%)** in this pair. The total
workflow did **not** improve: it waited 113 seconds longer to start
Build, and other lanes/aggregates also contribute. The overlapping setup
ran for 25.667s while Codex/Grok took 4.946s, leaving 20.719s to wait.
Actual installed Codex, Grok and Pi checks all passed with zero provider
calls. These are individual samples with filesystem/network/CPU
variance, not a claimed steady-state average. The earlier slower
cache-only run is retained above. No tests were removed and no jobs were
added.

## Risks

Shared-cache contention can reduce the benefit if warm-up is still
running. npm handles concurrent content-addressed cache writers and
checks integrity; misses still download normally. Two runtime containers
can now overlap and contend for host resources; the full CI run measures
that tradeoff. They retain separate network policies and per-container
bounds. Pi writes only its provider assets and a private receipt; the
other probes inspect Codex/Grok. No installed tree, lock, test result or
build output is reused. The consumer still starts empty and performs the
full lifecycle and runtime checks. Normal unconfigured producer cache
behavior is preserved.

## Model Used

OpenAI GPT-6 through Codex, with repository inspection, execution and
GitHub tools. The serving model suffix and context capacity are not
exposed to 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 linked existing issues or described the issue in
this PR
- [x] I have not referenced internal or instance-local Paperclip issues
or links
- [x] My branch name describes the change and contains no private ticket
identifier
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation
- [x] I have considered and documented the risks
- [ ] All Paperclip CI gates are green (prior head passed; rerunning
after master merge)
- [ ] Greptile is 5/5 with no open P2s, recommendations or follow-ups
(prior head 5/5; current head pending)
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 15:16:52 -05:00
DottaandPaperclip 3898f6a45f fix(native): honor duplex transport for GitHub callback bridges (#16455)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Native remote runners use a session-owned broker for managed GitHub
operations.
> - That broker uses the existing authenticated sandbox callback bridge.
> - The native caller omitted the server-selected duplex flag. An
enabled and capable target still used file polling.
> - Warm sessions must observe a changed flag and channel loss before
the next admission.
> - This pull request forwards the existing flag and retires unavailable
or changed bridges before retained instruction preparation.
> - The benefit is less idle remote traffic without changing credential
authority or the default transport.

## Linked Issues or Issue Description

**What happened?**

A native GitHub callback bridge selected `queue_v1` even when its
sandbox target had duplex enabled and supported it. The file bridge
continues remote queue checks while the warm session remains available.

**Expected behavior**

An enabled, capable target should use the existing HTTP/2 bridge.
Disabled or unsupported targets and failed channel startup must retain
the authenticated file fallback. A changed server flag must take effect
at the next normal warm-session boundary.

**Steps to reproduce**

1. Create native GitHub access on a sandbox target with the
server-selected duplex flag enabled, verified duplex capability and a
working channel.
2. Observe the selected callback transport.
3. Before this fix, it is `queue_v1`. The added real-wire regression
expects `http2_v1` and fails on the old source.

## What Changed

- Forward the existing server-selected duplex flag through the native
GitHub broker.
- Record that transport selection on the broker. Retire the warm
provider and broker through the existing cleanup path when the flag
changes.
- Read live channel failure when checking broker readiness. Mark normal
session cleanup as an orderly completion.
- Include the selected flag in instruction preparation identity. Retire
a failed broker before adopting retained instructions, while preserving
existing ownership and cleanup fences.
- Add real local HTTP/2 credential-rotation and file-fallback controls.
Add native warm-session flag-change controls.
- Document selection, fallback and warm-session behavior.
- Scan CI secret expressions in one forward pass, including quoted
braces and escaped apostrophes. Preserve direct, bracket, multiline and
whole-context references while rejecting filename and literal-string
false positives.

## Verification

- Current head `41440b07ea45e9e882e36ed495a66e501c8dd4df` resolves the
actual CI-policy conflict with master
`307eb16c0c59abd9e0626fde9201939b262e7f5f`. It retains upstream's
stricter whole-expression credential guard, including quoted secret
text, and uses the forward scanner instead of a backtracking regex. All
**16 CI policy tests** pass, including the bounded 28- and
10,000-apostrophe controls in both policy modes. The reported old regex
still has its recorded two-second timeout (14 passed, one failed). On
this final merged source, **809 affected native cases** pass with zero
selected skips (65.20s). Full repository typecheck (31.44s) and build
(22.13s) pass. Frozen source hashes stayed unchanged. Fresh exact-head
full CI, configured security and completed Apex remain pending.

- Before master integration, the frozen native repair passed repository
`pnpm -r typecheck` passed (33.0s) and `pnpm build` passed (32.1s).
- Before the latest master integration, all **800 affected cases passed
with zero selected skips**: complete native executor (725), resume (50),
GitHub broker (16), environment duplex-gate (4), and heartbeat
instruction-copy (5) suites. The final run took 95.3s. Source hashes
stayed unchanged through these checks.
- The initial head passed 788 affected cases and full CI, but Apex
scored it **3/5**. It found a dead HTTP/2 broker could remain reusable
and a flag change could fail after retained instruction preparation.
Both findings required the new repair. Three added before-fix
regressions failed on channel availability, orderly close, and
preparation identity.
- The first repair run failed three new warm-instruction fixtures
because fake provider close left its recorded state ready. The corrected
fixture writes a suspended checkpoint without weakening the production
ownership guard. A separate real-wire run then failed two availability
assertions because its helper spread had frozen the readiness getter.
The helper now preserves the getter. All failed attempts remain in the
local evidence.
- One disposable real Daytona sandbox exercised both transports on the
initial transport patch through the production native broker and
callback bridge. The provider shell wrapper used the then-current
production declarations. During equal two-second idle windows, file mode
issued **9 remote commands** and HTTP/2 issued **0**. Both variants
rotated synthetic credentials between two run bindings and denied idle
requests. Cleanup deleted the sandbox.
- Daytona component setup took 3.64s for file mode and 4.74s for HTTP/2.
This is an idle-traffic reduction, not a startup-speed claim. That
component run predates the availability and preparation repair; it does
not qualify the repaired paths on Daytona. The new failure controls use
a real local HTTP/2 channel. The credential resolver was synthetic and
no model was called. Real GitHub-account grants, staging replies, and
the end-to-end latency target remain unverified by this component test.
- Repaired-head CI found a policy-test false positive: a broad
`secrets.` regex matched an upstream filename. The unchanged test
reproduced the failure, and the corrected version passed all 15
controls. Master later supplied a stronger direct/bracket check, which
we retained when resolving the merge conflict. Review then found that
formatted expressions could stop that check at a quoted brace. The new
reported-case baseline failed (one failed, 14 passed). The final check
treats quoted strings as complete tokens, respects expression
boundaries, and passes all 15 cases. The later master conflict also
added `toJSON(secrets)` controls. The old branch pattern failed that
whole-context case. Review subsequently found exponential backtracking
with escaped apostrophes; the final forward scanner retains the
quoted-boundary and whole-context controls and passes all 15 tests,
including the bounded long-expression regression. No workflow or
credential handling changed. All failed attempts remain recorded.

- The full local repository test suite was not rerun. [Prior-head full
CI](https://github.com/paperclipai/paperclip/actions/runs/38775801821),
including `ci / verify` and `ci / e2e`, passed on previous head
`e5f8bdb425081cf08110c0f7423f96609e405920`. All 52 check runs succeeded,
two optional Storybook jobs skipped, and legacy Snyk passed. Completed
Apex review is **5/5** on that exact head, with no unresolved review
threads.

## Risks

- Only an explicit server-selected opt-in can use HTTP/2. The existing
provider-capability, channel-startup and authenticated file-fallback
checks remain in the shared bridge.
- Toggling the flag or losing the HTTP/2 channel replaces an idle
retained provider at the next run boundary. Instruction preparation must
make the same retirement decision. Normal ownership, settled history and
cleanup checks remain in effect.
- Lower idle traffic may reduce provider/controller pressure, but no
staging latency improvement is claimed. This feature remains inactive
when the existing flag is off. Other preparation and finalization costs
remain.
- No schema, API, UI, credential-selection, tracing endpoint or
default-setting changes.

## Model Used

- OpenAI Codex, based on GPT-6, with tool-assisted reasoning and code
execution. The exact hosted snapshot ID 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
- [ ] 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>
2026-10-15 15:15:55 -05:00
DottaandPaperclip 307eb16c0c perf(ci): avoid duplicate extraction in public install checks (#16460)
## Thinking Path

> - Paperclip manages AI agents for work.
> - Contributors wait for CI before they can deliver changes.
> - After #16434, Build is the longest CI job.
> - Its clean public npm install spends about 90 seconds installing
packed artifacts.
> - npm extracts local archives to read metadata before it installs
them.
> - Serve metadata from those same packed artifacts, then let normal npm
verify and install their bytes once.
> - Preserve the offline lifecycle and runtime checks, and measure the
complete workflow.

## Linked Issues or Issue Description

Refs #16434 and #16429.

**Current behavior:** The Linux Build check installs every staged
package by local tarball path. npm's file fetcher extracts an archive to
obtain its manifest. Installation then extracts it again. In the last
green run, Build took 408 seconds; consumer installation took 89.7
seconds. The full workflow took 8m06s.

**Proposed behavior:** Read manifests directly from the packed archives.
Serve those manifests and their SHA-512-bound tarballs from a temporary
registry on container loopback. Use normal npm installation into the
empty consumer. Other packages still resolve from the public npm
registry.

**Alternatives:** More parallel jobs would add setup and transfer work.
Skipping the install or runtime probes would remove useful coverage.
This change removes duplicate extraction instead. It does not add a
product feature or duplicate a roadmap item.

## What Changed

- Build a registry catalog from the actual tarball manifests and archive
hashes.
- Run the short-lived registry and npm in the existing unprivileged
download container. No host port is exposed.
- Preserve public dependency tarball URLs, archive integrity checks,
disabled initial lifecycle scripts, the offline rebuild, lock checks and
all Codex, Grok and Pi probes.
- Close the registry before offline verification. Keep native ARM and
Mac install qualification unchanged.
- Add real npm parity and failure tests. Record metadata preparation
time in the existing timing receipt.
- Fix an existing policy false positive: the filename
`docker-compose-secrets.test.mjs` is not a workflow credential. Inspect
GitHub expressions and retain rejection of Honeycomb keys, dot/bracket
secret reads and `toJSON(secrets)`.

## Verification

- 31 focused install-contract checks pass on Node 24.21.0. All 16
targeted CI profile-policy tests also pass.
- Real npm file and registry installs produce identical installed files,
bundled dependencies, optional dependencies and executable links. Both
defer lifecycle execution; offline rebuild works after the registry
closes and preserves the lock.
- npm rejects an archive whose gzip header changes while its extracted
payload remains valid. The CLI propagates the failure.
- The permanent real-npm parity test now includes non-catalog
`is-number@7.0.0`. Both paths install it from its official npmjs
tarball, and the test asserts the lock URL. Fetches have a 10-second
bound and no retries. This addresses the first Greptile finding. A
separate live probe also confirmed public provenance.
- The first local run hit the host sandbox's loopback `EPERM`; the same
checks passed with local listener access. An initial corrupted-gzip
negative fixture hit decompression failure before integrity
verification; the final fixture preserves valid gzip and specifically
proves integrity rejection. An old command-shape assertion was updated
for the new entry point without removing its ordering checks.
- The [first CI
run](https://github.com/paperclipai/paperclip/actions/runs/38778371043)
passed all test lanes and Build, but the existing credential-guard false
positive failed policy and both aggregates. Its 7m25s full duration is
**not** counted as a passing performance sample. The guard repair and
public-download regression are on the new head.
- The real Linux install passed all 18 packed packages, the lifecycle
sentinel, offline rebuild, unchanged lock, official Codex payload/lease
checks, Grok missing/present checks and Pi admission. The receipt
confirms `artifactTransport: loopback-registry`. No provider calls ran.
- Compared with the previous green run, consumer install fell **89.72s →
66.29s** (26.1%), including 1.87s to prepare metadata. Build fell **408s
→ 374s**. Both Build hosts were `m7i-flex.xlarge`; these are separate
runs, so registry/cache and upstream changes remain confounders.
- The base advanced since the previous 8m06s run, including runtime and
test changes. Treat that duration as historical context, not an
identical-source control.
- Pre-conflict head `d8f9de1c` [passes all 48 workflow
jobs](https://github.com/paperclipai/paperclip/actions/runs/38779549190),
including both required branch-protection checks. Greptile is **5/5** on
this head; its review thread is resolved. The non-required Superagent
Security Scan is still running.

| Measurement | Previous green run | Final green run | Observed change |
| --- | ---: | ---: | ---: |
| Full CI, workflow creation through final aggregate | 8m06s | **7m35s**
| **31s shorter (6.4%)** |
| Build job execution | 408s | **389s** | **19s shorter** |
| Clean consumer install, including catalog preparation | 89.72s |
**69.69s** | **20.03s less (22.3%)** |

The final catalog preparation took 1.87s and is included in the install
figure. Both Build hosts were `m7i-flex.xlarge`. Build began 42 seconds
after workflow creation instead of 53 seconds in the historical run, so
faster queue/setup admission explains part of the 31-second total.
Upstream code also advanced; these measurements are not a controlled
causal estimate of the complete gain. The two candidate install
measurements (66.29s and 69.69s) support the narrower reduction in
install work. No tests or runtime probes were removed.

- Conflict-resolution head `ea8287b81` [passes all 48 workflow
jobs](https://github.com/paperclipai/paperclip/actions/runs/38789785045),
including both required gates. Greptile re-reviewed this exact head at
5/5, with the sole earlier thread resolved. The conflict was the
independent filename-policy fix; the stronger expression guard is
retained. This run took **8m04s** overall, Build 423s, consumer
installation 80.56s and bundled-server staging 31.17s. This confirms
meaningful run variance: the earlier 7m35s is a sample, not a guaranteed
new wall-clock duration.

- A second independent master update touched the same credential test.
Final head `1c740b73e` resolves that conflict while retaining the same
stronger guard. [All 48 jobs
pass](https://github.com/paperclipai/paperclip/actions/runs/38792983313);
Greptile re-reviewed this exact head at 5/5. This run took **7m32s**
overall, Build **385s**, consumer install **67.62s**. Auto-merge is
enabled but GitHub requires code-owner approval.

## Risks

The initial install now uses registry package specs instead of file
specs. The parity test checks the resulting installed bytes. Full CI
must still exercise real bundled provider graphs and all offline probes.
The temporary consumer lock contains loopback artifact URLs; it is not
exported or reused for another installation. Native release consumers
retain their existing artifact install path. Queue, host and cache
variance limit attribution from separate workflow runs.

## Model Used

OpenAI GPT-6 through Codex, with repository inspection, execution and
GitHub tools. The serving model suffix and context capacity are not
exposed to 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 linked existing issues or described the issue in
this PR
- [x] I have not referenced internal or instance-local Paperclip issues
or links
- [x] My branch name describes the change and contains no private ticket
identifier
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation
- [x] I have considered and documented the risks
- [x] All Paperclip CI gates are green (48 jobs and both required gates
on conflict-resolution head)
- [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>
canary/v2026.1015.0-canary.20
2026-10-15 14:52:15 -05:00
Devin FoleyandPaperclip 341cfbcea8 fix(docker): remap the node user without walking the app home (#16475)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - The container image sets the node user's home to the app home,
`/paperclip`, which is the data volume in container deployments
> - When `USER_UID`/`USER_GID` differ from the image, the entrypoint
runs `usermod -u` and `usermod -g` before the app starts
> - `usermod` also re-owns every file under the user's home, so every
boot walks the whole data volume first
> - On a large volume this delayed each boot by about six minutes, and
platforms that stop the old container before starting the new one serve
errors for that whole time
> - This pull request runs the remap while the home points at a path
that does not exist, then restores it
> - The benefit is that a UID/GID remap takes milliseconds, and deploys
no longer wait for a full volume walk

## Linked Issues or Issue Description

Related: #15992 (skips the full-tree ownership probe on routine boots)
and #10530 (ownership before the privilege drop). This removes the
remaining per-boot full-tree walk.

**What happened?**
A deployment sets `USER_UID=1001`/`USER_GID=1001` on an image built with
the default 1000. Every boot logs `Updating node UID to 1001`, and the
next log line (`Updating node GID to 1001`) appeared six minutes later.
During that time the app was not running. The volume holds many agent
worktrees and dependency trees. No file had the old owner, so the walk
changed nothing.

**Expected behavior**
Remapping the node account should not depend on the size of the data
volume. Ownership repair belongs to the existing tiered ownership probe,
which records a marker and skips the full walk on routine boots.

**Steps to reproduce**
1. Build the image with the default `USER_UID=1000`.
2. Run it as root with `USER_UID=1001`, `USER_GID=1001` and a large app
home.
3. Every boot spends the time of a full home walk in `usermod -o -u`
before the app starts.

Measured in the runtime image (Debian trixie) with 200,000 files under a
user's home: `usermod -u` took 1,204 ms and re-owned every file. With
the home moved away first, the three `usermod` calls took 124 ms and
changed no file.

## What Changed

- `scripts/docker-entrypoint.sh`: when a UID or GID remap is needed,
read the node user's home with `getent passwd node` and point it at
`/nonexistent/paperclip-uid-remap`. Then run the same UID and GID
commands as before, and restore the home. Without a passwd entry, the
remap runs as before. The ownership probe and repair logic are
unchanged. After a real ID change, the home directory has the old owner,
so the shallow probe detects the mismatch on the same boot and repairs
the tree once.
- `server/src/__tests__/docker-entrypoint.test.ts`: stubs `getent` and
adds tests for the call order (UID+GID remap, GID-only remap), for
repair after the remap, and for the fallback without a passwd entry.

## Verification

- `pnpm exec vitest run src/__tests__/docker-entrypoint.test.ts` (in
`server/`): 22 passed.
- `sh -n scripts/docker-entrypoint.sh`: passed.
- Manual check in the runtime image with a throwaway user and 200,000
files (numbers above). The UID changed, file owners were not touched,
and the passwd home was restored.

## Risks

- `usermod -d` without `-m` only edits the passwd entry. The home is
restored right after the ID change. If the entrypoint fails between the
two calls, `set -e` stops the container before the privilege drop, and
the next boot sets the home again, so a partial state does not persist
past a restart.
- Ownership after a real remap now depends on the existing probe instead
of `usermod`. The probe's tests already cover the remap, fresh-mount,
deep-mismatch and marker cases.

## Model Used

- Claude Opus 5.5 (`claude-opus-5-5`), 1M context, through Claude Code
with tool use (shell, file edits, test runs, live measurement in a
running container).

## 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
- [ ] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 12:45:33 -07:00
DottaandPaperclip 69dded3230 fix: allow normal Daytona command status response latency (#16480)
Allow a normal completed Daytona status response up to 500ms within the unchanged caller deadline. Keep final separated logs, stream fallback and single dispatch.

Verified: 396 provider cases, full repository and standalone provider typecheck/build, matched real-Daytona component controls, and exact-head full CI/E2E, security and Apex 5/5. Whole-agent latency target remains open.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-10-15 14:42:36 -05:00
DottaandPaperclip 2aca41464b fix(workspaces): preserve compaction and expire standard Git bases (#16476)
## Thinking Path

> - Paperclip manages AI agents and their task workspaces.
> - Finished tasks can release reproducible Git files and restore them
later.
> - Unique work must stay on disk, while regenerable dependencies can be
removed.
> - Linux Git templates include an empty legacy directory that blocked
base cleanup.
> - The new expiration branch also skipped the existing guarded
dependency cleanup.
> - This change accepts the standard empty directory and retains that
cleanup order.
> - Private bases can expire, and protected workspaces still shed
regenerable files.

## Linked Issues or Issue Description

Refs: #16457

Live acceptance of #16457 removed a worktree but retained its private
base because Linux Git created an empty `.git/branches` directory. A
pending-base dry run then tried to resolve the already removed worktree
and hid the preservation reason.

A local integration comparison also showed that enabling Git expiration
skipped existing dependency compaction. It deferred pending startup
compaction by an hour. Both failures were reproduced before the fix.

## What Changed

- Accept `.git/branches` only when it is an empty real directory.
Preserve populated entries, files, and symlinks.
- Inspect pending base cleanup without resolving an absent worktree.
- Run existing guarded compaction before Git expiration. Exclude already
closed rows from compaction and retain its pending deadline.
- Keep failed expiration checks from reaching legacy whole-workspace
deletion. Existing compaction remains independent of Git expiration
dry-run mode.
- Extend real Git/PostgreSQL tests and retain the acceptance failures in
the delivery state note.

## Verification

- Linux-template baseline: private-base expiration failed before the
fix. The first sandboxed attempt could not bind PostgreSQL; the
authorized retry reproduced the behavior.
- Compaction baseline: two regression cases failed in 7.67 seconds. They
reproduced skipped dependency cleanup and the lost startup deadline.
- After the fixes, `pnpm exec vitest run
server/src/__tests__/execution-workspace-compaction.test.ts
server/src/__tests__/git-workspace-expiration.test.ts
server/src/__tests__/terminal-workspace-work.test.ts` passed all 49
cases in 43.79 seconds.
- Controls cover unique work, active runs, unfinished descendants,
previews, concurrent reopening, interrupted removal, exact-commit
restoration, and retryable upstream failures.
- Full `pnpm -r typecheck` and `pnpm build` passed for the final commit.
All exact-head CI and security checks passed. Greptile is 5/5 with all
findings resolved.
- Final staging acceptance will let the restarted worker resume the
retained base cleanup, then reopen normally at the recorded commit and
persist subsequent work. The base has not been manually removed. The
superseded preview build was cancelled before dispatching a replacement.

## Risks

- Legacy branch definitions can hold unique data. Only an empty real
directory qualifies for deletion.
- Compaction preserves its existing lifecycle guard and
regenerable-directory allowlist. It cannot fall through to legacy
deletion after an expiration failure.
- Already closed workspaces must only resume their recorded expiration;
they do not enter compaction.

## Model Used

OpenAI Codex, GPT-6.1-sol, with reasoning, code execution, Git,
database, and browser tools. The exact context-window size is not
exposed by 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>
2026-10-15 14:36:00 -05:00
DottaandPaperclip c53bdd9eb3 perf: capture sparse checkpoint files in bounded batches (#16473)
Capture sparse checkpoint files in bounded batches while retaining content and mutation checks. Prevent inserts after SQLite automatic rollback and drain active readers before database close.

Verified: 209 affected cases, final six capture controls, repository typecheck/build, real Daytona helper validation, and exact-head full CI/E2E, security and Apex 5/5. The matched component median saves 1.05s; the whole-agent latency target remains open.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-10-15 14:32:44 -05:00
DottaandPaperclip 5ec93dae01 fix(connectors): avoid redundant run preparation discovery (#16461)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Run preparation selects connector skills and tools under current
permissions.
> - An assignment check can build an unrelated company tool catalog and
wait for a shared discovery slot.
> - Native startup repeats assignment discovery to obtain static tool
definitions.
> - Slack also locks and reconciles an unchanged catalog, then repeats
task authorization.
> - This pull request removes that redundant startup work and preserves
live checks at tool execution.
> - The benefit is less preparation work, less contention, and unchanged
permission and approval enforcement.

## Linked Issues or Issue Description

Related: #16454 (detailed preparation tracing), #16425 (workspace
preparation performance).

**What happened?**

Connector configuration added avoidable work to run preparation. Browser
Use assignment authorized the whole company catalog, including other
connector families. Four connector resolvers ran in series. Native
controller startup repeated all assignment resolution when any connector
skill was pinned. Slack reconciled an unchanged catalog under an
advisory lock and checked task authority twice.

**Expected behavior**

Prepare only the connector data needed by the run. Reuse static tool
definitions from pinned skills. Preserve current company, assignment,
identity, profile, policy, grant, and approval checks when an operation
executes.

**Steps to reproduce**

1. Configure Browser Use and an unrelated MCP catalog with 500 tools for
one company.
2. Resolve Browser Use resources for an authorized task. The old path
reads and authorizes the unrelated catalog.
3. Occupy both full discovery slots. The old assignment check waits for
those slots.
4. Resolve a linked Slack task repeatedly with an existing current
catalog. The old path still acquires a catalog lock and repeats
authority checks.

**Paperclip version or commit**

Base: `68a09dcb5f50e3fb6ceaaeac2706d96db97fc9b3`.

**Deployment mode**

Observed in hosted native runs. The local reproduction uses a source
checkout and real embedded PostgreSQL.

## What Changed

- Restrict Browser Use catalog reads and policy decisions to active
Browser Use connections. Preserve guest restrictions, reviewed catalog
filters, live grants, and deterministic resource order. Keep assignment
checks out of the full discovery queue.
- Resolve the four independent connector families concurrently. Wait for
outstanding work to settle before propagating a failure, and retain
registration order.
- Register native direct connector tool definitions from pinned
connector skills. Keep live assignment resolution and governed execution
on every tool call.
- Compare Slack catalog hashes before reconciliation. Current catalogs
skip the catalog transaction and lock. Check task authority once after
current profile checks. Initial setup and upgrades retain locked
reconciliation and checks before and after it.
- Precompute immutable bundled Slack descriptor hashes. Preserve
disabled entries, profile state, removed bindings, and review metadata.
- Document the startup paths and add focused contention, revocation,
catalog upgrade, and failure-settlement regressions.
- Repair a pre-existing CI guard false positive: the filename
`docker-compose-secrets.test.mjs` matched `secrets.`. Check GitHub
secret expressions instead, with dot, bracket, and whole-context
controls. No workflow changes.

## Verification

- Conflict resolution: merge `b1566ca494f4af6e8d4418fa37393c5caee02582`
from master into head `55140b1609ae7bd21a038eb75a48c2683299e4b4`.
Combine both secret-expression guards and regression cases. Preserve
current workspace, native recovery, and Daytona changes. All 467 policy
tests, 787 focused native/connector/Browser Use tests, and server
typecheck passed locally after integration. Fresh full CI passed all 55
checks on this head, with two optional Storybook jobs skipped. Greptile
reviewed this exact head at 5/5 with no unresolved threads.

- `pnpm -r typecheck` — passed.
- `pnpm build` — passed.
- Focused native startup, connector concurrency, and AgentMail suites —
763 tests passed.
- Complete Browser Use suite — 33 tests passed. Focused Slack catalog,
linked task, retained provenance/revocation, and pinned native tool
tests passed. The complete runner tool authority suite passed (26
tests). The 1,337-case chat suite passed 1,335 tests and had two
failures: the original new transaction-count assertion and a 15-second
timeout in the publication-batch case. Both cases passed an isolated
rerun. The publication timeout occurred during concurrent local checks;
the passing rerun does not erase it. CI must still pass the chat shards.
- The first focused run found two incorrect new assertions: policy
evaluation performs a second catalog lookup, and an explicit allow
policy overrides a profile default. The tests now distinguish the scoped
catalog query and revoke the governing policy. The focused Browser Use
rerun passed all 33 cases after these assertion fixes.
- Full-suite test verification used the CI shards of `pnpm test:run`.
Local runs focused on the changed boundaries; the complete repository
test command was not duplicated locally.
- `node --test '.github/scripts/tests/*.test.mjs'` — all 467 policy
tests passed. The CI failure reproduced on the unchanged base guard
before this correction. Actual GitHub secret expressions still match the
guard.
- CI on the final head passed all chat shards, typecheck, build, Runner
checks, browser shards, and other test lanes. One existing
workspace-runtime case hit `EADDRINUSE` for a randomly selected test
listener in server shard 1/12 (1,162 tests passed in that shard). The
shard passed its single retry on the same SHA with no source changes.
The first failure remains recorded here. Previous reviewed head
`7191ac40691ddb1ef38b86665c95cc14c57ea390`: all 55 checks passed, two
optional Storybook jobs skipped, and no pending or failed checks.
Greptile is 5/5 on this head with no unresolved review threads. The
external security scan passed.

Local before/after measurements use the old and new implementations
against the same fixture. Both paths are warmed. Seven samples alternate
execution order. The database is real embedded PostgreSQL. No latency is
injected. These measurements do not establish hosted speed.

| Local path | Before median (range) | After median (range) | Work
reduction |
| --- | --- | --- | --- |
| Browser Use assignment with 500 unrelated MCP tools | 44.020 ms
(33.994–107.328) | 26.502 ms (20.385–99.037) | 26 → 22 statements;
unrelated catalog and discovery queue removed |
| Slack assignment with current catalog and linked responsible user |
49.723 ms (43.624–80.653) | 22.141 ms (19.781–30.818) | 5 → 2 database
transactions; no catalog lock on the current path |

The contention regression fails against the old implementation after a
bounded five-second wait, then passes against the optimized
implementation. It occupies the real global discovery scheduler and
verifies that Browser Use assignment completes without releasing those
slots. It records catalog SQL to verify connection scope. Revocation
cases remove policy, catalog availability, and grants between calls.
Existing Slack integration cases exercise retained provenance, removed
profile bindings, identity revocation, approved writes, and current
responsible-user restrictions.

## Risks

- Pinned native tool definitions can remain visible after access is
revoked. They confer no authority. Invocation rechecks current
assignments and fails closed before an operation executes. Newly
available connector families still require a newly admitted skill
selection.
- Concurrent resolution can increase instantaneous database reads to
four connector families per configuration call. It is a fixed bound.
Outstanding work settles before a failed preparation returns.
- Slack skips reconciliation only when all bundled version hashes and an
existing profile match. Missing or changed definitions still use the
existing locked path. Operator revocations remain effective.
- This PR addresses connector preparation. Workspace transfer, provider
startup, copyback, and queue delay can still keep total latency above
the user's goal. Hosted improvement needs a deployed before/after trace.
- No schema, lockfile, workflow, telemetry event, or authorization cache
changes.

## Model Used

OpenAI GPT-6 (Codex), with reasoning, repository inspection, code
execution, and GitHub tools. The runtime does not expose the exact
serving 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
- [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>
canary/v2026.1015.0-canary.19
2026-10-15 14:08:01 -05:00
DottaandPaperclip b1566ca494 perf(daytona): avoid log-follow delay for completed session commands (#16468)
A completed Daytona session command now reads final separated logs without waiting for a new log-follow socket. Running commands retain streaming, recovery, and the existing total deadline.

Verified with full repository typecheck/build, standalone provider typecheck/build, 395 passing provider cases, real immutable-image Daytona command controls, and fresh exact-head full CI/E2E and Apex 5/5.

Co-Authored-By: Paperclip <noreply@paperclip.ing>
2026-10-15 13:35:10 -05:00
DottaandPaperclip db11d899cf fix(native): recover remote sessions while preserving warm runs (#16451)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Native agents keep remote processes and conversation history across
warm turns.
> - A completed turn can leave handoff authority only in controller
memory.
> - Losing that controller can block a follow-up even while its sandbox
survives.
> - This pull request verifies durable ownership and reconnects the
exact prior process before handing it to the next run.
> - Healthy follow-ups stay warm. Recovery preserves saved work without
replaying a completed turn.

## Linked Issues or Issue Description

**What happened?**

A remote warm turn can finish without suspended backup authority. A
replacement controller rejects that prior owner even when its exact
process and completed checkpoint remain. A single unavailable identity
probe can also stop an otherwise valid reattachment.

**Expected behavior**

Keep healthy follow-ups warm. Recover a completed session after proving
that its controller stopped and that the successor holds current
authority. Reuse compatible processes; otherwise save and resume the
conversation. Retry unavailable identity reads within one shared
deadline.

**Steps to reproduce**

Use `doc/testing-native-remote-continuity.md`. Its Linux cases execute
real turns through PostgreSQL, TLS ingress, and the Rust runner. They
kill a separate controller process, recover old checkpoint metadata, and
change process configuration. The provider is deterministic.

Related: #16432 and #16441 fix live warm-owner handoffs. #16341 adds
recovery diagnostics. #14695 covers provider process retention.

## What Changed

- Preserve warm process reuse between healthy remote turns.
- Verify a committed prior result, stopped controller, matching
checkpoint and sandbox, and current task/coordinator ownership before
recovering an orphaned warm session.
- Reconnect through the prior run route, then use the existing
authenticated run attachment to change authority.
- Persist a process-configuration digest. Close and save recovered
sessions when old or changed configuration cannot support reuse.
- Retry unavailable state, marker, and process reads within one
30-second deadline. Keep signals and definitive identity failures
single-attempt.
- Record closed recovery diagnostics, including unreadable or malformed
saved state.
- Retire the recovery-only ownership check after verified attachment, so
later warm turns use their current authority.
- Add real-process Linux regressions and refusal controls.
- Expose the existing source-only file-recovery form for retained native
holds, with the same board authority, evidence, and exact stop-receipt
requirements as legacy holds. Recording recovered files does not change
task status or replay a run.

## Verification

- `pnpm -r typecheck` passed; the server check was repeated for the
third-turn fix.
- `pnpm build` passed after the final UI change. The UI typecheck, token
gates, and map checks also pass.
- Four Linux continuity cases passed: warm reuse, controller loss,
legacy checkpoint metadata, and changed configuration. Each creates one
conversation and starts exactly three turns, including a healthy
follow-up after recovery. The fixture uses expired prior leases; the
third turn keeps the runner and provider processes.
- Greptile caught the retained recovery gate; the third-turn regression
now covers it. An initial test omitted the heartbeat’s saved input and
left a test process after failure; the fixture was corrected and its
disposable container reset before the passing run.
- The current focused executor/restart group passes all 749 tests,
including the original failure classifications.
- Native file-recovery and UI tests pass (52 tests), including blocked
tasks and both native and legacy holds.
- After merging current master and retaining its equivalent CI
expression check, the CI policy tests pass (15 tests) and all four
three-turn Linux continuity cases pass again on
`dec418ae55ff21b4fb067132613658cce445f181`.
- `pnpm test:run` completed its general server group with 20,572 passes,
103 skips, and three failures: the skill-audit child process and two
HTTP test timeouts. The same three suites then passed in isolation (89
tests) without code changes. That local command stopped before later
groups; the complete final-head CI, including general, serialized,
Runner, build, and browser gates, is green.
- Greptile reviewed the combined head
`dec418ae55ff21b4fb067132613658cce445f181` at 5/5 with no actionable
findings; both earlier findings are resolved. All final-head CI gates
and the security scan passed. Staging deployment and retained-incident
disposition remain deployment acceptance work.

## Risks

- Recovery requires exact durable evidence. Live conflicting
controllers, replacement sandboxes, Stop/pause, and uncertain effects
must remain blocked.
- After controller loss, tool-contract or process-configuration changes
can restart the provider. Normal healthy follow-ups retain their
processes.
- The new idle-recovery path has Linux fake-provider evidence. Live
Codex/OpenCode and retained quarantined-state recovery still need
staging qualification.
- No database schema, telemetry, or runner protocol changes.

## Model Used

OpenAI GPT-6 through Codex, with reasoning, repository inspection, code
execution, and browser tools. The session does not expose a more
specific model version 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 (targeted checks and
isolated reruns; full-run limitation recorded 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 on
`dec418ae55ff21b4fb067132613658cce445f181`
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-10-15 13:26:09 -05:00
DottaandPaperclip 59a70dc9e2 fix(workspaces): expire reproducible Git files and restore exact commits (#16457)
## Thinking Path

> - Paperclip manages AI agents and their task workspaces.
> - Isolated Git worktrees and private repository copies remain on the
host after tasks finish.
> - These files can fill the disk even when every commit is available
upstream.
> - Cleanup must retain unique files, local Git state, live work, and
recovery data.
> - This pull request records and verifies an exact-commit restoration
recipe before expiration.
> - Normal reopening restores that commit even after upstream advances.
> - The benefit is lower host disk use while finished tasks remain
available for later work.

## Linked Issues or Issue Description

Refs #10285 and #2022. Follows #16433 for skill-cache expiration.
Related #11936 provides separate host-local cleanup tooling; this change
extends the existing company-scoped lifecycle worker and normal
workspace reopening. ROADMAP.md does not specify a competing
implementation.

## What Changed

- Add opt-in expiration for verified Paperclip-owned Git worktrees after
their whole task tree has been done or cancelled for 24 hours.
- Preserve active and scheduled runs, previews, pending reopening,
unresolved recovery, dirty files, unknown ignored files, and unsupported
or unique Git state.
- Verify an authenticated fetch in a fresh object store. Save repository
identity, exact commit, branch, and ownership before any deletion.
- Rename eligible files into recorded managed trash. Resume interrupted
cleanup under source and lifecycle locks.
- Expire private base clones only after consumer, file, reference,
reflog, and object checks pass. Preserve shared project base clones.
- Rebuild missing bases and worktrees through normal reopening at the
recorded commit. Return an explicit retryable error when repository
access fails.
- Add independent workspace/base switches, dry-run reports,
reclaimed-byte counts, and operational documentation. No table, public
API, UI, or recovery-retention change.

## Verification

- Real local bare remote plus Postgres: create at A, advance upstream to
B, expire the worktree and private base, reopen at A, then make and
retain a subsequent commit.
- Final lifecycle suite: all 20 tests passed in 46.41 seconds at
`d72947a2e45be5d0c912debb03c46b15863b4798`. Review fixes cover
second-cycle expiration, newer-branch recovery, normal preparation after
restoration, branch adoption, and Git administration path controls.
Eleven existing branch reconciliation controls also passed. Covers
unique files and Git state, live descendants, scheduled runs, recovery,
previews, unauthorized access, upstream failure, concurrent reopening,
interrupted deletion, shared bases, and nested private worktrees.
- Final guard regressions: 3 affected tests passed. Existing
workspace/runtime/preparation/source controls: 328 tests passed in
238.69 seconds.
- Full repository typecheck and build passed locally. The full local
test attempt did not pass: initial native-session cases hit macOS
Postgres shared-memory exhaustion, source changes invalidated two
discovery cases, and the checkout disappeared near the end. The
final-code retry of the remaining skill and unrelated controls passed
all 103 tests. All checks passed on this exact head, including
typecheck, general and serialized tests, Runner checks, build, canary
dry-run, browser E2E, and security scans. Greptile reviewed the head at
5/5 with all findings resolved.
- Fixed a blocking CI policy false positive for
`docker-compose-secrets.test.mjs`. The test still rejects GitHub secret
expressions, including dot, bracket, and multiline forms. Its full
15-test suite passes.
- Map validation and `git diff --check` passed.
- Staging dry-run inspection, measured reclamation, and ordinary product
acceptance remain pending. No live acceptance is claimed.

## Risks

- Git restoration depends on continued upstream availability and
credentials. Cleanup skips unverified commits; restoration never
substitutes the default branch.
- File deletion requires multiple conservative proofs. Unknown or
unsupported state is retained and can limit reclamation.
- Source and lifecycle locks serialize preparation, reopening, and
expiration. Remote verification has a deadline but can delay work on the
same source.
- Start with both expiration switches disabled. When enabled, dry-run
remains the default. Rollback disables further deletion while retaining
restoration support.

## Model Used

OpenAI GPT-6 through Codex, with reasoning, repository inspection, tool
use, and code execution. The exact backend model ID 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 (focused tests; full local
limitation documented 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>
canary/v2026.1015.0-canary.18
2026-10-15 13:09:59 -05:00