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DottaandPaperclip dd777f4b73 feat(dot): complete onboarding and expand governed Runner capabilities (#15414)
## Thinking Path

> - Paperclip manages AI agents, their work, and their permissions.
> - Paperclip Runner supplies the same admitted tool authority to each
provider.
> - The Dot provider in #15402 needs reliable onboarding and useful
agent capabilities.
> - An idle Dot could not start work, assign a human, read skills, or
produce a workspace artifact.
> - Pairing also relied on a second configuration save before ordinary
admission could work.
> - This pull request adds governed idle admission and shared Runner
tools, and completes pairing atomically.
> - Operators can test Dot with fresh data while keeping normal company,
approval, budget, and run ownership checks.

## Linked Issues or Issue Description

**Subsystem affected**

Paperclip Runner, dedicated Dot MCP access, OAuth onboarding,
experimental settings, and empty worktree startup. This PR builds on
merged provider PR #15402. It reuses the merged MCP gateway from #14846
and assistant connection work from #14933 and #15380.

**Problem or motivation**

An idle Dot could see assignments but could not act on a conversation
request until someone created a task first. Its Runner catalog could not
assign tasks to humans or read pinned skills and workspace files.
First-time OAuth discovery and pairing also needed browser fixes, and a
completed pairing did not persist its binding reference on the agent.

**Proposed solution**

Keep Dot within the existing Runner. Admit a visible agent-authored
intake task for idle requests. Add people, human assignment, cross-task,
skill, and optional sandbox workspace tools through shared authority.
Relay assigned app calls through the configured MCP gateway. Add lease
renewal and follow-up references. Save pairing and its configuration
revision atomically. Show prerequisites and provide a complete copy
prompt.

**Roadmap alignment**

This extends the experimental provider in #15402. It uses the existing
governed gateway, task model, skills, artifact path, and native Runner.
It adds no separate execution subsystem.

## What Changed

- Add a standalone OpenAI Dot agent choice with an independent
experimental opt-in. It works with the general Runner option off.
Require Assistant connections (MCP), authenticated sign-in, and public
HTTPS for pairing.
- Use Dot’s own option for company package import. Allow an unpaired Dot
configuration to save after external billing acknowledgement; task
admission still requires pairing. Prepare the shared dev binary for
Dot-only opt-in.
- Label saved Dot agents as OpenAI Dot. Use prerequisite-check copy in
setup and runtime configuration.
- Route Dot creation directly to pairing after explicit external billing
acknowledgement. Hide local CLI, model, and harness setup for Dot.
Preserve the shared Runner implementation and canonical API type. Other
Runner providers still require their general opt-in.
- Add an empty worktree option with fresh signing keys and no production
data copy.
- Fix public-client OAuth negotiation, discovery compatibility, and
optional separate browser authorization origin.
- Add one-use pairing consent preview, clear copied setup instructions,
and atomic binding persistence and cleanup.
- Add idle request admission with stable request IDs and normal
scheduling, permissions, budgets, and task ownership.
- Add identity and people discovery, human task assignment and
reassignment, and authorized cross-task comments and documents.
- Read assigned skill files from pinned manifests. Relay assigned app
calls through the merged gateway without exposing credentials.
- Add an off-by-default workspace bridge. Constrain paths and writes.
Run commands in a deny-by-default OS sandbox with no network or injected
credentials. Reserve mutations before effects and never blindly repeat
uncertain work.
- Add rolling lease renewal, task pagination, bounded operation limits,
and deduplicated follow-up references without comment bodies in
webhooks.
- Add an off-by-default attachment reading setting. Restrict reads to
files on the current assigned task. Verify size and hash, cache bounded
verified copies per run, paginate text or binary bytes, and recheck live
authority before returning.
- Keep file grants operator-owned. Reject agent self-grants across
configuration routes. Preserve attachment consent in create/import
forms. Close generic API file bypasses while retaining current-run
response snapshots and permitted uploads.
- Keep provider limits explicit. Do not inherit a Dot binding,
attachment permission, or workspace permission when hiring another
agent.
- Include the required Markdown format in cross-task document writes and
validate the API title limit. Verify real creation and revision
persistence.
- Restrict command execution to Linux bubblewrap with descendant
containment. macOS retains workspace file tools and artifact publishing,
while refusing command calls. Explain the platform limit in setup.
- Exclude Paperclip instance state from workspace files, uploads,
artifact publication, and sandbox commands. Protect nested directories
and case variants. Fail closed when the directory protection scan
exceeds 4,096 directories.
- Add static UI compression for slow public tunnels. Document setup, the
complete tool inventory, and qualification limits.

## Verification

- Merge preparation on `00ca2c75b` integrates merged base #15402 and
master `fc6304dfe`. The ancestry commit preserves the reviewed follow-up
source tree. The subsequent security fix excludes instance state from
file tools, uploads, artifact publication, and sandbox commands. It
preserves private task authorization and task monitors. It regenerates
the combined tool catalog, seeded catalog digest, and protocol manifest.
Workspace typecheck, full build, and UI token gates pass. All sixteen
real Dot broker cases and 93 company import cases pass after the review
fixes and creator-attribution test correction. The exported
human-assignment catalog and Unicode page boundaries are also fixed. All
ten catalog tests and nine workspace/skill bridge tests pass. All 35
workspace bridge and authority tests passed after the instance-state
fix, including real macOS commands in that intermediate version. The
subsequent document and descendant-containment fixes pass 44 focused
tests across bridge, authority, and setup UI, with six Linux command
cases skipped on macOS. Real cross-task documents pass the route
validator and persist two revisions. macOS refuses command execution and
does not advertise the tool. Full workspace typecheck and build, changed
server/UI typechecks, and token gates pass again on the final commit.
Greptile rates final head 00ca2c75b 5/5 and its completed check
concludes success; all review threads are resolved. All 58 current-head
checks are complete: 54 passed and 4 intentionally skipped. This
includes full tests, typecheck, build, Runner, browser E2E, release
verification, and Canary Dry Run. The older full local root attempt
finished with 16,602 passes, 93 skips, and ten failures across two
suites: it began before source edits and retained earlier imported
implementations while loading later tests. Both suites pass a clean
final-head rerun (25 passed, six Linux-only command cases skipped on
macOS). This mixed-source full attempt is not a final-head full-suite
pass; use the fresh CI evidence below.
- Full workspace typecheck and build pass for the standalone Dot change
on head `392d54f80`. UI token gates are clean. The full workspace
typecheck passed before the final importer UI edit; the changed UI
typecheck, build, and token gates pass again on the final commit. The
server build passes for its unchanged final source.
- Standalone selection, creation, settings, harness visibility,
inventory, and runtime admission checks pass. OAuth onboarding and the
real Rust/PostgreSQL broker suite pass 27 cases with the general Runner
option disabled. Dot and MCP revocation still block pairing; other
Runner providers remain disabled. Create, hire, conversion, and
inherited-hire route regressions pass 68 cases. The runtime selection
suite passes 20 cases. The setup UI suite passes 50 cases. Company
import and dev binary checks pass 97 cases. Import UI checks pass 29
cases, including Dot-only selection, preservation of imported Dot
agents, generic Runner fallback, canonical configuration serialization,
and required billing acknowledgement. A read of the synthetic instance
reports the native binary required with Dot enabled, the general rollout
disabled, and no persisted native work.
- The latest attachment, operator-consent, generic API file-guard, and
bridge checks pass 80 tests. Cache and native lifecycle checks pass 550
tests; create/import builders pass 45 tests; attachment setup UI checks
pass 16 tests. The real Rust/PostgreSQL Dot broker suite passes 15
cases.
- Earlier authority, human assignment, pinned skill, confinement,
cancellation, inheritance, onboarding, replay, OpenAPI, and gateway
regressions pass their focused rechecks. Workspace writes reject
concurrent stale hashes.
- In the live empty test-drive, turn the general Runner option off and
leave Dot and MCP on. Add agent shows a separate OpenAI Dot choice.
Create rejects missing billing acknowledgement, saves the canonical Dot
configuration, and opens pairing. The existing paired Dot remains ready
and passes its prerequisite checks. No new plugin pairing was needed for
this UI change. The final browser import preview keeps a Dot source
agent as OpenAI Dot, falls back a generic Runner agent while its switch
is off, and offers Dot independently.
- Real Dot completed OAuth, signed MCP Events readiness, and an
event-only assigned document task in an empty synthetic instance.
Pairing saved its binding without a second configuration save.
- Real Dot verified human assignment, cross-task comments and documents,
pinned skill reading, sandbox commands, lease renewal, follow-up input,
and a downloaded artifact whose bytes and hash matched its receipt. An
idle conversation request created an intake, created a task for its
human owner, continued after a definite missing-file read error, and
finalized Done with exit code 0.
- After operator approval, real Dot read a synthetic assigned-task
attachment and wrote its file-only random proof into an agent-authored
document. Its first test required accepting review because the existing
document tool removed the final newline.
- On head `2626c8f9b`, real Dot read a 13,849-byte synthetic attachment
in two pages, used `expectedSha256` on page two, saved exactly its final
random marker, verified readback, and finalized Done with exit code 0. A
direct inbox check was required for this attachment qualification; it
does not claim event-only delivery.
- Previous head `392d54f80` passes all 55 checks (53 passed, two
intentionally skipped), including the full test, typecheck, build,
native Runner, browser, and release verification gates. Greptile rates
this head 5/5; all review threads are resolved.
- Head `2626c8f9b` passed all 56 checks: 54 passed and two intentionally
skipped. This includes full typecheck, build, native Runner, server
tests, serialized suites, browser E2E, and Canary Dry Run. The unchanged
Cursor managed-runtime test exceeded its five-second deadline on the
first attempt; its focused local suite passed all eight cases, and the
single CI rerun plus dependent verify gate passed.
- A prior full local serial test attempt reported 19 failures (16,141
passed, 88 skipped) and stopped before later wrapper groups. It began
before the final source edits. Every failed suite has a passing fresh
recheck; the macOS snapshot stress case passes alone in 227 seconds. The
previous head `000fb9261` passed all 56 CI checks. PRs leave
`pnpm-lock.yaml` unchanged; CI and the refresh bot own dependency
resolution.

## Risks

- Dot remains off by default. Its own opt-in does not enable other
Runner providers. It still requires the MCP option; disabling Dot blocks
new work while keeping existing recovery and saved bindings.
- Dot requires a stable public HTTPS origin. Its base provider in #15402
is merged. Temporary tunnels are useful for testing but are not
permanent deployments.
- Idle intake creates a visible agent-authored task. It does not
fabricate a human message or bypass ordinary admission.
- Workspace commands require Linux bubblewrap with a private PID
namespace; deployment qualification is still needed. macOS file tools
and artifact publishing remain available, but commands are disabled
because sandbox-exec does not contain detached descendants. There is no
unrestricted fallback. Command protection fails closed above 4,096
workspace directories. The historical macOS command walkthrough does not
qualify the current Linux implementation.
- Provider model choice, token usage, cost, native thread control, and
global external stopping remain unavailable. Known Paperclip budget
gates still apply.
- The workspace bridge and attachment reader are separate opt-in
settings. Reading assigned task files sends their contents to OpenAI.
Revocation prevents future reads but cannot withdraw bytes already sent.
Files are read on request; automatic inbound attachment staging remains
disabled.
- An existing event registration can retain earlier instructions that
prohibit extra tasks. Dot asked for permission before a second intake
after the final event-only bootstrap; that extra no-nudge continuation
is not live-qualified under that earlier registration. The later
attachment qualification submitted normally through the composer. The
revised onboarding prompt describes the new idle entry point, and its
protocol polling path is tested.
- OpenAI event delivery can be delayed; a webhook acknowledgement is not
proof that Dot has begun work.
- A running Dot can retain an old plugin catalog after tool refresh.
Refresh and actual tool exposure must be checked before using new
top-level actions.
- Hosted and remote controller modes are not qualified.

## Model Used

OpenAI Codex, based on GPT-6. The exact deployment ID and context window
size are not exposed in this session. Capabilities used: reasoning,
repository editing, code execution, test inspection, and browser
control.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either linked existing issues or described the issue in-PR
following the relevant issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links
- [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 (focused suites and all
fresh failure rechecks pass; the earlier full attempt is 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
- [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>
2026-10-07 19:44:17 -05:00
Nicky LeachandPaperclip 8ed1f51f75 fix(scripts): silence pnpm DEP0169 at provisioning install call sites (#12228)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Worktree provisioning prepares the dependencies and tools that these
agents need.
> - The pinned pnpm version calls the deprecated `url.parse()` function
during each install.
> - Node.js 24 reports this call as `DeprecationWarning [DEP0169]`.
> - The provisioning scripts run more than one install, so the warning
repeats in each run.
> - This pull request disables only `DEP0169` at each affected pnpm
install call site.
> - The benefit is a clear provisioning log while other deprecation
warnings remain visible.

## Linked Issues or Issue Description

**What happened?**

The worktree provisioning scripts printed `DeprecationWarning [DEP0169]`
during each pnpm install. The warning came from pnpm 9.15.4 and its
`toNerfDart` call to `url.parse()`.

**Expected behavior**

The provisioning scripts should hide this known warning from the pinned
pnpm version. They should keep other deprecation warnings visible.

**Steps to reproduce**

1. Use Node.js 24 with pnpm 9.15.4.
2. Run worktree provisioning with a base-workspace repair or dependency
install.
3. Observe the repeated `DeprecationWarning [DEP0169]` output.

**Paperclip version or commit**

Commit `5cd41b1a9996713efdfdc62373da8045664c7f30`.

**Deployment mode**

Built from source.

**Installation method**

Built from source with pnpm.

**Agent adapter(s) involved**

Not adapter-specific (core bug).

**Database mode**

Not database-related.

## What Changed

- Add `--disable-warning=DEP0169` to each affected pnpm install call
site.
- Append the flag to `NODE_OPTIONS` so the scripts keep existing values.
- Add comments that name the source of the warning and the removal
condition.
- Add a regression test for all affected scripts and warning codes.

## Verification

- `bash -n scripts/provision-worktree.sh` passes.
- `bash -n scripts/provision-worktree-runtime.sh` passes.
- `node --test scripts/__tests__/provision-worktree-self-heal.test.mjs`
passes with 15 tests.
- GitHub Actions must pass all required checks before merge.

## Risks

This change has low risk. It changes warning output only for `DEP0169`.
It does not overwrite existing `NODE_OPTIONS` values. Revert commit
`5cd41b1a9996713efdfdc62373da8045664c7f30` to restore the prior output.

## Model Used

OpenAI Codex, GPT-5. The model used tool calls and code execution. The
runtime did not expose a context-window value.

## 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>
2026-08-26 10:42:13 -07:00
scotttongandPaperclip dc5b070709 fix(runtime): guard empty Bash 3.2 array expansion (#11891)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agents can run in isolated worktrees with a separate Paperclip
runtime.
> - Runtime provisioning uses a Bash script on macOS hosts.
> - macOS ships Bash 3.2, where an empty array expansion fails under
`set -u`.
> - The source-config argument array is empty when the base workspace
already has a config.
> - This pull request guards that expansion and tests the normal
base-config path on Bash 3.2.
> - The benefit is that managed worktree provisioning no longer fails
before database seeding.

## Linked Issues or Issue Description

No public GitHub issue exists for this problem. PR #11752 added the
conditional source-config argument that exposed the failure.

**What happened?**

`scripts/provision-worktree-runtime.sh` expands an empty
`source_config_args` array while `set -u` is active. Bash 3.2 reports
`source_config_args[@]: unbound variable` and stops provisioning when
the registered base workspace already has `.paperclip/config.json`.

**Expected behavior**

Runtime provisioning must call `worktree ensure-seeded` without a source
override when the base workspace config exists. It must work with the
Bash 3.2 version that macOS supplies.

**Steps to reproduce**

1. Use macOS system Bash 3.2.
2. Create a base workspace with `.paperclip/config.json`.
3. Run `scripts/provision-worktree-runtime.sh` with `set -u` active in
the script.
4. Observe the unbound-variable error before `worktree ensure-seeded`
runs.

**Paperclip version or commit**

Reproduced on `origin/master` before this change.

**Deployment mode**

Local managed worktree runtime on macOS.

## What Changed

- Guard all three optional source-config array expansions with Bash
3.2-compatible parameter expansion.
- Add a regression test that uses the base-config path and verifies that
no `--from-config` argument is sent.
- Document the Bash 3.2 compatibility requirement in the runtime script.

## Verification

- `/bin/bash -n scripts/provision-worktree-runtime.sh`
- `node --test --test-name-pattern='runtime provisioning invokes
ensure-seeded once|runtime provisioning omits the source
override|runtime provisioning guards every optional source-config
expansion' scripts/__tests__/provision-worktree-self-heal.test.mjs`
- `git diff --check`

## Risks

Low risk. The change only affects expansion of an optional two-element
CLI argument array. The regression tests cover both the empty and
non-empty paths.

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

## Model Used

OpenAI Codex with model ID `gpt-5`. The runtime did not expose the
context-window size. Reasoning, tool use, and code execution were
enabled.

## Checklist

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

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-08-21 17:26:51 -07:00
Nicky LeachandClaude Opus 5 a9d1f740f0 fix(workspaces): seed managed worktrees when the base checkout has no config (#11752)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Agents do that work in isolated git worktrees, and a managed
worktree runs its own Paperclip instance with a cloned database
> - That clone needs a seed source, and the source must come from
server-owned registration, never from state the workspace itself can
rewrite
> - The seed-source resolver requires the registered base project
workspace to hold its own `.paperclip/config.json`
> - A managed project workspace is a plain `git clone`, and no code
writes that file into it
> - Every isolated worktree provision, deferred seed, and workspace
repair therefore fails on a managed checkout
> - This pull request lets a named source supply the config when the
base checkout has none
> - The benefit is that managed worktrees provision again, and the seed
source stays server-owned

## Linked Issues or Issue Description

No public GitHub issue exists for this problem. It is described below.

**What happened?**

Agent runs that need an isolated worktree fail during provisioning. The
provision command exits with this error (paths redacted):

```
Execution workspace provision command "bash ./scripts/provision-worktree.sh" failed:
Registered base project workspace has no canonical Paperclip config:
<instance-home>/instances/default/projects/<company-id>/<project-id>/<repo>/.paperclip/config.json
```

`resolveRegisteredWorktreeSeedSource` sets `registeredConfigPath` to
`<baseCwd>/.paperclip/config.json` whenever the caller names a
registered base workspace. It then requires that file to exist.
`scripts/provision-worktree.sh` applies the same rule.

A managed project workspace never has that file.
`materializeManagedProjectWorkspace` creates it with `git clone` and a
rename, so the checkout holds repository content only. The control plane
keeps its config at `<home>/instances/<id>/config.json` instead.

The failure reaches three paths: worktree provisioning, deferred seeding
through `worktree ensure-seeded`, and workspace repair.

The behavior changed in #11671. That pull request replaced a fallback
chain with a single hard requirement. Fixture code in
`scripts/__tests__/provision-worktree-self-heal.test.mjs` writes a
config into the fake base workspace, so tests kept passing.

**Expected behavior**

A managed worktree provisions and seeds from the registered source. The
seed manifest still never selects that source.

**Steps to reproduce**

1. Register the Paperclip repository as a project with a `repoUrl`, so
the server materializes a managed checkout.
2. Assign an issue to an agent whose workspace strategy is
`git_worktree`.
3. Watch the workspace operation log for the provision command.
4. The command exits non-zero with the error above.

**Paperclip version or commit**

Reproduced on `master` at 01ddc26a3.

**Deployment mode**

`local_trusted`, single instance.

**Database mode**

Embedded PostgreSQL.

**Operating system**

Linux, Node.js 22.

**Related pull requests**

- Refs #11671 — introduced the requirement this pull request relaxes.
- Refs #11733 — open work on seed-source preflight. It reads the same
base-workspace config path and skips when the file is absent. It does
not change source selection.
- Refs #11735 — open work on provisioning reliability. It edits the same
four files and will need a rebase after either lands.

## What Changed

- `resolveRegisteredWorktreeSeedSource` sets the registered config path
only when `<baseCwd>/.paperclip/config.json` exists. This makes the
existing `registeredConfigPath ?? explicitSource` branch reachable for a
plain checkout.
- A base workspace that does hold its own config stays authoritative. A
mismatched explicit source is still rejected.
- The resolver throws a named error when the base workspace has no
config and no source is named.
- `readInstanceId` accepts an instance-root config at
`<home>/instances/<id>/config.json`. That layout names its instance by
directory and has no adjacent `.env`. Validation reuses
`resolvePaperclipInstanceId`.
- `scripts/provision-worktree.sh` and
`scripts/provision-worktree-runtime.sh` name the control plane's
instance config as the source when the base workspace has none. The
canonical-path and symlink checks stay.
- The workspace repair route supplies the same fallback, and only when
the base workspace has no config of its own.
- `doc/DEVELOPING.md` records the two source layouts.

## Verification

- `node --test scripts/__tests__/provision-worktree-self-heal.test.mjs`
— 10 tests pass. The fixture no longer writes a config into the base
workspace, so it models a real managed checkout. One test now creates
that config mid-test, which covers both layouts.
- `npx vitest run src/worktree-seed-source.test.ts` in `packages/shared`
— 4 tests pass. Two are new: one resolves an instance-root source, and
one still fails closed when no source exists.
- `npx vitest run src/__tests__/workspace-runtime.test.ts
src/__tests__/execution-workspaces-routes.test.ts
src/__tests__/execution-workspace-runtime-control-conflict.test.ts
src/__tests__/workspace-operations-reconciliation.test.ts
src/__tests__/worktree-seed-server-spawn.test.ts` in `server` — all
pass. Run them one file at a time. They share one test database, and
concurrent runs fail teardown.
- `npx vitest run src/__tests__/worktree.test.ts` in `cli` — 63 tests
pass.
- `pnpm --filter @paperclipai/shared typecheck` — clean.
- Manual check on a live instance: the resolver now returns the instance
config as the source for a managed checkout, with the source instance
`default` and a distinct target instance.

## Risks

Low to moderate.

- The relaxed rule applies only when the base workspace holds no config.
A base workspace that holds one keeps full authority, so the trust model
from #11671 is unchanged. The seed manifest still never selects the
source.
- The instance-id fallback reads a directory name. It applies only to
the `<home>/instances/<id>/config.json` layout, and
`resolvePaperclipInstanceId` rejects an unsafe segment.
- #11735 edits the same four files. Whichever pull request lands second
needs a rebase.
- `pnpm --filter @paperclipai/server typecheck` currently fails on this
checkout with duplicate `drizzle-orm` type instantiations. The failure
is present with and without this change, and the error count is
identical. It comes from an unrelated lockfile state, not from this pull
request.

## Model Used

Claude Opus 5 (`claude-opus-5`), by Anthropic, running in Claude Code.
Extended thinking was on. The model used file, search, and shell tools
to diagnose the failure on a live instance and to run the test suites.

## 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

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

---------

Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
2026-08-20 08:42:16 -07:00
bd059a073d fix(workspaces): make managed runtimes reliable across restarts (#11740)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work
> - Execution workspaces need isolated databases, ports, and runtime
services
> - Concurrent workspaces could reuse ports or lose service ownership
after a restart
> - A markerless worktree also needed seed recovery, but normal
markerless instances still needed to boot
> - This pull request makes seed, port, and service ownership state
explicit and recoverable
> - It also checks live process and listener identity before it reclaims
shared resources
> - The benefit is reliable workspace startup, restart, adoption, and
concurrent provisioning

## Linked Issues or Issue Description

**What happened?**

Managed workspaces could lose runtime service ownership after a
control-plane restart. Concurrent worktrees could also reuse a port when
their parent paths differed. A seed recovery change made every
markerless instance resolve a worktree seed source, so normal instances
without a source could not start.

**Expected behavior**

Paperclip must preserve healthy managed services across restarts. It
must reserve unique ports across worktree parents. It must provision a
registered markerless worktree, but it must skip seed work for a normal
markerless instance.

**Steps to reproduce**

1. Start two managed worktrees under different parent paths at the same
time.
2. Restart the control plane while a managed service stays alive.
3. Start Paperclip with a config that has no seed markers and no
registered worktree source.
4. Observe duplicate port selection, lost service adoption, or a
seed-source startup error.

**Paperclip version or commit**

Current `master` plus the workspace runtime reliability changes in this
pull request.

**Deployment mode**

Local development with managed execution workspaces and embedded
Postgres.

## What Changed

- Added a shared port registry with lease heartbeats, process identity
checks, and live listener probes.
- Reserved worktree ports across custom parent paths and repaired
duplicate legacy assignments.
- Preserved and adopted healthy managed services across control-plane
restarts.
- Reconciled guest bind modes and verified listener ownership before
termination or reuse.
- Provisioned registered markerless worktree databases and kept normal
markerless instance startup as a no-op.
- Added CLI, shared, server, and shell regression tests for seed, port,
listener, restart, and adoption behavior.
- Updated the worktree development documentation.

## Verification

- `pnpm exec vitest run cli/src/__tests__/worktree.test.ts
--reporter=verbose` — 63 tests passed.
- `pnpm exec vitest run
packages/shared/src/worktree-port-registry.test.ts --reporter=verbose` —
5 tests passed.
- Focused runtime Vitest set — 199 tests passed across 37 suites.
- `node --test scripts/__tests__/provision-worktree-self-heal.test.mjs`
— 10 tests passed.
- `git diff --check` passed.

## Risks

- Port reservation now depends on lease and process identity data. The
fallback listener probe prevents early reclamation when process metadata
is incomplete.
- Runtime adoption is stricter about bind and owner identity. The tests
cover healthy adoption, stale records, PID reuse, and unrelated
listeners.
- Markerless seed detection now separates registered worktrees from
normal instances. The tests cover both paths.
- There are no database schema migrations.

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

## Model Used

- OpenAI Codex with the `gpt-5` model family. The serving snapshot and
context-window size are not exposed. The agent used reasoning,
repository tools, code execution, and test execution.

## Checklist

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

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Dev Agent <dev@paperclip.ing>
2026-08-19 14:55:16 -05:00
DottaandPaperclip a2bf936f9a feat(workspaces): sign the workspace login handoff and gate readiness (#11671)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Managed worktree services run isolated Paperclip instances with
cloned databases.
> - A reachable service was reported as ready even when its database,
runtime identity, or login path was not usable.
> - The first candidate added verified database seeding and managed
repair in #11665.
> - This pull request consolidates that candidate with signed login
handoff and a complete readiness contract.
> - Post-QA fixes close five defects in repair identity, repair
responses, UI retry, seed journal handling, and seed-source trust.
> - The benefit is a workspace that either opens safely or reports one
accurate recovery action.

## Linked Issues or Issue Description

No public GitHub issue exists for this work, so the problem is described
here.

**What happened**

Managed workspace URLs could return HTTP 200 and report ready while
login failed. QA also found cases where repair used the wrong instance
identity, returned a generic error, left the UI stuck, rejected a safe
journal lag, or trusted a mutable workspace manifest.

**Expected behavior**

Opening a ready workspace signs the board user in to the correct
isolated instance. Provisioning and repair use a registered source and
report a structured recovery state.

**Actual behavior**

Entry depended on a password copied into the clone. Several failure
paths could publish stale readiness, hide the repair precondition, or
trust state that the workspace could modify.

**Additional context**

This pull request includes the commits first published in #11665. That
pull request keeps the original base head for review history. This
consolidated pull request is the merge candidate. Related open readiness
work includes #11575 and #11621.

## What Changed

- Adds a short-lived, signed, single-use login ticket. It binds the
user, workspace, instance, and runtime origin.
- Exchanges the ticket through Better Auth. It creates the session and
cookie through the supported adapter path.
- Adds protected workspace readiness fields for the database, clone
data, login handoff, seed phase, and runtime identity.
- Fails readiness closed when the guest has no company or
execution-workspace binding.
- Binds ticket issuance to the exact cloned user and active company
membership selected for the handoff.
- Verifies every current active board identity through the exact-user
handoff before publication or reuse.
- Gates managed runtime publication on the readiness contract and the
recorded worktree instance identity.
- Refreshes runtime work products from the live runtime row after a port
change.
- Adds one workspace access card with ready, degraded, repairing, and
failed states.
- Uses the runtime response identity for repair. It returns structured
repair precondition errors.
- Lets a valid source journal lag converge during provisioning.
- Binds seed and repair manifests to a source registered outside the
agent-writable worktree.
- Clears recovered UI errors so a successful retry can open the
workspace.
- Makes runtime tests register canonical sources and avoid ports owned
by live host listeners.
- Keeps Vitest on source suites when compiled `dist` trees exist.
- Isolates CLI and adapter tests from ambient AWS and runtime API
environment variables.
- Preserves a 404 response for cross-company workspace ID lookups before
runtime authorization.
- Makes concurrent single-flight coverage independent of
path-canonicalization scheduling order.

## Verification

The following checks passed on the integrated head:

```sh
pnpm -r typecheck
pnpm build
pnpm check:token-gates
pnpm --filter @paperclipai/db check:migrations
```

- The server source lane passed 420 files and 4,953 tests. Five tests
were skipped.
- The CLI lane passed 57 files and 385 tests.
- The database lane passed 26 files and 97 tests.
- The shared package passed 58 files and 506 tests.
- The adapter utility lane passed 640 tests. Four tests were skipped.
- The Claude adapter passed 220 tests. One test was skipped.
- The Codex adapter passed 323 tests.
- The OpenClaw adapter passed 13 tests.
- The OpenCode adapter passed 42 tests.
- The plugin SDK passed 45 tests.
- The workspace runtime suite passed 124 tests.
- The caller-scoped readiness and handoff suite passed 52 tests.
- The workspace provisioning shell suite passed 7 tests.
- The runtime exposure suite passed 17 tests while live host mappings
occupied fixed test ports.
- `git diff --check` passed and the worktree is clean.

The serialized route lane will run in GitHub CI with its normal shards.
No deployment or active-workspace migration was performed.

## Risks

- This is a medium-risk authentication and runtime-readiness change.
- The login ticket uses exact origin, workspace, instance, and user
binding. It has a short expiry and a one-time nonce.
- Runtime publication is stricter. A real readiness, identity, per-user
handoff, or control-plane database disagreement now blocks publication.
- This pull request supersedes #11665 as the merge candidate. Close
#11665 after this pull request merges.
- No new database migration is included. The lockfile and workflow files
are unchanged.
- Deployment and active-workspace migration are intentionally outside
this pull request.

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

## Model Used

Claude Opus 5 (`claude-opus-5[1m]`), 1M context, extended thinking, tool
use, and code execution produced the main candidate. OpenAI GPT-5
(`gpt-5`) through Codex, with agentic reasoning, tool use, and code
execution, integrated the post-QA fixes and hardened the test gates. The
Codex context-window size 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 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>
2026-08-19 02:37:02 -05:00
dcac49a4fd feat(workspaces): defer isolated setup until runtime start (#10653)
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Isolated workspaces give each task a safe and reproducible checkout.
> - The existing setup cloned the development database before an agent
needed to run the app.
> - This made worktree creation slower and heavier for tasks that never
start a service.
> - Runtime services already use one server start path for heartbeat,
operator, and startup recovery flows.
> - This pull request moves heavy setup to that start path and keeps
worktree creation lean.
> - The benefit is faster isolated workspace creation with the same
reliable runtime setup when a service starts.

## Linked Issues or Issue Description

Related pull request: #10652 covers the initial deferred
database-seeding slice. This pull request supersedes it with end-to-end
runtime provisioning and safe cleanup.

**What existing behavior does this improve?**

This improves isolated worktree creation, runtime service startup, and
isolated instance cleanup.

**Subsystem affected**

Cross-cutting: CLI worktree setup, server runtime orchestration, shared
workspace contracts, and development scripts.

**Current behavior**

Paperclip seeds an isolated development database during worktree
creation. It can also leave an isolated instance directory after
workspace teardown. This work happens even when no runtime service
starts.

**Proposed behavior**

Paperclip creates the worktree with a lean eager setup. It runs an
idempotent runtime provision command before the first managed service
spawn. Concurrent starts share one provision attempt. Teardown removes
the isolated instance safely.

**Reason and benefit**

Many agent tasks only edit and test code. They do not need a running
Paperclip instance. Deferring the database seed reduces workspace
startup cost while preserving automatic setup for tasks that start the
app.

**Breaking changes**

None. The new runtime provision command is optional. Existing workspace
behavior is unchanged when it is absent.

## What Changed

- Split Paperclip worktree setup into a lean eager script and an
idempotent runtime provision script.
- Added `runtimeProvisionCommand` to project, issue, realized workspace,
and persisted workspace contracts.
- Added a per-workspace provision mutex before local service spawn for
heartbeat, operator, and startup recovery flows.
- Added a persisted `provisioning` service state and the
`workspace_runtime_provision` operation phase.
- Kept provision time outside the service readiness timeout and made
failed attempts visible and retryable.
- Reclaimed isolated instance data during safe workspace teardown.
- Serialized deferred database seeding across processes and bound
teardown to the instance root captured in persisted workspace metadata.
- Added tests for config flow, concurrency, retry, no-op behavior,
readiness timing, scripts, CLI commands, and cleanup.
- Documented the eager and runtime provisioning contracts.

## Verification

- `pnpm -r typecheck`
- `pnpm build`
- `pnpm test:run` (server: 3,201 passed; UI: 3,345 passed; the CLI phase
exposed one environment-sensitive AWS doctor assertion because the agent
runtime injects static AWS credentials)
- `env -u AWS_ACCESS_KEY_ID -u AWS_SECRET_ACCESS_KEY pnpm exec vitest
run cli/src/__tests__/secrets.test.ts -t 'passes AWS doctor checks when
non-secret provider config is present'`
- Focused runtime tests cover serialized provisioning, retry after
stderr failure, absent-command no-op behavior, operation logging,
persisted state order, and readiness timeout exclusion.
- Focused CLI and cleanup tests cover concurrent seed serialization,
stale-lock fail-closed behavior, persisted instance ownership, and
rewritten sibling pointers.

## Risks

- A faulty runtime provision script blocks service startup. Paperclip
records stderr, marks the service failed, and retries on the next start.
- Concurrent service requests share an in-process provision attempt,
while the seed command uses an atomic filesystem lock across processes.
A stale lock fails closed and requires an operator to verify no seed is
running before removing it.
- Isolated instance cleanup is destructive. The cleanup service
validates ownership and path containment before removal.

> 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-5.6-sol`, with agentic reasoning, tool use, and
code execution. The service does not expose the context-window size.

## Checklist

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

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
2026-08-02 10:37:10 -05:00