## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The board UI is the main daily navigation surface for agents,
projects, and their related resources.
> - Operators need a lightweight way to keep frequently used agents and
projects close without changing company-wide ordering or ownership.
> - Resource memberships already model per-user relationships to
projects and agents, so they are the right place to store user-specific
starred state.
> - This pull request extends that membership contract with a starred
timestamp and exposes star controls in list/detail views.
> - The sidebar then uses those starred memberships to show compact,
user-specific shortcuts.
> - The benefit is faster navigation without introducing a separate
favorites system or leaking preferences across users.
## Linked Issues or Issue Description
No public GitHub issue exists.
Feature request:
## Problem or motivation
Users cannot pin frequently used agents or projects into the main
sidebar. Returning to important resources requires scanning full
project/agent lists or navigating through detail pages, which adds
friction to repeated daily workflows.
## Proposed solution
Store a per-user `starred_at` timestamp on agent and project
memberships, expose API actions to set or clear that state, add star
toggle controls to list/detail pages, and render starred projects and
agents as compact sidebar shortcuts.
## Alternatives considered
A separate favorites table would work, but it would duplicate membership
scoping and require another resource relationship model. Keeping starred
state on memberships preserves existing company/user boundaries and
avoids a second source of truth.
## Roadmap alignment
Checked `ROADMAP.md`; no overlapping planned core work for starred
resource/sidebar navigation was found.
## Additional context
The affected subsystems are `packages/db`, `packages/shared`, `server/`,
and `ui/`. The migration is idempotent with `IF NOT EXISTS` guards so
environments that saw an earlier local migration name can still apply
the final ordered migration safely.
## What Changed
- Added idempotent migration `0133_resource_membership_stars` for
`starred_at` columns and lookup indexes on agent/project memberships.
- Extended shared resource membership types and validators with starred
metadata and actions.
- Updated server resource membership services/routes to read and mutate
starred resource state.
- Added reusable star toggle UI and resource membership hook support for
starred state.
- Added starred projects and agents sidebar rendering, plus star
controls on list and detail pages.
- Added focused shared, server, and UI coverage for starred membership
behavior and sidebar rendering.
## Verification
- Rebased and force-with-lease pushed current PR head
`a086fc965391c9e50a51b5b83b5b44a797b2a6f4` onto current
`paperclipai/paperclip:master`; `gh pr view` reports `MERGEABLE` with no
merge conflicts. GitHub checks are green for this fresh head.
- `pnpm exec vitest run packages/shared/src/resource-memberships.test.ts
server/src/__tests__/resource-memberships-routes.test.ts
server/src/__tests__/workspace-runtime.test.ts
ui/src/components/Sidebar.test.tsx
ui/src/components/SidebarAgents.test.tsx
ui/src/components/SidebarStarredProjects.test.tsx
ui/src/components/StarToggle.test.tsx
ui/src/pages/InstanceExperimentalSettings.test.tsx` passed after the
rebase: 8 files, 143 tests.
- Greptile re-review is 5/5; the remaining screenshot thread was
resolved as non-blocking because this task explicitly requested no
screenshots/images in the PR.
- `pnpm exec vitest run
ui/src/components/SidebarStarredProjects.test.tsx` passed after the
mobile pending-spinner fix.
- `pnpm exec vitest run packages/shared/src/resource-memberships.test.ts
server/src/__tests__/resource-memberships-routes.test.ts
ui/src/components/Sidebar.test.tsx
ui/src/components/SidebarAgents.test.tsx
ui/src/components/SidebarStarredProjects.test.tsx
ui/src/components/StarToggle.test.tsx
ui/src/pages/InstanceExperimentalSettings.test.tsx` passed: 7 files, 68
tests.
- `pnpm --filter @paperclipai/db typecheck && pnpm --filter
@paperclipai/shared typecheck && pnpm --filter @paperclipai/server
typecheck && pnpm --filter @paperclipai/ui typecheck` passed
db/shared/server, then failed in pre-existing UI code outside this PR:
`src/pages/CompanyEnvironments.tsx` missing `@xterm/*` type declarations
and `previous` possibly null.
- Checked that the PR diff does not include `pnpm-lock.yaml` or
`.github/workflows` changes.
- Checked `ROADMAP.md` and found no overlapping planned core work for
starred resource/sidebar navigation.
- Searched existing GitHub PRs for duplicate starred-resource/sidebar
work and found none.
## Risks
- Migration touches membership tables. The SQL uses `IF NOT EXISTS` for
columns and indexes so environments that saw an earlier local migration
name can still apply this safely.
- Sidebar ordering and visibility changes could affect users who rely on
the previous flat sidebar layout.
- Starred state is per-user membership metadata; code paths must
continue preserving company/user scoping around memberships.
> 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, tool-enabled coding agent with shell/GitHub access.
Context window not disclosed by the runtime.
## 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - The database layer runs migrations during server startup via
`server.listen`; migrations that block this path delay instance
availability
> - Migration `0126_issue_comment_derived_attribution.sql` backfills
derived attribution columns on `issue_comments` using a LIMIT-5000 loop
with no index or keyset cursor — it re-scans the full table from the
start each batch, giving O(n²) complexity
> - On instances with millions of issue comments this blocked
`server.listen` for ~5 minutes during upgrade, causing CPU pegs and
unavailability
> - Editing 0126 in place is unsafe: the migration runner keys its
applied-set on file **content hash**, so any edit changes the hash,
causing the runner to re-apply the migration on already-migrated
databases and blocking startup
> - The safe remedy is delete-and-relocate: remove 0126 and add a new
forward migration 0132 that uses a temporary partial index + keyset
pagination (`id > last_comment_id ORDER BY id LIMIT 5000`) so every row
is visited exactly once — O(n)
> - This pull request implements that delete-and-relocate with
idempotency guards (IF NOT EXISTS DDL, backfill WHERE clause that skips
already-attributed rows) so it is a safe near-noop on already-migrated,
partially-migrated, and fresh databases alike
## Linked Issues or Issue Description
No pre-existing public GitHub issue. Inline bug report:
**What happened?**
The `0126_issue_comment_derived_attribution` migration runs during
server startup and uses a LIMIT-5000 batch loop that re-scans
`issue_comments` from row 1 each iteration (no index, no keyset cursor).
The result is O(n²) I/O that blocked `server.listen` on large instances.
**Expected behavior**
Backfill migrations should advance with a keyset cursor so each batch
reads a new slice; total work is O(n) and startup is not blocked.
**Steps to reproduce**
Run a Paperclip upgrade on an instance with ≥200k issue comments;
observe `server.listen` blocked for several minutes and CPU peg during
migration.
**Paperclip version or commit**
Reproduced on the current `master` branch prior to this fix.
**Deployment mode**
All deployment modes that run the migration runner at startup.
## What Changed
- **Deleted**
`packages/db/src/migrations/0126_issue_comment_derived_attribution.sql`
— the O(n²) LIMIT-5000 loop with no index/cursor
- **Added**
`packages/db/src/migrations/0132_issue_comment_derived_attribution_fast.sql`:
- Creates a temporary partial index over the eligible predicate before
backfilling
- Uses keyset pagination (`id > last_comment_id ORDER BY id LIMIT 5000`)
— each batch advances to the batch-max id, so every row is visited once
- Drops the temporary index at the end
- Columns/FKs guarded with `IF NOT EXISTS`; Option-A timing-tier cleanup
preserved; human-authored comments never touched
- `WHERE` clause in the backfill excludes rows already attributed (safe
near-noop on already-migrated DBs)
- **Updated** `packages/db/src/migrations/meta/_journal.json` — dropped
0126 entry, appended 0132
- **Added**
`packages/db/src/issue-comment-derived-attribution-migration.test.ts`
(345 lines) — covers fresh-install, already-0126-migrated idempotency,
and partial-backfill completion scenarios using embedded Postgres
## Verification
```bash
# Migration numbering guard
pnpm --filter @paperclipai/db check:migrations
# Migration tests (embedded Postgres, 3 scenarios)
pnpm --filter @paperclipai/db vitest run issue-comment-derived-attribution-migration.test.ts
```
Both pass locally. CI results will appear on this PR.
## Risks
**Migration safety — already-migrated databases:** Deleting 0126 leaves
an orphan row in the runner's applied-set. The runner only checks the
set for "has this been applied" — orphan rows are never re-applied. 0132
runs as a near-noop: IF NOT EXISTS DDL is skipped, and the backfill
WHERE clause excludes rows that already have attribution.
**Migration safety — partially-migrated databases:** Keyset pagination
is idempotent. 0132 picks up from the highest attributed row id, so a
partial prior run is completed correctly.
**No data loss:** The migration never deletes or overwrites
user-authored content. It only writes to derived attribution columns on
rows where attribution is absent.
**Rollback:** 0132 is a forward-only migration. If a rollback is needed,
the attribution columns remain (no harm) and can be ignored or cleaned
up in a subsequent migration.
## Model Used
Claude Sonnet 4.6 (`claude-sonnet-4-6`) via the Paperclip AI agent
harness, with tool use and extended context enabled. Implementation
authored by Priya Raman; PR opened via the Paperclip Git Expert agent.
## 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
_(branch is the preserved implementation branch from the authoring
engineer; the internal task id is present in the branch name by workflow
convention — not a content risk)_
- [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 _(pending — CI running)_
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
_(pending — will be driven to terminal-green before merge)_
- [ ] I will address all Greptile and reviewer comments before
requesting merge _(pending — will action all findings)_
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Paperclip stores heartbeat run ownership context so operators can
audit which user was responsible for agent work
> - A migration backfills missing heartbeat run `responsible_user_id`
values from issue references in each run's context snapshot
> - Some context snapshots can store issue identifiers as public ticket
strings rather than UUIDs
> - The migration needs to resolve both UUID issue ids and issue
identifiers without trying to cast identifier strings to UUID
> - This pull request tightens the migration query so UUID matching only
casts validated UUID-shaped values and identifier matching remains a
separate fallback
> - A companion repair migration is needed so installations that already
recorded `0130` still get the corrected heartbeat-run backfill
> - The benefit is that existing installations can apply the
responsible-user invariant migrations without failing on non-UUID issue
references and without leaving already-migrated databases unrepaired
## Linked Issues or Issue Description
No public GitHub issue was found in a quick search for this migration
failure.
Bug report context following `.github/ISSUE_TEMPLATE/bug_report.yml`:
**Pre-submission checklist**
- I searched existing open and closed issues and did not find a
duplicate.
- I can reproduce against current `master` plus the responsible-user
invariant migration path.
- The error originates in Paperclip's database migration, not in an
adapter, API provider, or local configuration.
**What happened?**
Applying the heartbeat run responsible-user backfill migration could
fail when `heartbeat_runs.context_snapshot->>'issueId'` or `taskId`
contained an issue identifier such as `PAP-123` instead of a UUID. The
migration attempted to use issue refs for UUID matching and identifier
fallback, but the UUID path needed to avoid casting non-UUID identifier
strings. Because `0130` may already have been applied in some
installations, a follow-up repair migration is needed as well.
**Expected behavior**
The migration should backfill from UUID issue ids when present, from
issue identifiers when present, and fall back to the company default
responsible user without unsafe UUID casts. Already-migrated
installations should receive the repaired heartbeat-run context-ref
backfill through a new migration.
**Steps to reproduce**
1. Use a migrated database with a company, issue, agent, and heartbeat
run.
2. Store a null `heartbeat_runs.responsible_user_id` and a
`context_snapshot` like `{"issueId":"PAP-123"}`.
3. Replay/apply the run responsible-user repair migration.
4. Observe that the migration must not cast `PAP-123` to UUID and should
backfill from the matching issue identifier.
**Paperclip version or commit**
Current `master` plus this migration fix branch.
**Deployment mode**
Database migration during server startup or explicit migration command.
**Installation method**
Built from source / self-hosted migration path.
**Agent adapter(s) involved**
Not adapter-specific; core database migration bug.
**Database mode**
Postgres migration path, including embedded Postgres in development.
**Access context**
Not applicable; migration-time data backfill.
**Relevant logs or output**
Unsafe UUID casts can surface as Postgres invalid input syntax errors
when a context snapshot issue ref is an identifier rather than a UUID.
**Privacy checklist**
No private logs, paths, API keys, tokens, company names, or internal
Paperclip issue links are included.
## What Changed
- Split heartbeat run context issue reference extraction into reusable
CTEs.
- Only cast `issueId` / `taskId` values to UUID after a UUID-shape regex
check.
- Preserve fallback matching by issue identifier within the same
company.
- Keep deterministic candidate priority with `issueId` before `taskId`
and UUID matches before identifier matches.
- Added `0131_repair_run_responsible_user_context_refs.sql` so
installations that already applied `0130` still receive the corrected
heartbeat-run backfill.
- Added a DB migration regression test that replays the repair migration
with an identifier-style heartbeat run issue ref.
## Verification
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm --filter @paperclipai/db exec vitest run src/client.test.ts`
- Isolated embedded Postgres migration run with a temporary
`PAPERCLIP_CONFIG`: `pnpm --filter @paperclipai/db migrate` applied all
pending migrations successfully.
- GitHub Actions PR workflow is green on commit
`1c2655bc457cef3716a43e66463e1e5bc2fdcfab`.
- Greptile is 5/5 with no unresolved threads on commit
`1c2655bc457cef3716a43e66463e1e5bc2fdcfab`.
- Searched for duplicate public issues/PRs with GitHub search; no direct
duplicate found.
- Checked `ROADMAP.md` for overlap; no related roadmap item found.
## Risks
- Low-to-medium migration risk because this modifies an existing data
backfill migration and adds a companion repair migration.
- The query still relies on `context_snapshot` containing either issue
UUIDs or identifiers that match issues in the same company.
- Installations with unusual malformed context snapshots now skip unsafe
UUID casts and fall through to identifier/default backfill behavior.
> 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 coding agent with tool use and local command
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, or
confirmed no docs update is needed for this migration-only fix
- [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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agent runs often need provider credentials, API tokens, and other
environment-bound secrets.
> - Company-level secrets work for shared credentials, but they do not
model values that should differ by human operator.
> - Without a user-scoped model, a run can dispatch without knowing
whether the responsible human has supplied the needed value.
> - Paperclip also needs run attribution to make those user-scoped
runtime checks deterministic and auditable.
> - This pull request adds user-specific secret definitions, per-user
values, environment bindings, responsible-user attribution, and runtime
resolution gates.
> - The benefit is that teams can define the secret once, let each user
provide their own value, and block runs before dispatch when required
user secrets or active definitions are unavailable.
## Linked Issues or Issue Description
Refs #224
Refs #6057
This PR implements user-specific secret support as a core
secret-management capability rather than a one-off adapter setting. It
is related to existing public work on company secrets UI and runtime
secret refs, but is distinct because the value is owned by the
responsible user and resolved at run dispatch time.
Related PR search before opening found existing secrets work such as
#1550, #8256, #8614, #8634, and #8647; none of those add the full
user-secret definition/value/runtime gate covered here.
## What Changed
- Added user-secret definitions and per-user "My secrets" values,
keeping stored values out of access metadata.
- Added `user_secret_ref` environment bindings and UI affordances to
pick them alongside existing secret refs.
- Added responsible-user runtime resolution so user-secret refs resolve
against the human responsible for the run.
- Added pre-dispatch missing-secret gates so runs fail before adapter
dispatch when required user values are absent or definitions are
inactive.
- Added low-trust allowlist hardening for user-secret runtime access.
- Added issue, routine, run, and agent API key responsible-user
attribution and fail-closed dispatch behavior when attribution cannot be
resolved.
- Added denial-copy mapping so responsible-user authorization failures
surface as actionable run outcomes instead of opaque setup failures.
- Added OpenAPI documentation for the user-secret routes.
- Rebases cleanly on current `master`; migrations were renumbered
incrementally as `0128_user_specific_secrets`,
`0129_agent_api_key_responsible_user`, and
`0130_run_responsible_user_invariant` after upstream `0126`/`0127`
migrations.
- Removed previously committed local design screenshots so the PR
contains code/docs/tests only.
## Verification
- PASS: PR head `2527febd106bcf3ca264ca0da7fca491084192d6` is based on
`paperclipai/paperclip:master`.
- PASS: `git diff --check`
- PASS: `git diff --name-only public/master...HEAD | rg
'^(pnpm-lock\\.yaml|\\.github/workflows/|screenshots/)' || true`
produced no files.
- PASS: migration journal audit confirmed unique indexes through `130`
with tail entries `0126_issue_comment_derived_attribution`,
`0127_environment_custom_images_instance_scoped`,
`0128_user_specific_secrets`, `0129_agent_api_key_responsible_user`, and
`0130_run_responsible_user_invariant`.
- PASS: `pnpm --filter @paperclipai/ui typecheck`
- PASS: `pnpm --filter @paperclipai/server typecheck`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-responsible-user-invariant.test.ts`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-active-run-output-watchdog.test.ts
src/__tests__/heartbeat-stale-queue-invalidation.test.ts
src/__tests__/heartbeat-workspace-finalize-branch.test.ts
src/__tests__/issue-monitor-scheduler.test.ts`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-comment-wake-batching.test.ts
src/__tests__/heartbeat-retry-scheduling.test.ts
src/__tests__/heartbeat-accepted-plan-workspace-refresh.test.ts
src/__tests__/heartbeat-plugin-environment.test.ts`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/low-trust-red-team-routes.test.ts`
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/secrets-service.test.ts` (55 tests)
- PASS: `pnpm vitest run server/src/__tests__/secrets-routes.test.ts
server/src/__tests__/secrets-service.test.ts` (89 tests after final
Greptile cleanup fixes)
- PASS: `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/heartbeat-issue-liveness-escalation.test.ts` (17 tests
after the final rebase CI fix)
- PASS: focused server Vitest batches covering heartbeat recovery,
project env, plugin env, routines, low-trust, pipelines, monitors,
watchdog, and stale queue paths.
- PASS: GitHub checks are green on
`2527febd106bcf3ca264ca0da7fca491084192d6`, including Typecheck +
Release Registry, Build, General tests, serialized server suites, e2e,
Canary Dry Run, verify, security checks, and Greptile Review.
- PASS: Greptile Review completed successfully on
`2527febd106bcf3ca264ca0da7fca491084192d6` with Confidence Score 5/5,
and GraphQL review-thread audit returned zero unresolved non-outdated
threads.
## Risks
- Runtime behavior now depends on a run having a correct responsible
user; missing or incorrect responsibility assignment can block runs
before adapter dispatch.
- `user_secret_ref` bindings intentionally expose metadata without
values, but UI/API callers may need to handle the new binding kind
explicitly.
- External secret providers and IAM policies are not automatically
provisioned by this PR; operators still need to configure provider-side
access for non-local vaults.
- The PR is broad across db/shared/server/UI/runtime paths, so release
validation should include both API and UI secret workflows before merge.
- The migration renumbering is intentionally incremental after upstream
migrations; the branch migrations use guarded
column/table/index/constraint creation so users who tested the older
draft numbering should not hit duplicate DDL for the existing objects.
> 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 (`gpt-5`), Codex local adapter
with shell/tool use and code execution. Context window and internal
reasoning mode are not exposed by the runtime.
## 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Environments are now managed as instance-level runtime resources
rather than per-company rows
> - The custom environment image setup tables were introduced with their
own `company_id` columns and route query parameters
> - That split made one saved environment image state depend on an extra
company context even though the environment itself is the durable owner
> - It also made saved-environment probes harder because applying the
active custom image template could require a company context when no
secret-backed config needed one
> - This pull request scopes custom image templates and setup sessions
directly to the saved environment
> - The benefit is that reusable environment images follow the same
instance-scoped model as environments while secret resolution still uses
company context only when secrets require it
## Linked Issues or Issue Description
No matching public GitHub issue was found.
Bug report:
### What happened?
saved environment custom-image routes and persistence required a
`companyId` even though environments are instance-scoped, and saved
sandbox probes did not opt into active custom-image template application
unless a company context was present.
### Expected behavior
custom-image templates and setup sessions should be owned by the saved
environment, and saved sandbox probes should apply the active template
while still requiring a company context only for secret-backed runtime
config.
### Steps to reproduce
1. Configure an instance-scoped sandbox environment with custom-image
setup support.
2. Start or inspect a custom-image session or template for that saved
environment.
3. Probe the saved environment without a custom-image-specific
`companyId` query parameter.
### Paperclip version or commit
current `master` after the environment custom-image template migration.
### Deployment mode
Local dev (pnpm dev) or authenticated local Paperclip instance.
### Installation method
Built from source (pnpm dev / pnpm build).
### Agent adapter(s) involved
Not adapter-specific (core bug).
### Database mode
Embedded PGlite/Postgres dev database.
### Access context
Board human operator.
### Privacy checklist
No logs, secrets, tokens, private URLs, or local machine paths are
included.
Duplicate search performed:
- `gh search prs "environment custom image companyId
repo:paperclipai/paperclip" --state open --limit 20`
- `gh search prs "custom image environment scoped
repo:paperclipai/paperclip" --state open --limit 20`
- `gh search issues "environment custom image
repo:paperclipai/paperclip" --state open --limit 20`
The returned results were unrelated adapter, Docker, auth, or
stale-workspace items.
## What Changed
- Removed redundant `company_id` columns from environment custom-image
templates and setup sessions.
- Added migration `0127_environment_custom_images_instance_scoped` to
collapse duplicate active rows per environment before dropping the old
company-scoped indexes/columns.
- Updated custom-image services, route handlers, shared validators, and
UI API/query keys to use environment-scoped custom-image state.
- Kept runtime secret resolution company-aware only when secret refs or
bindings require a company context.
- Made saved sandbox environment probes opt into active custom-image
template application.
- Updated DB, shared, server, and UI tests for the new
environment-scoped contract.
## Verification
- `pnpm --filter @paperclipai/db run check:migrations`
- `pnpm exec vitest run
packages/db/src/environment-custom-images-schema.test.ts
packages/shared/src/environment-custom-images.test.ts
server/src/__tests__/environment-custom-image-routes.test.ts
server/src/__tests__/environment-custom-images-service.test.ts
server/src/__tests__/environment-routes.test.ts
ui/src/pages/CompanyEnvironments.test.tsx`
- `pnpm -r typecheck`
- `pnpm test:run` before rebasing onto latest `master`; after the rebase
only the migration number changed, and the migration check plus focused
suite, typecheck, and build were rerun.
- `pnpm build`
## Risks
- Migration safety: the migration supersedes duplicate active templates
per environment and fails duplicate active setup sessions before adding
environment-only unique indexes. Operators with duplicate historical
active rows should review which active template is kept.
- Behavior shift: plugin custom-image setup calls now receive
`companyId: "instance"` when no secret binding determines a concrete
company context.
- Secret-backed configs still require an explicit or uniquely inferable
company context; environments with secret bindings spread across
multiple companies continue to fail fast.
> 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 via the `codex_local` adapter, GPT-5-based coding model
with tool-enabled repository inspection, editing, testing, git, and
GitHub CLI access. Exact context-window metadata was not exposed by the
runtime.
## 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Task/issue threads render each comment as a chat bubble; the author
determines whether it shows as a left-aligned agent bubble (name + icon)
or a right-aligned "Board" bubble
> - Comments posted by an agent from a local execution environment are
written with a non-human author id (`local-board`/system), so they were
mis-rendered as blue "Board" bubbles instead of being attributed to the
authoring agent
> - This misattribution is confusing (it looks like the human board said
something an agent actually said) and it can drive false
wake/reconciliation behavior on the affected threads
> - This pull request adds server-side attribution derivation (lossless
run-id join first, then an explicit run-log post marker), persists the
derived agent so the read path stops re-scanning run logs, and stops the
client from labeling agent-derived comments "Board"
> - The benefit is agent comments render as the correct agent, genuine
human board comments are never reattributed, and reads get cheaper after
a one-time persistence
## Linked Issues or Issue Description
<!-- No public GitHub issue — describing the problem in-PR (bug report
shape). -->
**What happened?**
In a task/issue comment thread, comments authored by an agent from a
local execution environment are stored with a non-human author id
(`local-board`/system). The UI renders these as right-aligned blue
"Board" bubbles, implying a human board member authored them. The
mislabeling is also a wake/reconciliation hazard: an agent comment that
reads as "Board" can look like human board input.
**Expected behavior**
Such comments should render as the authoring agent (left-aligned bubble
with agent name + icon). Genuine human/board comments must continue to
render as "Board" and must never be reattributed to an agent.
**Steps to reproduce**
1. Have an agent post a comment on an issue from a local execution
environment (author id `local-board`).
2. Open the issue comment thread in the UI.
3. Observe the agent's comment rendered as a right-aligned blue "Board"
bubble instead of the authoring agent.
**Root cause**
The read path did not resolve the authoring agent for these comments,
and the client fell back to a "Board" label for the `local-board`
author.
## What Changed
- **Server derivation (`server/src/services/issues.ts`):**
- Resolve the authoring agent from the comment's run id first
(`createdByRunId`/`derivedCreatedByRunId` → `heartbeatRuns.agentId`) —
lossless when present.
- Second tier `run_log_comment_post`: read the run log lazily (only for
still-unresolved comments) to match the explicit `comment id:` post
marker.
- **Guard:** never reattribute a comment whose author maps to a genuine
user profile. Only the non-human sentinel (`local-board`, which is
itself a `user` row) and authors absent from the `user` table are
eligible.
- Pure timing-overlap tiers are intentionally **not** used (Option A) —
an agent comment and a human board comment posted during the same run
are indistinguishable rows, so any timing guess risks mislabeling a real
human comment.
- **Persistence
(`packages/db/src/migrations/0126_issue_comment_derived_attribution.sql`,
`packages/db/src/schema/issue_comments.ts`):** add stored `derived_*`
attribution columns and write the resolved agent back with a single bulk
`UPDATE ... FROM (VALUES ...)`, so reads stop recomputing from run logs.
Migration is additive (new nullable columns) with a batched, idempotent
backfill of the lossless run-id tier over historical rows.
- **Types (`packages/shared/src/types/issue.ts`):** expose the persisted
attribution fields and the `IssueCommentDerivedAuthorSource` union.
- **Client (`ui/src/lib/issue-chat-messages.test.ts`):** the message
builder already prefers a resolved agent id (`authorAgentId ??
runAgentId ?? derivedAuthorAgentId`), so once the server persists the
derived agent the bubble renders as the agent automatically — no client
code change needed. Adds a regression guard confirming a genuine board
comment with no derived agent is still rendered as "Board".
- **Tests:** derivation + message-building tests, including assertions
that genuine board/user comments are **not** reattributed.
## Verification
- `cd server && npx vitest run issues-service` — 94 tests pass: run-id
resolution, no-attribution on timing overlap alone (Option A), multi-run
ambiguity, same-agent multi-run, and the genuine-user guard. Exercises
the real persistence path (bulk UPDATE) against the test DB.
- `cd ui && npx vitest run issue-chat-messages` — 27 tests pass; client
no longer labels agent-derived comments "Board", and a genuine board
comment with no derived agent is not re-labeled.
- `cd server && npm run typecheck` — passes (exit 0).
- Manual: on a thread containing old agent-authored comments, the blue
"Board" bubbles render as the authoring agent; a genuine board comment
on the same thread still renders as "Board".
## Risks
- **Mis-reattributing a genuine board comment made during an agent run**
→ mitigated by the human-profile guard (only `local-board`/system
authors are eligible) and by dropping pure timing tiers (Option A): only
the lossless run-id join and the explicit run-log post marker attribute
history.
- **Backfill volume / run-log reads** → the migration backfill is
batched (5000 rows/loop) and results are persisted so reads stop
recomputing; the read-path persistence is a single bulk UPDATE rather
than per-comment round-trips. Migration adds only nullable columns (no
destructive change).
- The persistence/backfill has **not** been run against any production
database as part of opening this PR.
## Model Used
Claude Opus 4.8 (`claude-opus-4-8`), extended thinking, via Claude Code
with tool use.
## 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 — related open
PRs (#6006 narrow attribution run scan, #4729 attribution roll-up, #7014
reaped-run attribution) address different attribution paths; none fix
the `local-board` "Board" bubble rendering this PR targets. Supersedes
#8832 (same change; branch renamed to drop an internal ticket id per
CONTRIBUTING → Branch Naming)
- [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
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - A growing part of that work runs in sandboxed environments rather
than on the operator's local machine.
> - Today sandbox providers can start fresh workspaces and run probes,
but they do not have a shared contract for capturing and reusing
prepared sandbox state.
> - Operators need a way to set up tools, credentials, and project
dependencies once, then reuse that prepared image for later agent runs.
> - This pull request adds reusable sandbox custom images across the
provider contract, server runtime, and board UI.
> - It also keeps probes and sandbox copy flows aligned with
pre-authenticated/custom-image environments.
> - The benefit is faster, more reliable sandbox runs without repeatedly
rebuilding the same environment setup.
## Linked Issues or Issue Description
No public GitHub issue was found for this change. Inline feature request
follows.
### Problem or motivation
Sandboxed agents need reusable prepared runtime state so repeated runs
do not require manual setup every time. Operators often need system
packages, CLIs, SDKs, dependency caches, credentials, and project
tooling available before an agent can work productively.
### Proposed solution
Add a provider-level custom-image capability, server-side setup/capture
lifecycle, Daytona/fake provider support, and board UI controls for
creating, testing, selecting, and deleting custom images.
### Alternatives considered
Leaving this as provider-specific setup outside Paperclip would keep the
control plane blind to image state and would not give agents consistent
environment metadata. Re-running setup commands for every lease is
simpler, but slower and less reliable for interactive or credentialed
setup.
### Roadmap alignment
Checked `ROADMAP.md`; this aligns with the Cloud / Sandbox agents
roadmap area and does not duplicate any related public issue or PR found
by search.
Additional context:
- Subsystem affected: cross-cutting (`packages/db`, `packages/shared`,
`packages/plugins`, `server`, `ui`).
- Duplicate search: searched GitHub for `sandbox custom image` and
`sandbox template environment`; no related public issues or PRs were
found.
## What Changed
- Added custom-image shared types, validators, constants, API paths, and
database schema/migration.
- Added server services/routes for custom-image templates and setup
sessions, including runtime cleanup and provider metadata handling.
- Extended plugin/sandbox provider capabilities for interactive setup,
template capture, and template deletion.
- Implemented custom-image support in the fake sandbox provider and
Daytona provider.
- Updated environment runtime/config handling so active custom images
flow into leases, probes, and agent execution.
- Added board UI controls and API client support for custom-image setup,
capture, selection, status, and error states.
- Hardened sandbox copy/probe behavior for insecure clipboard contexts
and pre-authenticated sandbox images.
- Added targeted coverage across shared validators, DB schema, server
routes/services, provider plugins, adapter probes, and UI flows.
## Verification
- `pnpm install --frozen-lockfile --ignore-scripts`
- `pnpm vitest run
packages/adapters/claude-local/src/server/test.probe.test.ts
packages/adapters/claude-local/src/server/test.ts
packages/adapters/codex-local/src/server/test.remote.test.ts
packages/adapters/codex-local/src/server/test.ts`
- `pnpm --filter @paperclipai/adapter-claude-local typecheck`
- `pnpm --filter @paperclipai/adapter-codex-local typecheck`
- `pnpm vitest run
packages/db/src/environment-custom-images-schema.test.ts
packages/shared/src/environment-custom-images.test.ts
packages/shared/src/validators/plugin.test.ts
server/src/__tests__/environment-custom-images-service.test.ts
server/src/__tests__/workspace-runtime.test.ts
packages/plugins/sandbox-providers/daytona/src/plugin.test.ts
ui/src/pages/CompanyEnvironments.test.tsx
ui/src/pages/CompanySettings.test.tsx`
- `pnpm -r typecheck`
- `pnpm build`
- `rm -rf packages/db/dist && pnpm test:run`
- Public-safety scan of the final diff found no internal Paperclip issue
links, private instance URLs, or real secret patterns.
## Risks
- Adds a database migration and new environment runtime tables, so
migration ordering and rollback need care.
- Provider implementations may differ in how reliably they can
capture/delete images; unsupported providers surface capability-gated UI
states.
- Custom-image state can contain operator-prepared tooling and
credentials inside the provider image, so providers must enforce their
own access controls and cleanup semantics.
- Broad surface area across shared contracts, server runtime, plugins,
adapters, and UI means CI and Greptile review should be watched closely.
> 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 (`gpt-5`) via Codex CLI with tool use and code execution.
Assisted with branch cleanup, conflict resolution, local verification,
and PR preparation. Earlier branch implementation work was assisted by
Paperclip-managed Claude/Codex agents.
## 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The core server and database packages should only carry features
that are ready to remain in the product surface.
> - The X mention poller backend added database tables, Drizzle schema
exports, a server service, and a server test suite.
> - That backend work needs to be removed from core for now so the main
app does not carry unused X mention poller infrastructure.
> - A clean revert is safer than leaving partially unused database and
service code behind.
> - This pull request removes the poller backend artifacts and keeps the
migration journal aligned with the reverted migration history.
> - The benefit is that fresh environments no longer create or expose
the X mention poller backend tables or service code.
## Linked Issues or Issue Description
No public GitHub issue exists for this revert.
Duplicate PR search: searched open PRs in `paperclipai/paperclip` for "x
mention poller"; only this PR matched.
### What happened?
Core contained X mention poller backend infrastructure that should not
remain in the main Paperclip product surface right now.
### Expected behavior
Fresh core installs and migrations should not create the X mention
poller tables, and the server/db packages should not expose the removed
poller service or schema exports.
### Steps to reproduce
1. Inspect the prior migration journal after the original poller backend
commit.
2. Inspect the Drizzle schema exports.
3. Inspect the server services and tests for X mention poller backend
artifacts.
### Paperclip version or commit
This PR reverts the backend artifacts from the current `master` history.
### Deployment mode
Local development and CI.
## What Changed
- Deleted the `0125_x_mention_poller` migration and removed its journal
entry so fresh environments do not create the X mention poller tables.
- Removed the X mention Drizzle schema file and schema exports from the
db package.
- Removed the X mention poller server service and its server test suite.
- Left the functional diff unchanged from the original revert.
## Verification
- `rg -n "x_mentions|x-mention-poller|mention
poller|0125_x_mention_poller|xMention" packages server` returned no
matches.
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- Current functional CI checks are green; this metadata update is
intended to re-run and clear the `commitperclip PR Review` gate.
## Risks
- Developers who already applied migration `0125_x_mention_poller`
locally will keep four stale tables that Drizzle no longer tracks:
`x_mention_sources`, `x_mention_author_allowlist`, `x_mentions`, and
`x_mention_budget_ledger`.
- Manual local cleanup for those developers is to drop the stale
`x_mention_*` tables from their local database after confirming they do
not need that local data.
- Fresh environments that have not applied the removed migration should
be unaffected.
## Model Used
OpenAI Codex, GPT-5 family, via the ACPX-backed Codex local adapter.
Tool use included local shell inspection and GitHub CLI metadata
updates.
## 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
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Agents and operators increasingly need external event sources to
become durable Paperclip work inputs
> - X mentions are one such source, but intake needs to be safe before
any downstream automation consumes them
> - The backend needs stable source state, idempotent mention storage,
author gating, rate-limit handling, and budget accounting
> - This pull request adds the database contract and service layer for X
mention polling and hydration queueing
> - The benefit is that future X-triggered workflows can build on a
controlled, test-covered ingestion path instead of calling the X API
directly
## Linked Issues or Issue Description
- No public GitHub issue exists for this exact backend extraction.
- Problem: Paperclip does not yet have a durable, budget-aware backend
path for ingesting X mentions as external work inputs.
- Proposed solution: add X mention source, mention, allowlist, and
budget ledger tables plus a poller service that stores mentions
idempotently, queues only allowlisted authors for hydration, tracks
cursor state, records spend decisions, and fails closed when cost
estimates are unavailable.
- Related but not duplicate: #8609, #8199, and #7316 touch internal
mention wake behavior rather than X API mention ingestion.
## What Changed
- Added X mention poller database tables and schema exports for sources,
stored mentions, author allowlists, and budget ledger entries.
- Added a server-side X mention poller service with cursoring,
idempotent upsert behavior, allowlist gating, hydration queue handling,
rate-limit backoff, and budget pause behavior.
- Added focused Vitest coverage for intake gating, duplicate retries,
cursor safety, rate limits, budget failures, and hydration budget
pauses.
## Verification
- `pnpm exec vitest run server/src/__tests__/x-mention-poller.test.ts`
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm --filter @paperclipai/server typecheck`
## Risks
- Migration ordering matters because this adds migration
`0125_x_mention_poller.sql`; it should merge after the existing `0124`
migrations on `master`.
- The service is backend-only and adapter-driven in this PR, so product
behavior should not change until callers wire it into a runtime path.
- Budget accounting intentionally fails closed when estimates are
missing, which may pause a source rather than risk unbounded API spend.
## Model Used
- OpenAI Codex, GPT-5-based coding agent, tool-enabled local repository
and terminal workflow.
## 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agent adapters are the boundary between the control plane and the
runtimes that actually do work.
> - Hermes support needs to be available as first-class local and
gateway adapters while still preserving the adapter-manager override
path for external packages.
> - The adapter work touches runtime execution, UI adapter metadata,
onboarding prompts, scoped credentials, release packaging, and smoke
coverage, so the handoff needs concrete verification rather than only
unit tests.
> - This pull request adds built-in Hermes local and Hermes gateway
support, keeps external adapter overrides compatible, and
documents/tests the gateway flow end to end.
> - The benefit is that operators can hire Hermes-backed agents without
a manual plugin install, while self-hosted installs can still
override/shadow the built-ins through Adapter manager packages.
## Linked Issues or Issue Description
No public GitHub issue exists for this exact Hermes built-in adapter,
gateway onboarding, and release-source work.
Problem description:
- Hermes local and gateway adapters need a public, reviewable source
path in the monorepo so package artifacts and built-in adapter behavior
match the application source.
- Operators need built-in `hermes_local` and `hermes_gateway` adapter
choices without losing the ability to install external Hermes packages
as overrides.
- Gateway onboarding needs secure defaults for API server URLs, API
keys, and generated agent setup text.
- Hermes-originated task bridge credentials need narrower API-key scope
configuration.
- Related public PRs found during duplicate search include #3027, #2363,
#7544, #7950, #8095, and #8543.
## What Changed
- Added the unified Hermes adapter package with local and gateway
server/UI/CLI exports, config schemas, transcript parsing, model
detection, and package metadata.
- Registered `hermes_local` and `hermes_gateway` as built-in adapters
across shared constants, server registries, CLI packaging, and UI
adapter registries.
- Kept the external adapter override path compatible so installed Hermes
packages can shadow built-ins and restore the built-in parser when
disabled.
- Added Hermes gateway onboarding docs, board-operator docs, Docker
smoke assets, and shell smoke harnesses for join/e2e validation.
- Added scoped task-bridge API-key support, authorization checks,
issue-origin handling, and tests for Hermes-created Paperclip tasks.
- Hardened gateway transport and redaction behavior for API keys,
headers, session data, and smoke diagnostics.
- Updated release packaging/bootstrap checks for the Hermes packages
while leaving `pnpm-lock.yaml` out of the PR per repository policy.
## Verification
Targeted local verification recorded before PR handoff:
- `pnpm --filter @paperclipai/hermes-paperclip-adapter exec vitest run
src/gateway/server/execute.test.ts` — 14/14 passed.
- `pnpm test:hermes-gateway-smoke` — 6/6 passed.
- Hermes package typecheck/build checks passed.
- Focused server/UI adapter tests passed — 31/31.
- Release helper Node tests passed — 18/18.
- `git diff --check origin/master..HEAD` passed.
Fresh Docker E2E smoke evidence:
- Ran `pnpm smoke:hermes-gateway-e2e` on 2026-06-26 with a fresh state
directory and fresh Docker container against a live Paperclip dev
server.
- Hermes direct execution reached `completed`.
- Hermes stop/cancel path reached `cancelled`.
- Hermes gateway created a Paperclip task, Paperclip ran the Hermes
agent, and the task reached `done` with the expected marker response.
- Temporary board auth keys, token files, smoke state, and Docker
containers were cleaned up after the run.
PR checks on head `b5eae40ce`:
- GitHub Actions passed: `policy`, `review`, `Typecheck + Release
Registry`, all general test shards, all serialized server shards,
`Build`, `Canary Dry Run`, `e2e`, and aggregate `verify`.
- External checks passed: Snyk and Socket Project Report.
- External Socket Pull Request Alerts remained pending after the
first-party CI matrix completed.
## Risks
- Medium risk: this spans adapter registration, package publishing,
gateway execution, onboarding docs, API-key scoping, and UI adapter
metadata.
- Migration risk is low: the scope-config migration adds a nullable
column and does not rewrite existing keys.
- Gateway execution depends on operator-provided Hermes API
configuration; the smoke covers the Docker gateway path but real
deployments may differ by network/auth setup.
- Direct Greptile review on the latest expanded diff is file-count
limited, although the commitperclip review gate passed.
> 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 coding agent, tool use enabled in a local repository
workspace. Context window size is not exposed in this environment.
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with 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] Commitperclip review gate is green; direct Greptile review is
file-count limited on the latest expanded diff
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The pipeline subsystem models repeatable work as items moving
through stages, with agent automation, review gates, blockers, drift
notices, and linked work.
> - Operators need this to be usable as one coherent workflow surface,
not just as backend primitives or disconnected route experiments.
> - The branch now carries the pipeline data model, service/routes,
CLI/tutorial path, aggregation feeds, operator UI, stage automation
controls, liveness/retry handling, and follow-up polish that make the
primitive reviewable end to end.
> - This pull request is the single review target for that pipeline
workflow primitive stack.
> - The benefit is that reviewers can evaluate the full operator
experience and server contract together against `master`.
## Linked Issues or Issue Description
No public GitHub issue exists for this work. The underlying feature
request is described inline.
### Problem or motivation
Paperclip needs a first-class way to model multi-stage agent/company
workflows where upstream items can spawn downstream work, request
review, carry fields across pipelines, surface drift, retry automation,
and show operators where work is blocked or active. Without a unified
pipeline primitive, these workflows spread across ad hoc issues,
routines, and comments, making the state hard to inspect or operate.
### Proposed solution
Add the pipeline workflow primitive stack: database schema and
migrations, shared validators/types, server services and REST routes,
aggregation and liveness helpers, CLI/tutorial smoke support, and the
React operator UI for pipeline lists, boards, item detail,
review/learnings views, settings, stage automation, secrets, carry-over
fields, and retry/recovery flows.
### Alternatives considered
- Keep workflows as loosely linked issues and routines: rejected because
operators need a single board/detail/settings surface for repeated
workflow patterns.
- Ship backend primitives first and defer UI: rejected for this branch
because the operator experience is the main way to validate the
primitive.
- Add a narrower one-off content workflow: rejected because the same
primitives are useful across future company processes.
## What Changed
- Added and evolved pipeline schema, migrations, shared contracts,
server services, REST routes, route tests, and CLI/tutorial smoke
support.
- Added pipeline aggregation, health/liveness, drift acknowledgment,
blocker/carry-over, automation retry, stage automation environment, and
permission recovery behavior.
- Added the operator UI for pipeline index/board/item
detail/settings/review/learnings flows, including stage secrets,
automation controls, markdown/item descriptions, linked issue assets,
liveness banners, and source automation metadata.
- Refactored issue document frame rendering through the shared
`DocumentFrameHeader` component to keep document controls consistent
with the pipeline document surfaces.
- Kept this PR as the single base-branch review target for the current
pipeline branch.
## Verification
Current branch refresh:
- `pnpm vitest run server/src/__tests__/pipelines-service.test.ts` — 31
passed
- `pnpm vitest run server/src/__tests__/pipelines-routes.test.ts` — 19
passed
- `pnpm --filter ./server typecheck` — passed
- `pnpm --filter ./ui typecheck` — passed
- Verified Pipelines remains gated by `enablePipelines === true`:
sidebar item is hidden unless the flag is enabled, direct pipeline
routes redirect to `/dashboard` when disabled, and the Experimental
settings UI still has no Pipelines toggle.
- GitHub status checks on `df071c710646de625131064c3fb6588b5e97964a` —
all complete with no failing conclusions, including Actions, Socket,
Superagent/Security, and Greptile Review
- Greptile summary on `df071c710646de625131064c3fb6588b5e97964a` —
Confidence Score 5/5
- GitHub review-thread sweep — 0 unresolved Greptile threads
Previously recorded during branch development:
- Server pipeline service/route and aggregation tests
- Shared validator tests
- UI pipeline page/settings/item-detail/learnings/liveness tests
- Pipeline tutorial smoke path
## Risks
- High review surface: this is a large feature branch spanning database,
shared contracts, server behavior, CLI/docs, and UI.
- Migration ordering and schema compatibility need reviewer attention
because this branch has been kept current across multiple `master`
syncs.
- GitHub still reports merge state `BLOCKED` because the PR is awaiting
normal human review/branch-protection completion; all current status
checks are green.
- Branch-name checklist exception: this PR uses the pre-existing
requested branch name, which predates the current public-branch naming
rule. The PR title/body avoid internal issue references.
> 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 coding agent based on GPT-5, with repository tool use,
shell execution, git/GitHub CLI operations, and local verification
commands. Earlier commits in this branch were assisted by Paperclip
agents and other AI coding agents as recorded in commit authorship.
## 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
- [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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Agents and board users operate inside a company-scoped control plane
where permissions decide which mutating actions they can perform
> - Company skills are part of the reusable agent-company setup surface,
but skill mutation had been coupled to broader agent-creation authority
> - That coupling meant importing or managing skills required a
permission that also implies hiring power, which is broader than the
operation needs
> - Paperclip already has a grant-based permission vocabulary, so skill
mutation should be authorized through a dedicated `skills:create`
capability while preserving existing default behavior for trusted agents
> - This pull request adds the skill creation permission contract,
enforces it on company skill mutations, exposes it in agent permission
management, and documents the changed CLI/API expectations
> - The benefit is a narrower, auditable permission path for skill
import/create/update/delete flows without forcing agents to receive
broader agent-creation authority
## Linked Issues or Issue Description
No public issue is linked.
Problem: company skill mutation APIs were effectively tied to broader
agent creation authority. This PR splits skill mutation authorization
onto the public `skills:create` permission while keeping existing
default skill creation behavior for agents unless explicitly disabled.
Related public PR found during duplicate search: #5330. That PR uses an
older `canManageSkills` shape; this PR implements the `skills:create`
grant path instead.
## What Changed
- Added `skills:create` to shared permission constants and agent
permission types/validators as `canCreateSkills`.
- Backfilled default human/member role grants for `skills:create`.
- Updated company skill mutation routes to require board/user or agent
access to `skills:create`, while preserving legacy/default agent
behavior through `canCreateSkills` unless explicitly disabled.
- Updated agent permission update handling, UI permission controls,
duplicate-agent payloads, plugin SDK fixtures, and agent detail API
surfaces for `canCreateSkills`.
- Added regression coverage for skill route authorization, permission
schema/default behavior, invite grants, omitted permission updates, and
duplicate-agent payloads.
- Updated CLI and Paperclip skill documentation for the new skill
creation permission.
## Verification
- `pnpm exec vitest run
server/src/__tests__/agent-permissions-service.test.ts
server/src/__tests__/agent-permissions-routes.test.ts
server/src/__tests__/company-skills-routes.test.ts
server/src/__tests__/invite-join-grants.test.ts
ui/src/lib/duplicate-agent-payload.test.ts` — 5 files, 90 tests passed.
- `pnpm --filter @paperclipai/shared typecheck && pnpm --filter
@paperclipai/server typecheck && pnpm --filter @paperclipai/ui
typecheck` — passed.
- `pnpm test:run ...changed files...` was attempted first, but the
stable wrapper rejects explicit file arguments; direct Vitest was used
for the same targeted files.
## Risks
- Moderate authorization risk: this changes the gate for company skill
mutations, so the tests cover board grant checks, agent explicit grant
checks, legacy default allowance, and explicit denial.
- Migration/backfill risk is low: the migration only grants
`skills:create` to existing human roles that already need broad
management capability.
- UI/API compatibility risk is low: `canCreateSkills` remains default-on
for full agent permissions, and the update validator preserves omitted
values so unrelated permission edits do not re-enable disabled skill
creation.
> 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 coding agent with terminal/tool use 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI-agent
companies.
> - The control plane coordinates issues, workspaces, documents,
routines, and board review flows across company-scoped data.
> - The local source branch contained related schema, service, and UI
changes for workspace issue scoping and document/routine annotations.
> - These changes need to move together because db schema, shared types,
server services, and UI consumers form one contract.
> - This pull request extracts the migration-bearing control-plane work
from the source branch onto `origin/master`.
> - The benefit is a standalone branch with deterministic migration
order and focused review for the highest-risk part of the split.
## Linked Issues or Issue Description
No GitHub issue exists for this branch split. Internal source task:
[PAP-11234](/PAP/issues/PAP-11234).
Problem/motivation:
- Workspace operations need explicit issue scoping so readiness and
blocker handling can be derived correctly.
- Document annotations need reliable live updates, save failure
surfacing, normalized activity keys, and better comment panel behavior.
- Routine descriptions need the same annotation contract as issue
documents so operators can discuss and edit routine text without
special-case infrastructure.
Proposed solution:
- Add the workspace-operation `issueId` migration and readiness scoping.
- Add routine document/annotation schema, shared types, services,
routes, and UI editing support.
- Keep the related migrations in one PR so the renumbered `0106` and
`0107` migrations land in a deterministic order after current `master`.
Alternatives considered:
- Split migrations into separate PRs, rejected because that would create
migration-numbering conflicts and make each branch less standalone.
- Merge this with UI polish, rejected because this branch needs deeper
server/db review.
Roadmap alignment:
- Checked `ROADMAP.md`; the roadmap mentions future recurring routine
capabilities generally, but no duplicate implementation PR for these
annotation/workspace changes was found.
## What Changed
- Added `0106_workspace_operations_issue_id.sql` and
`0107_routine_description_annotations.sql`, plus schema exports.
- Scoped workspace readiness to blocker issues and attached workspace
operation issue ids.
- Scoped issue-thread interaction accept finalization to the source run.
- Added routine document annotation contracts across
db/shared/server/UI.
- Improved document annotation live updates, activity-key normalization,
save failure surfacing, and comment panel behavior.
- Added issue workspace property controls and compact
blocked-by/quick-control UI updates.
- Added focused server and UI regression tests for the new contracts.
## Verification
- `CI=true NODE_ENV=development pnpm install --frozen-lockfile
--prefer-offline`
- `NODE_ENV=test pnpm exec vitest
server/src/__tests__/document-annotation-routes.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts
server/src/__tests__/issues-service.test.ts
server/src/__tests__/routine-document-annotation-routes.test.ts
server/src/__tests__/routines-routes.test.ts
server/src/__tests__/workspace-runtime.test.ts
ui/src/components/IssueDocumentAnnotations.test.tsx
ui/src/components/IssueProperties.test.tsx
ui/src/components/WorkspaceRuntimeControls.test.tsx
ui/src/context/LiveUpdatesProvider.test.ts --run` — 10 files, 273 tests
passed.
- `NODE_ENV=test pnpm -r --filter @paperclipai/db --filter
@paperclipai/shared --filter @paperclipai/server --filter
@paperclipai/ui typecheck` — passed, including db migration numbering
check.
## Risks
- Migration-bearing PR; merge this branch before any later PR that adds
migrations with higher numbers.
- Cross-layer contract risk across db/shared/server/ui, mitigated with
targeted tests and affected-package typecheck.
- Review should pay special attention to company scoping in new
routine/document annotation 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 GPT-5 Codex via Paperclip `codex_local` / CodexCoder, GPT-5-class
coding model with tool use and shell execution. Exact runtime snapshot
and context-window setting were not exposed by the Paperclip run
context.
## 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 available from the run context)
- [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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots (N/A per source task: do not add screenshots/images unless
specifically part of the work)
- [x] I have updated relevant documentation to reflect my changes (N/A;
no public docs 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
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - This change touches several already-shipped subsystems —
document-comment annotations, the selected-agent Conference Room chat
surface, routine description annotations, workspace-operation tracking,
and the board polling/inbox UI
> - A batch of incremental fixes and two small backend additions had
accumulated on a local mainline and were deployed to a live instance,
but never landed upstream — so each `origin/master` sync kept
re-diverging
> - Leaving them un-upstreamed means the same delta has to be re-merged
on every sync and risks being lost or silently reverted
> - This pull request rebases that delta cleanly on top of current
`origin/master` (preserving recent upstream work such as reusable
sandbox leases and the relation-list collapse controls) and brings it up
for review
> - The benefit is that mainline and the deployed instance converge, and
these fixes/additions get normal review + CI + Greptile coverage
## Linked Issues or Issue Description
No single GitHub issue tracks this; it is a bundle of bug fixes and two
small feature additions. Following the issue-template fields:
**Bug fixes (what was wrong → what this does):**
- Document comments rendered out of document order, didn't live-update
across clients, swallowed save failures, and lost the markdown text
selection on re-render. Now: doc-order sort, live updates, surfaced
save-failure state, stable selection across re-renders.
- The board polling hot path returned oversized payloads on every poll.
Now: an opt-in `summary` projection trims the heartbeat-run list
payload.
- Assorted UI fixes: sidebar nav peek/streamlining edge cases, markdown
file-viewer re-mount/line-height issues on iOS Safari, inbox badge/skill
deep-link tab selection, and `⌘.` work-mode cycling on iOS.
**Feature additions:**
- `workspace_operations.issue_id` — associate a workspace operation with
the issue that triggered it (new migration `0106`, schema, service,
shared type).
- Routine **description annotations** — comment threads on a routine's
description document, mirroring issue document annotations (new
migration `0107`, `routine_documents` schema, routes/service,
editable-sections UI).
- Selected-agent **Conference Room chat** surface wiring and live
issue-thread updates.
**Related PR:** #8229 (`feat(control-plane): add annotation and
workspace controls`, draft) covers overlapping
annotation/workspace-control territory — flagging it so a reviewer can
reconcile the two rather than double-merging.
## What Changed
- `feat(workspace)`: `workspace_operations.issue_id` migration +
schema/service/type; issue workspace property controls reconciled with
upstream's evolved "Service" row.
- `feat(routines)`: routine description annotations —
`routine_documents` schema, migration `0107`, routes/service,
`editable-sections` UI.
- `fix(document-comments)`: doc-order sort, live updates, save-failure
surfacing, stable markdown selection (+ storybook story, rerender test).
- `feat(chat)`: selected-agent Conference Room chat surface and live
issue-thread updates (`LiveUpdatesProvider`, `issue-chat-messages`,
interactions service).
- `perf(board)`: opt-in `summary` projection for the board
polling/heartbeat-run list payload, plus assorted sidebar / file-viewer
/ inbox / IssueProperties UI fixes.
Organized into 5 logical commits. Migrations are numbered incrementally
after upstream's latest (`0105`) — `0106` then `0107`, no journal
collision.
## Verification
- Built by 3-way merging the deployed delta onto current
`origin/master`; the only merge conflict (`IssueProperties.test.tsx`,
two adjacent test blocks) was resolved in favor of upstream's evolved
"green service link above the workspace row" layout, which matches the
merged component's rendered output.
- Confirmed recent upstream work is preserved post-merge: reusable
sandbox lease teardown (`#8513`), the IssueProperties relation-list
collapse controls, and the sidebar streamlined-nav default.
- Confirmed the net diff vs `origin/master` is exactly the intended
feature delta (65 files) and that overlapping server files (`issues.ts`,
`agents.ts`, `heartbeat.ts`) only add feature code without disturbing
upstream logic.
- This delta is already running on a live deployed instance.
- Full typecheck/test suite + Greptile to run in CI (see checklist).
## Risks
- Two new migrations (`0106`, `0107`). Both are additive (new table /
new nullable column) and ordered after upstream's `0105`; no data
backfill, low risk. If another migration-bearing PR merges first,
renumber before merge.
- Largest blast radius is in the merged overlapping UI/service files;
covered by the existing test suites for those files plus CI.
- Overlaps thematically with draft PR #8229 — reviewers should reconcile
rather than merge both blindly.
## Model Used
Claude Opus 4.8 (`claude-opus-4-8`), extended thinking, with tool use
(git, shell). Agentic coding workflow.
## 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)
- [ ] 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>
## Thinking Path
> - Paperclip is the open source control plane people use to coordinate
AI agents, issues, approvals, comments, and work products.
> - The involved subsystem is issue context: markdown links, issue
properties, related work, lists, filters, inbox/sidebar status, and
plugin-provided external context.
> - The gap is that URLs to external systems currently remain mostly
plain links, so humans and agents must manually open them to understand
status, identity, and liveness.
> - This matters because external work objects such as GitHub issues and
pull requests are part of the operational state of a Paperclip company.
> - The implementation keeps core provider-neutral: shared contracts,
storage, sync, routes, and UI surfaces live in core while providers can
contribute detection and status resolution.
> - This pull request adds the external object reference foundation,
GitHub provider support, issue-surface rendering, filters,
sidebar/list/inbox signals, and test/story coverage.
> - The benefit is that linked external work becomes inspectable
Paperclip context without hardcoding every provider directly into the
UI.
## Linked Issues or Issue Description
No public GitHub issue exists for this work.
Feature request:
- Problem: URLs in Paperclip issues, comments, documents, and related
surfaces do not expose provider status or object identity inline.
- Proposed behavior: detect supported external object URLs, persist
normalized references, refresh provider status, and render concise
status-aware links across issue surfaces.
- Users affected: board users, agents, and maintainers who triage issues
containing external work links.
- Acceptance: external object references are company-scoped,
provider-extensible, visible in key issue surfaces, filterable where
relevant, and covered by focused shared/server/UI tests.
Related PR search:
- No open duplicate PRs found for `external object references`.
- Closed related prior attempt: #4556.
## What Changed
- Added shared external-object contracts, validators, status/liveness
helpers, and plugin protocol declarations.
- Added database schema and additive migrations for external objects,
source mentions, and display metadata.
- Added server services/routes for detecting, syncing, summarizing,
refreshing, and resolving external objects across issues, documents,
comments, projects, and plugins.
- Added a GitHub external-object provider plus plugin SDK authoring
docs.
- Wired UI presentation across markdown links, comments, issue chat,
documents, properties, related work, issue rows, filters, inbox/sidebar
badges, and Storybook stories.
- Rebasing cleanup: moved the branch onto current `master`, repaired
stale worktree provision config, hardened environment-sensitive
tests/mocks, and removed committed screenshot artifacts from the PR
branch to keep the reviewable file set below tool limits.
## Verification
- `pnpm exec vitest run packages/shared/src/external-objects.test.ts
server/src/__tests__/external-object-routes.test.ts
server/src/__tests__/external-objects-service.test.ts
ui/src/components/ExternalObjectPill.test.tsx
ui/src/lib/external-objects.test.ts` passed after rebasing: 5 files, 56
tests.
- Historical branch verification before this PR creation included `pnpm
test:run`, `pnpm -r typecheck`, and `pnpm build`; this PR body does not
claim those were rerun after the final rebase.
## Risks
- Medium: this adds a new cross-surface sync path on
issue/document/comment writes. The implementation uses safe sync
wrappers so external-object failures warn instead of blocking core
mutations.
- Medium: the migrations introduce new tables and indexes. They are
additive and company-scoped.
- Medium: provider-specific URL parsing can miss or misclassify edge
cases. Shared canonicalization tests and provider tests cover current
GitHub shapes.
- Low: UI badge/filter behavior could add visual noise for object-heavy
issues; component tests and Storybook stories cover the intended
surfaces.
> Roadmap checked: `ROADMAP.md` references the plugin system as the
current extension path and does not list a duplicate core feature.
Related long-range docs discuss external references, work products,
preview URLs, and plugin extension points; this PR implements the scoped
external-object reference foundation.
## Model Used
OpenAI Codex, GPT-5 coding-agent runtime, with shell and GitHub CLI tool
use. Reasoning mode: medium. Exact deployed runtime model ID and context
window were not exposed in the environment.
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with 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>
## Thinking Path
> - Paperclip is the control plane for AI-agent companies, so execution
environment selection has to stay inspectable and predictable across
companies, agents, and runs.
> - The environment subsystem decides where an agent heartbeat actually
runs and how remote sandbox state is realized and restored.
> - That subsystem previously mixed company-scoped environment catalogs
with issue-level environment stamping, so a reassigned issue could keep
executing in the previous assignee's sandbox.
> - That behavior breaks the control-plane contract: changing the
assignee should change the executing agent/environment path unless there
is an explicit current override.
> - Fixing it cleanly required more than a narrow patch; the environment
model had to move to instance scope with a single inherited default and
per-agent override semantics.
> - This pull request rewires the schema, server/API surface, runtime
resolution, and UI around that model, then adds regression coverage for
cross-company inheritance and per-agent isolation.
> - The benefit is that environment choice now follows the approved
instance/agent configuration path instead of stale issue state, while
shared environments only need to be configured once per instance.
## Linked Issues or Issue Description
- No directly matching public GitHub issue or PR was found while
searching for this refactor.
### What happened?
Reassigning work between agents with different execution environments
could keep running in the previous sandbox because environment choice
was stamped onto the issue and outranked the current assignee. The same
subsystem also forced environment catalogs to be duplicated per company
even though the underlying execution environments were instance-wide
resources.
### Expected behavior
Execution should resolve through the current instance and agent
configuration path, with one instance-scoped environment catalog, one
instance default, optional per-agent override, and no stale issue-level
environment authority surviving reassignment.
### Steps to reproduce
1. Configure two agents to use different execution environments.
2. Assign an issue to the first agent so the issue records execution
state in that environment.
3. Reassign the same issue to the second agent and run another
heartbeat.
4. Observe that the pre-fix runtime can still sync or execute in the
original sandbox instead of the second agent's environment.
### Paperclip version or commit
Current `master` before this PR.
### Deployment mode
Self-hosted server.
### Installation method
Built from source (`pnpm dev` / `pnpm build`).
### Agent adapter(s) involved
- Claude Code
- Not adapter-specific (core bug in environment authority / resolution)
### Database mode
External Postgres.
### Access context
Both board reassignment and agent heartbeats were involved.
## What Changed
- Moved environments and their default selection contract to instance
scope in DB/shared types, including the migration that dedupes legacy
per-company environments and seeds the instance local default.
- Reworked environment CRUD/auth flows to use instance-scoped APIs and
added route/service coverage for instance-level environment management.
- Changed runtime resolution to prefer `agent default -> instance
default -> built-in local`, removed issue-level environment stamping
from the active execution path, and isolated sandbox/plugin leases by
`(executionWorkspaceId, agentId)`.
- Added environment env-var runtime precedence so environment-provided
values act as the baseline for agent execution.
- Moved the environment UI into instance settings and updated agent
configuration surfaces to reflect inherit/override behavior.
- Added regression coverage for instance-default inheritance across
companies and for the new runtime resolution behavior.
- Fixed a rebase-only duplicate `enableTaskWatchdogs` flag regression in
instance settings types/validators/services so the branch typechecks
cleanly on current `master`.
- Updated stale server tests so CI matches the shipped instance-scoped
environment contract.
## Verification
- `git diff --check`
- `pnpm --filter @paperclipai/shared typecheck`
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm exec vitest run
server/src/__tests__/environment-runtime-driver-contract.test.ts
server/src/__tests__/agent-permissions-routes.test.ts
server/src/__tests__/environment-routes.test.ts
server/src/__tests__/environment-instance-routes.test.ts
server/src/__tests__/execution-workspace-policy.test.ts
server/src/__tests__/heartbeat-plugin-environment.test.ts
server/src/__tests__/instance-settings-routes.test.ts`
## Risks
- The migration changes environment scope and dedupes existing rows, so
installs with unusual legacy environment combinations should be reviewed
carefully during upgrade.
- Remote execution behavior now depends on instance-default inheritance
semantics instead of issue-level stamping, so any remaining code paths
that still assume issue-scoped environment authority would surface as
follow-up bugs.
- This PR includes both server/runtime behavior and UI relocation, so
reviewers should watch for authorization edge cases around instance
settings and environment management.
> I checked [`ROADMAP.md`](ROADMAP.md). This work fits the existing
Cloud / Sandbox agents direction as a bug-fix/refactor to current
behavior, not a new parallel product surface.
## Model Used
- OpenAI Codex coding agent in this Paperclip/Codex session; GPT-5-class
tool-using model with code execution and shell access. The exact backend
model ID is not exposed to the session runtime.
## 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
- [ ] If this change affects the UI, I have included before/after
screenshots
- [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
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The task lifecycle and recovery subsystems decide when agent work is
still productive, stalled, or ready for review.
> - Existing recovery paths can observe stopped or incomplete work, but
there was no first-class per-task watchdog model with scoped review
permissions.
> - Watchdog follow-ups also need strict boundaries so
recovery/status-only runs cannot mutate approvals or perform deliverable
work.
> - This pull request adds the task watchdog data model, API/service
layer, scheduler/review flow, adapter wake context, UI configuration
surfaces, and docs.
> - The branch has been rebased onto current `paperclipai/paperclip`
`master`; the watchdog migration is now ordered after master's latest
migrations as `0104_issue_watchdogs`.
> - The benefit is a more explicit task-review loop that preserves
Paperclip's single-assignee and governance invariants while making
stalled work easier to route.
## Linked Issues or Issue Description
No linked GitHub issue. Paperclip task:
[PAP-11275](/PAP/issues/PAP-11275).
## Problem or motivation
Task recovery needs a first-class watchdog path that can inspect stopped
work and create scoped follow-ups without bypassing normal task
ownership. Board/UI users need a way to configure watchdogs on tasks and
see watchdog-related live work. Recovery/status-only runs must remain
limited to status reporting and must not create approvals, link
approvals, or submit approval comments.
## Proposed solution
Add a task-watchdog data model, scheduler/classifier, scoped mutation
guard, adapter wake context, API/UI configuration surfaces, and
documentation so watchdog agents can review stopped task subtrees under
explicit boundaries.
## Alternatives considered
Reuse the existing recovery-action flow only. That would keep
stopped-work detection implicit, make per-task watchdog assignment
harder to expose in the UI, and would not provide a durable
scoped-review issue for stalled task trees.
## Roadmap alignment
This is Paperclip control-plane lifecycle infrastructure for task
execution and recovery. I checked `ROADMAP.md`; this PR does not
duplicate an existing planned core item.
## What Changed
- Added issue watchdog schema, migration, shared contracts, validators,
CRUD API, and service support.
- Added task watchdog scheduler/classifier behavior, scoped mutation
enforcement, adapter wake context, and default watchdog mandate
guidance.
- Added UI surfaces for configuring watchdogs on new/existing tasks,
viewing watchdog activity, and exposing the experimental setting.
- Added docs for the user-facing task watchdog workflow and
implementation semantics.
- Gated new-task watchdog setup behind `enableTaskWatchdogs` and blocked
cheap status-only recovery runs from approval mutations.
- Rebased onto current `master` and renumbered the idempotent watchdog
migration from the branch-local `0102_issue_watchdogs` slot to
`0104_issue_watchdogs`.
- Addressed Greptile feedback by loading watchdog classifier input with
a recursive subtree query and centralizing the watchdog origin-kind
constant.
- Added and updated focused server/UI tests for watchdog routes,
scheduler/classifier behavior, scope boundaries, live task visibility,
settings, and new issue dialog behavior.
## Verification
- `pnpm vitest run server/src/__tests__/task-watchdogs-scheduler.test.ts
server/src/__tests__/task-watchdogs-classifier.test.ts`
- `pnpm vitest run
server/src/__tests__/approval-routes-idempotency.test.ts
server/src/__tests__/issue-agent-mutation-ownership-routes.test.ts`
- `pnpm vitest run ui/src/components/NewIssueDialog.test.tsx`
- `pnpm --filter @paperclipai/server typecheck`
- `git diff --check`
- Verified the PR diff does not include `pnpm-lock.yaml` or
`.github/workflows`.
## Risks
- Medium risk: this introduces a new task lifecycle surface touching DB
schema, server routes/services, adapter wake context, and UI task
configuration.
- Watchdog scheduling behavior depends on the new experimental setting
and runtime context checks behaving consistently across local and
production agents.
- The watchdog migration is idempotent (`IF NOT EXISTS` /
duplicate-object guards) so users who tried the previous branch-local
migration number should not get duplicate-object failures.
- CI and the second Greptile pass are pending after the latest
review-fix push.
> 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-class coding agent in the Paperclip workspace. Exact
runtime model id and context window were not exposed to the agent; tool
use and local command 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots — N/A per Paperclip task instruction: do not add
screenshots/images to this PR unless they are specifically part of the
work.
- [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>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
## Thinking Path
> - Paperclip is the control plane people use to create, configure, and
run AI agents for work.
> - This change sits in the server-side agent lifecycle and
secret-binding subsystem, where adapter config `env` entries can
reference company secrets.
> - An incident (while trying to configure a Novita sandbox) showed that
an agent can reach a broken runtime state if `adapterConfig.env`
contains `secret_ref` entries but the matching `company_secret_bindings`
rows are missing.
> - The immediate run-path guard and error-surfacing work made the
failure diagnosable, but they did not fully prevent new broken agents
from being created.
> - The risk came from create and approval flows being responsible for
remembering to sync bindings at each call site, which is easy to miss as
new flows are added.
> - This pull request moves the invariant into `agentService`
create/update/activate paths, keeps the existing hire-flow fix, and adds
regression coverage for create, update, and legacy pending-approval
recovery.
> - The benefit is that agent secret binding integrity is enforced
closer to the data mutation point, so future callers inherit the
protection automatically.
## Linked Issues or Issue Description
Refs #8309
### What happened?
A Paperclip agent could persist `adapterConfig.env` `secret_ref` entries
without matching agent-scoped `company_secret_bindings` rows. When that
happened, the config UI could still look configured, but the real run
path failed pre-dispatch because the secret was not actually bound to
that agent.
### Expected behavior
Every normal agent create, config-update, and pending-approval
activation flow should leave the agent with secret bindings that match
its persisted secret-ref env config.
### Steps to reproduce
1. Create or activate an agent through a flow that persists
`adapterConfig.env` secret refs without synchronizing
`company_secret_bindings`.
2. Observe that the config state can still appear populated.
3. Start a run for that agent.
4. Observe that pre-dispatch binding validation fails because the secret
reference exists but the agent binding does not.
### Deployment mode
Local dev (`pnpm dev`)
### Installation method
Built from source (`pnpm dev` / `pnpm build`)
### Agent adapter(s) involved
- Claude Code
- Not adapter-specific (core bug)
### Database mode
Embedded PGlite / embedded local dev database flow
### Access context
Board (human operator) created or approved the agent; agent runtime
later consumed the config.
### Additional context
This PR focuses on preventing new broken states from normal service
flows and on backfilling the covered legacy pending-approval activation
path.
## What Changed
- Kept the existing branch-local hire-flow fix that synchronized
bindings for route and approval paths.
- Moved the binding integrity invariant into `agentService.create()`,
`agentService.update()` when `adapterConfig` changes, and
`agentService.activatePendingApproval()`.
- Added `server/src/__tests__/agents-service-secret-bindings.test.ts`
covering create-time sync, update-time resync, and backfill for legacy
pending-approval agents.
- Removed now-redundant route-layer and approval-layer binding sync
calls once the service layer became authoritative.
- Simplified the affected unit tests so route/approval tests no longer
assert service-owned binding writes directly.
## Verification
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run
server/src/__tests__/agents-service-secret-bindings.test.ts
server/src/__tests__/approvals-service.test.ts
server/src/__tests__/agent-skills-routes.test.ts`
## Risks
- Low to medium risk.
- This changes where secret-binding synchronization is enforced, so any
unexpected caller that relied on upper-layer manual sync behavior could
behave differently.
- Agent create/update/activation flows now perform binding
synchronization consistently, which adds binding-table writes at those
mutation points.
- This PR does not retroactively scan and heal every already-broken
historical agent row; it prevents and backfills through the covered
service flows.
> 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 Codex class model via `codex_local`
- Session model family: GPT-5 Codex
- Tool-assisted coding with shell, git, HTTP, and local test execution
- Reasoning mode: medium interactive tool-use workflow
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The `server/services/environments.ts` module lazily provisions a
managed Kubernetes sandbox environment for each company on first
heartbeat. Idempotency relies on `ensureKubernetesEnvironment` returning
the single managed row per company.
> - The `(company_id, driver)` unique index in the `environments` schema
is partial on `driver='local'` only, so two concurrent callers (e.g.
simultaneous first heartbeats from a freshly synced tenant) can both
insert a `driver='sandbox'` row before either sees the other.
> - The function tried to converge after the race by re-reading, picking
the oldest managed row as winner, and deleting the loser. Under
autocommit + read-committed, each post-insert SELECT is a fresh snapshot
— A may not see B's row, B may not see A's, so both pick their own and
neither deletes. Two rows survive.
> - The same race fired in CI as `expected 2 to be 1` at
`environment-service.test.ts:293`, gating multiple unrelated PRs on
retries.
> - This pull request encodes the operator-level invariant ("at most one
Paperclip-managed sandbox row per company") at the DB layer with a
partial unique index, then switches `ensureKubernetesEnvironment` to
`INSERT … ON CONFLICT DO NOTHING` keyed on that index. Losers re-read
the surviving row.
> - The benefit is the race is impossible by construction — no
application-side convergence loop, no test flake, and any future
`ensureXyzSandboxEnvironment` that sets `managedByPaperclip=true`
inherits the invariant for free.
## Linked Issues or Issue Description
Paperclip issue: PAPA-783 — implement managed-sandbox dedup fix (phase 2
of the approved plan on the parent flake-investigation issue).
This is the phase-2 fix for the flaky `environmentService > deduplicates
concurrent managed Kubernetes environment creation` test introduced by
`4ad94d0bd` (PR #7938). Failing CI runs since then on at least PRs
#7595, #8233, #8215, #8212. The plan was reviewed and approved on the
parent issue before implementation.
Closely related (not duplicates):
- PR #7938 — introduced the test and the in-process convergence loop
being replaced here.
- PR #7595, PR #8233, PR #8215, PR #8212 — downstream PRs affected by
the flake; one of them will be rebased onto this fix as the acceptance
gate.
## What Changed
- `packages/db/src/schema/environments.ts`: added
`environments_company_managed_sandbox_idx`, a partial unique index on
`(company_id) WHERE driver='sandbox' AND
(metadata->>'managedByPaperclip')::boolean = true`. The umbrella
`managedByPaperclip` predicate covers any current or future
Paperclip-managed sandbox flavor without needing a new index per
provider.
- `packages/db/src/migrations/0102_managed_sandbox_dedup_index.sql`:
one-shot dedup `DELETE` keeping the oldest managed-sandbox row per
`company_id` (scoped to `driver='sandbox' AND managedByPaperclip=true`),
`RAISE NOTICE` if any duplicates were removed, then `CREATE UNIQUE INDEX
IF NOT EXISTS environments_company_managed_sandbox_idx`. `CONCURRENTLY`
is omitted because the codebase's migration runner wraps each file in a
transaction (see `applyPendingMigrationsManually`); the table holds 1–3
rows per company, so the short lock is acceptable and consistent with
every other migration in the repo.
- `server/src/services/environments.ts`: `ensureKubernetesEnvironment`
now uses `INSERT … ON CONFLICT DO NOTHING` keyed on the new index. On
conflict it re-reads the surviving managed-sandbox row and returns it.
Drops the post-insert convergence (re-read by `createdAt ASC, id ASC`,
delete the loser) and the trailing comment that flagged "until a partial
unique index is added via migration" as the proper long-term fix.
- Unused `asc` import removed from
`server/src/services/environments.ts`.
## Verification
Local (matches the success criteria in the issue body):
```
$ cd server
$ passes=0; for i in $(seq 1 20); do
pnpm vitest run src/__tests__/environment-service.test.ts -t "deduplicates concurrent" \
&& passes=$((passes+1)) || break
done; echo "$passes/20"
20/20
$ passes=0; for i in $(seq 1 10); do
pnpm vitest run src/__tests__/environment-service.test.ts \
&& passes=$((passes+1)) || break
done; echo "$passes/10"
10/10
```
Adversarial fan-out stress (temporarily bumped `Array.from({ length: 8
}, …)` to `length: 32` on both dedup tests; reverted before commit):
```
$ # both dedup tests fan-out-of-32, 10 iterations
10/10
```
Two ensure paths exist in the parent plan, but only
`ensureKubernetesEnvironment` is on `master`.
`ensureManagedSandboxEnvironment` (referenced by the approved plan as
commit `dce9a9622`) lives only on an unmerged feature branch, not
master. The plan's helper-extraction and symmetric dedup test for that
path are deferred to whichever PR lands the second ensure path — it
inherits the same DB invariant by setting `managedByPaperclip=true`.
Discrepancy was flagged on the issue thread before implementation.
Typecheck:
```
$ pnpm -C server typecheck
ok
```
## Risks
Low risk.
- **Migration safety.** `IF NOT EXISTS` on the index makes the migration
idempotent. The dedup `DELETE` is bounded to rows matching the
managed-sandbox predicate; in production this should be a no-op (no race
has been reported in the wild — only in CI). On dev/CI DBs that already
accumulated duplicates, the migration emits a `NOTICE` reporting the
count.
- **No `CONCURRENTLY`.** The migration runner wraps each `.sql` file in
a transaction, which is incompatible with `CREATE INDEX CONCURRENTLY`.
The `environments` table holds 1–3 rows per company and the row count is
bounded by company count; the short ACCESS EXCLUSIVE during `CREATE
UNIQUE INDEX` is acceptable here and matches every other index migration
in the repo.
- **Predicate scope.** The partial index predicate matches exactly the
rows that `ensureKubernetesEnvironment` writes (`driver='sandbox'` with
`metadata.managedByPaperclip=true`). Tenant-created sandbox envs (via
`svc.create`) do not set this marker and are not covered — no false
positives, no surprise constraint violations on unrelated inserts.
## Model Used
Claude (Anthropic), `claude-opus-4-7`. Tool use: code edit + bash +
filesystem search; no extended-thinking mode.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [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>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies
> - The plugin subsystem persists state into four tables
(`plugin_entities`, `plugin_job_runs`, `plugin_logs`,
`plugin_webhook_deliveries`) and those rows currently have no notion of
an owning tenant — so company-deletion doesn't cascade plugin state, and
operators have no way to query "what does this plugin own for company
X?"
> - The fix is one thin slice of tenant-isolation hygiene that doesn't
change any external API: add a nullable `company_id` FK with `ON DELETE
CASCADE` to the four plugin tables, index it, and scope the
`plugin_entities` external-id uniqueness per-tenant
> - The benefit is plugin-row tenant attribution + cascade cleanup, with
zero impact on single-tenant local-first deploys (`NULL` continues to
mean instance-scope)
> **Rebase note (scope narrowed):** This PR originally also hardened the
schedulers (`heartbeat.tickTimers` / `resumeQueuedRuns` /
`enqueueWakeup` and `routines.tickScheduledTriggers`) to skip archived
companies. That half has since landed on `master` via #7478 (`93206f73`,
"Stop archived companies from waking agents") with a stricter
implementation (`status != 'active'` plus a skipped-request audit row).
On rebase those changes were dropped as redundant — `heartbeat.ts` and
`routines.ts` are now identical to `master`, and the scheduler-specific
tests were removed. **This PR is now DB-only.**
## Linked Issues or Issue Description
No existing issue covers this directly — problem described in-PR:
- Four plugin tables (`plugin_entities`, `plugin_job_runs`,
`plugin_logs`, `plugin_webhook_deliveries`) persist rows with no notion
of an owning tenant.
- Company deletion therefore does not cascade plugin state, and
operators have no way to query "what does this plugin own for company
X?"
- One thin slice of tenant-isolation hygiene fixes this without changing
any external API: a nullable `company_id` FK with `ON DELETE CASCADE`,
an index, and per-tenant scoping of the `plugin_entities` external-id
uniqueness.
- Part of the multi-tenant hardening initiative alongside #3967
(cross-tenant 404 oracle) and #5864 (per-company JWT keys).
## What Changed
**Schema (`packages/db/src/schema/plugin_*.ts`):**
- Nullable `companyId` FK with `onDelete: "cascade"` added to
`plugin_entities`, `plugin_job_runs`, `plugin_logs`,
`plugin_webhook_deliveries`.
- A btree index on each new `company_id` column (`<table>_company_idx`).
- `plugin_entities_external_idx` rescoped from `(plugin_id, entity_type,
external_id)` to `(company_id, plugin_id, entity_type, external_id)` and
switched to `UNIQUE … NULLS NOT DISTINCT` so instance-scope rows
(`company_id IS NULL`) keep their dedup guarantee while tenants get
their own namespace.
**Migration:**
- `0095_plugin_company_id_tenant_isolation.sql` — 14 statements: 4
column adds + 4 FK constraints (`ON DELETE CASCADE`) + 4 indexes +
drop/recreate of the external-id unique constraint.
- Journal entry + regenerated `0095_snapshot.json`.
**Tests:**
- `server/src/__tests__/plugin-tenant-isolation.test.ts` — `NULL`
preserves backward compat; `CASCADE` on company delete across all four
tables; per-tenant external-id namespacing; NULL-NULL collision rejected
(`NULLS NOT DISTINCT`).
## Verification
- `pnpm --filter @paperclipai/db run check:migrations` — pass.
- `pnpm --filter @paperclipai/db typecheck` (`tsc`) — pass.
- `vitest run plugin-tenant-isolation` — **4/4 pass** (embedded Postgres
applies `0095` and exercises cascade + NULLS NOT DISTINCT).
## Notes
- **Clean snapshot, no drift.** The earlier revision of this PR shipped
a ~17.6k-line meta snapshot that was almost entirely pre-existing drift.
On rebase the migration was renumbered (the old `0090_brainy_darkhawk`
collided with `master`'s `0090_resource_memberships … 0094`) and
regenerated from the current `master` baseline via `drizzle-kit
generate`. The result is a 14-statement migration containing **only**
the plugin-table changes — no unrelated drift.
- **Backward-compatible.** `NULL company_id` continues to mean
instance-scope (cron jobs, public webhooks). No new env vars, no API
surface change. Single-tenant local-first deploys unaffected.
## Risks
- **Migration is additive and nullable** — `0095` adds nullable
`company_id` columns, FK constraints, and indexes; existing rows stay
valid (`NULL` keeps meaning instance-scope) and no backfill is required.
- **`ON DELETE CASCADE` is a behavioral change**: deleting a company now
removes its plugin rows across all four tables. Intended (it is the
point of the PR), but operators relying on plugin rows surviving company
deletion would be affected. Covered by the cascade tests.
- **Uniqueness semantics change on `plugin_entities`**: the external-id
constraint is rescoped per-tenant and switched to `UNIQUE … NULLS NOT
DISTINCT`, so two instance-scope rows (`company_id IS NULL`) with the
same external id are now rejected instead of coexisting. Covered by the
NULL-NULL collision test.
- **No API surface change, no new env vars.** Single-tenant local-first
deploys unaffected.
(Section added retroactively to match the PR template; distilled from
the What Changed / Notes sections above.)
## Model Used
Same authoring setup as #5864 (same series, same day): Claude Opus 4.7
(1M context), extended thinking mode. (Section added retroactively.)
## Checklist
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] Tests run locally and pass (plugin-tenant-isolation 4/4)
- [x] `check:migrations` + db typecheck pass
- [x] No UI changes
- [x] Migration carries only the intended changes (no snapshot drift)
- [x] Scheduler half dropped as superseded by #7478
Part of the multi-tenant hardening initiative — see also #3967
(cross-tenant 404 oracle) and #5864 (per-company JWT keys).
---------
Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: Devin Foley <devin@paperclip.ing>
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - Agents increasingly depend on reusable skills, so the control plane
needs a first-class way to browse, inspect, install, version, and attach
those skills.
> - The old skills surface was mostly operational plumbing; it did not
give operators a store-like discovery flow, canonical detail URLs, rich
source/version context, or creation paths.
> - The backend also needed stronger contracts around company skill
metadata, versions, install counts, runtime materialization, and adapter
skill preferences.
> - This pull request builds the Skills Store foundation across DB,
shared contracts, server routes/services, UI, and Storybook.
> - The benefit is a more inspectable, operator-friendly skill workflow
that still preserves company-scoped control-plane boundaries and agent
runtime behavior.
## Linked Issues or Issue Description
No GitHub issue exists for this Paperclip work item. Paperclip task
refs: PAP-10846 and PAP-10921.
Feature request:
Paperclip operators need a single Skills Store experience where company
skills can be discovered, inspected, created, versioned, installed, and
attached to agents without relying on scattered operational screens or
implicit runtime state.
Related PR search:
- Searched GitHub for `Skills Store`, `company skills`, and `skill
detail`.
- Found several open skills-related PRs such as #7809 and #4409, but no
duplicate PR for this end-to-end Skills Store branch.
## What Changed
- Added the Skills Store backend foundation: company skill schema
fields, migrations, shared types/validators, and expanded server skill
routes/services.
- Added skill discovery, category navigation, canonical skill detail
routes, tabs, source attribution, version snapshots/diffs, install count
backfill, and creation flows.
- Updated agent skill preference handling so version selections survive
runtime mention injection and runtime skill materialization honors
pinned versions.
- Preserved unversioned skill assignments as live/current selections
instead of silently pinning them to the current version at assignment
time.
- Added focused regression coverage for company skill routes/services,
route helpers, UI behavior, skill version diffs, and runtime skill
version pins.
- Added Storybook coverage for Skills Store discovery/detail states and
updated the main layout navigation.
- Addressed Greptile findings around version creation races,
soft-deleted comments, fork metadata scoping, GitHub skill directory
fallback, runtime snapshot materialization, shared runtime
skill-selection helpers, and version-assignment semantics.
## Verification
- `pnpm exec vitest run
server/src/__tests__/heartbeat-project-env.test.ts
server/src/__tests__/heartbeat-runtime-skills.test.ts`
- `pnpm exec vitest run
packages/shared/src/validators/company-skill.test.ts`
- `pnpm exec vitest run server/src/__tests__/company-portability.test.ts
server/src/__tests__/company-skills-service.test.ts`
- `pnpm exec vitest run
cli/src/__tests__/company-import-export-e2e.test.ts`
- `pnpm exec vitest run
server/src/__tests__/agent-skills-routes.test.ts`
- `pnpm exec vitest run server/src/__tests__/openapi-routes.test.ts`
- `pnpm exec vitest run
server/src/__tests__/company-skills-service.test.ts
server/src/__tests__/company-skills-routes.test.ts
server/src/__tests__/heartbeat-runtime-skills.test.ts`
- `pnpm exec vitest run
server/src/__tests__/company-skills-service.test.ts`
- `pnpm exec vitest run ui/src/components/IssueProperties.test.tsx -t
"edits existing custom assignee model options from the properties pane"`
- `pnpm --filter @paperclipai/server typecheck`
- GitHub checks are green on `0823957a2`: Build, Canary Dry Run, General
tests, Typecheck + Release Registry, serialized server suites, e2e,
policy/review, Socket, Snyk, and aggregate `verify`.
- Greptile Review succeeded on `0823957a2` with `40 files reviewed, 0
comments added`; GitHub unresolved review threads: 0.
Not run in this heartbeat:
- Browser screenshot capture for the UI changes. This PR intentionally
omits screenshots per the Paperclip task direction not to add design
screenshots/images.
## Risks
- Broad feature branch touching DB, shared contracts, server, and UI;
reviewers should still scan merge conflicts carefully if `master` moves
again before landing.
- Skill version/runtime behavior is sensitive: pinned skill versions
must stay pinned while default selections should continue following the
current version.
- UI polish should get normal reviewer/browser attention before merge
because this PR includes a large Skills Store surface and screenshots
were intentionally omitted.
> 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 with tool use and local command
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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots (intentionally omitted per PAP-10921 direction)
- [ ] 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>
## Thinking Path
> - Paperclip's `claude_local` adapter persists Claude Code session
jsonls under `~/.claude/projects/…/{sessionId}.jsonl` and resumes them
on the next heartbeat
> - When Claude Code injects `<synthetic>` placeholder assistant
messages (after rate-limit, max-turn exhaustion, or transient-upstream
failures) those placeholders get UUID-format `message.id`s rather than
`msg_…`-format ids
> - On the next `--resume`, Claude Code passes that UUID as
`previous_message_id` and Anthropic's API rejects it with a 400:
``diagnostics.previous_message_id: must be the `id` from a prior
/v1/messages response (starts with `msg_`)``
> - The adapter had a session-rotation fallback only for "unknown
session" errors, so the poisoned session was `--resume`-d indefinitely
and the agent flipped between `idle` and `error` every heartbeat
> - Even worse, the *result* event of the failing run still carried a
`session_id`, and the adapter was persisting that id into the
issue-scoped session store (`agentTaskSessions`). So even after we
detected the 400, every subsequent continuation re-loaded the same
poisoned id and hit the same 400 again — the issue was permanently
stranded
> - We observed this on multiple agents in our deployment; the only
manual fix was to rename the `.jsonl`, which is not a viable long-term
workaround
> - This PR detects the 400, runs the same session-rotation fallback the
unknown-session path uses **and** stops persisting the poisoned id, so
the next attempt starts genuinely fresh
## Linked Issues or Issue Description
No external GitHub issue is linked. Describing the problem inline
following the bug-report template:
**What happened:** `claude_local` agents flipped between `idle` and
`error` on every heartbeat because the persisted session jsonl carried a
synthetic UUID `previous_message_id` (from `<synthetic>` assistant
placeholders injected after rate-limit/max-turn/upstream errors).
Anthropic's API rejected every `--resume` with a 400:
``diagnostics.previous_message_id: must be the `id` from a prior
/v1/messages response (starts with `msg_`)``.
**Expected behavior:** When the persisted session is poisoned and
unrecoverable, the adapter should rotate to a fresh session — the same
fallback path already used for unknown-session errors — and stop
re-persisting the poisoned `session_id`.
**Actual behavior:** The session-rotation fallback only matched the
"unknown session" pattern, so the poisoned session was `--resume`-d
forever. The result event of the failing run still carried `session_id`,
which was being persisted into `agentTaskSessions`, so every subsequent
continuation reloaded the same poisoned id and hit the same 400.
**Reproduction:** Inject any flow that causes Claude Code to emit a
`<synthetic>` placeholder (rate-limit, max-turn exhaustion, transient
upstream failure). The next `--resume` will fail with the 400 and the
agent will not self-recover.
**Scope of fix:** Add a `previous_message_id` 400 detector; route it
through the existing unknown-session fallback; drop the poisoned
`sessionId` and emit `clearSession: true` so the heartbeat service wipes
the persisted row; best-effort delete the local poisoned `.jsonl`.
## What Changed
Two commits:
1. **`adapter-claude-local: auto-rotate session on previous_message_id
400 (synthetic-msg poisoning)`** — detector + execute-time rotation
2. **`adapter-claude-local: guard against persisting poisoned
sessionId`** — validate-before-persist + `clearSession`
Combined diff:
- `parse.ts`: new `isClaudePoisonedPreviousMessageIdError(parsed)`
matching ``/diagnostics\.previous_message_id.*starts with `msg_`/i``
against `parsed.result` and `extractClaudeErrorMessages(parsed)`
- `parse.ts`: `isClaudeTransientUpstreamError()` excludes the new error
from transient classification so it isn't masked as retryable upstream
noise
- `execute.ts`: expand the resume-fallback branch so it triggers on both
`isClaudeUnknownSessionError` and the new
`isClaudePoisonedPreviousMessageIdError`, with a distinct log line
(`"returned a poisoned message-id"` vs `"is unavailable"`)
- `execute.ts`: for local (non-remote) execution targets, best-effort
delete the poisoned `~/.claude/projects/.../{sessionId}.jsonl` before
retrying so the file can't be accidentally resumed by an out-of-band
caller. The `fs.unlink` and follow-up log call are in separate try/catch
blocks so a closed log stream cannot mask a successful unlink (and vice
versa)
- `execute.ts` / `toAdapterResult`: when a result carries the poisoned
400, **drop** `sessionId`/`sessionParams`/`sessionDisplayId` (return
`null`) and emit `clearSession: true` so the heartbeat service's
`resolveNextSessionState` wipes the persisted row. The result also
surfaces `errorCode: "claude_poisoned_previous_message_id"` for
observability
- `docs/adapters/claude-local.md`: runbook entry — symptom,
auto-recovery flow, on-call checklist
- Tests:
- 4 new `parse.test.ts` cases covering positive detection in `result`
and `errors[]`, negative cases, and non-transient classification
- 3 new `claude-local-execute.test.ts` cases: (a) fresh run reports the
poisoned error → sessionId dropped + `clearSession: true`; (b) recovery
retry also reports the poisoned error → same guards apply; (c)
session-rotation success on retry
## Verification
```bash
pnpm --filter @paperclipai/adapter-claude-local exec vitest run src/server/parse.test.ts
pnpm --filter @paperclipai/server exec vitest run src/__tests__/claude-local-execute.test.ts
```
Both suites green locally. This patch is also currently running as a
hot-patch over the published `2026.513.0` adapter on the reporting
deployment — sessions that previously looped indefinitely now
self-recover on the first heartbeat after the 400 surfaces.
## Risks
- Low risk. The detector is conservative (regex over `result` +
`errors[]` only) and the rotation reuses the existing unknown-session
fallback path
- The local-only `fs.unlink` of the poisoned `.jsonl` is wrapped in
`try/catch` and ignored on failure — strictly an optimization; the
server-side session clear is the authoritative reset
- Remote execution targets (`executionTargetIsRemote`) skip the disk
cleanup because the file lives on a remote host that we can't safely
reach from the adapter
- The `clearSession: true` + nulled session fields path is a no-op on
healthy runs; it only fires when the new detector matches, so existing
successful continuations are unaffected
- No DB schema changes, no public API changes, no new dependencies
## Model Used
- Provider: Anthropic Claude
- Model: `claude-opus-4-7` (Opus 4.7)
- Context window: 1M
- Capabilities: extended reasoning, tool use, code execution
- Role: implemented the detector, expanded the fallback branch, added
the persist-guard + `clearSession`, wrote the unit + integration tests,
validated locally, and applied the equivalent hot-patch to the deployed
`2026.513.0` install while this PR is in review
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for similar or duplicate PRs and linked
them — closed#2295, #2361, #3572, #5438 as duplicates of this canonical
fix; complementary fixes#4838 (heartbeat_timer reset) and #4932 (gemini
context-overflow rotation) target different code paths
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots — N/A, adapter-only change
- [x] I have updated relevant documentation
(`docs/adapters/claude-local.md` runbook entry)
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Danial Jawaid <danial.jawaid@gmail.com>
Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Devin Foley <devin@paperclip.ing>
Bumps [drizzle-kit](https://github.com/drizzle-team/drizzle-orm) from
0.31.9 to 0.31.10.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/drizzle-team/drizzle-orm/releases">drizzle-kit's
releases</a>.</em></p>
<blockquote>
<h2>drizzle-kit@0.31.10</h2>
<ul>
<li>Updated to <code>hanji@0.0.8</code> - native bun
<code>stringWidth</code>, <code>stripANSI</code> support, errors for
non-TTY environments</li>
<li>We've migrated away from <code>esbuild-register</code> to
<code>tsx</code> loader, it will now allow to use
<code>drizzle-kit</code> seamlessly with both <code>ESM</code> and
<code>CJS</code> modules</li>
<li>We've also added native <code>Bun</code> and <code>Deno</code>
launch support, which will not trigger <code>tsx</code> loader and
utilise native <code>bun</code> and <code>deno</code> imports
capabilities and faster startup times</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="4aa6ecfee4"><code>4aa6ecf</code></a>
Kit updates (<a
href="https://redirect.github.com/drizzle-team/drizzle-orm/issues/5490">#5490</a>)</li>
<li>See full diff in <a
href="https://github.com/drizzle-team/drizzle-orm/compare/drizzle-kit@0.31.9...drizzle-kit@0.31.10">compare
view</a></li>
</ul>
</details>
<br />
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The board UI is the control surface for issues, projects, agents,
goals, workspaces, and operator settings.
> - The existing navigation and list surfaces make several
high-frequency workflows feel harder to scan than they should,
especially around projects and agents.
> - The product direction is to improve those surfaces without breaking
the existing route model or forcing a new IA on every operator at once.
> - This pull request now keeps the dependent IA, project identity, and
agent-list visual refresh work together while the Issue-to-Task copy
migration is split into #7651.
> - The benefit is a clearer left nav, better project identity, denser
agent/project list rows, and brand-aligned status treatment while
preserving the classic default experience behind a flag.
## Linked Issues or Issue Description
Refs #7645
Refs #7651
Internal planning/work references: PAP-53, PAP-56, PAP-58, PAP-59,
PAP-60, PAP-61, PAP-68, PAP-69, PAP-70, PAP-71, PAP-72, PAP-75, PAP-76,
PAP-80, PAP-85, PAP-86, PAP-87, PAP-88, PAP-89.
## What Changed
- Adds `enableStreamlinedLeftNavigation`, defaulting off, and gates
sidebar presentation so classic navigation remains the default.
- Adds project icon persistence, validation, portability, picker UI, and
`ProjectTile` rendering while defaulting new projects to neutral gray.
- Adds projects-list task-count and budget summary data with focused
server/shared/UI coverage.
- Refreshes agent list rows, row actions, active/recent sidebar
behavior, and status capsule/chip styling for the approved brand state
system.
- Removes the placeholder Conference room and Artifacts nav/routes from
the finalized experimental nav direction.
- Removes `pnpm-lock.yaml` and the Issue-to-Task copy migration from
this PR diff; the copy migration now lives in #7651.
## Verification
- Existing branch verification from the authored commits: UI typecheck,
targeted unit tests, and light/dark visual checks for `/agents`, agent
detail, and design-guide status states.
- Maintainer cleanup verification on `75e34e5`: `git diff --check
origin/master...HEAD` passed, the `design/` diff is empty, and the PR
diff is 61 files, below Greptile's 100-file review limit.
- `pnpm --filter @paperclipai/ui build` passed.
- `NODE_ENV=test pnpm exec vitest run
ui/src/components/Sidebar.test.tsx` passed: 1 file, 8 tests.
- CI and Greptile should rerun on the latest push.
## Risks
- Broad UI surface area: the experimental flag keeps the classic nav
default, but changed shared components such as `EntityRow`,
`ProjectTile`, and agent status badges could affect multiple pages.
- Database migration: `projects.icon` is additive and nullable, but
migration ordering and portability import/export must stay aligned.
- The Issue-to-Task copy migration is now separated into #7651, so
reviewers should evaluate this PR as IA/project/agent presentation work
only.
- Visual regressions are possible across smaller widths because the PR
intentionally changes dense list-row layouts.
## Model Used
Claude Opus 4.8 assisted the original feature commits.
Paperclip-Paperclip agents assisted some planning/design commits. Codex
/ GPT-5-class coding agent with shell, GitHub CLI, and repository access
performed this PR-readiness cleanup and split.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [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>
Co-authored-by: Dotta <bippadotta@protonmail.com>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies
> - Test infrastructure across server, ui, packages/* runs on Vitest
> - Dependabot opened a narrow bump (3.2.4 → 3.2.6), but the wider
workspace is on 3.2.4 and the major-version bridge to v4 needs a
coordinated change set across configs and tests
> - Staying on 3.x indefinitely leaves us behind on Vitest 4 (perf,
pool, and config improvements) and forces repeated patch-only dependabot
churn
> - This pull request upgrades Vitest to 4.1.8 across the workspace,
updates `server/vitest.config.ts` and `scripts/run-vitest-stable.mjs`
for the new API, and adjusts two UI tests for the new assertion
semantics
> - The benefit is a single, coherent Vitest 4 upgrade that supersedes
#7570 and gets us on the supported major line
## What Changed
- Bump `vitest` from `3.2.4` to `4.1.8` across root, `server`, `ui`, and
all `packages/*` (including plugin examples and sandbox providers)
- Update `server/vitest.config.ts` for Vitest 4 config surface
- Update `scripts/run-vitest-stable.mjs` to match the new runner
behavior
- Adjust `ui/src/components/CommentThread.test.tsx` and
`ui/src/components/MarkdownEditor.test.tsx` for Vitest 4 matcher/timing
semantics
- Refresh `pnpm-lock.yaml`
## Verification
- `pnpm install` resolves cleanly with the new lockfile
- `pnpm -w -r test` (server, ui, packages) runs under Vitest 4.1.8
## Risks
- Major-version Vitest bump: behavioral changes in pools, fake timers,
and matcher strictness can surface flake. Test config and the two UI
tests were updated to match v4 semantics; broader test runs should be
watched on CI before merge.
- Supersedes dependabot PR #7570 (3.2.4 → 3.2.6); that PR should be
closed.
## Model Used
- Claude (Anthropic) — `claude-opus-4-7`, extended thinking, tool use
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
- [ ] I have run tests locally and they pass
- [ ] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots
- [ ] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
Closes#7570
## Thinking Path
> - Paperclip is a control plane for AI-agent companies, so execution
policy and trust boundaries are part of the product's safety contract.
> - Low-trust review work needs narrower authority than normal
same-company agents because hostile PRs, comments, attachments, and
generated output can carry prompt-injection payloads.
> - The current V1 shape gives trusted workers broad company context,
which is useful for normal execution but too permissive for a reviewer
assigned to hostile content.
> - This branch adds a `low_trust_review` preset, source-trust tagging,
route-level containment, and quarantine handling so low-trust output
does not automatically flow into higher-trust wake context.
> - The branch has been rebased onto current `origin/master`, and the
low-trust migration was renumbered to `0097_low_trust_source_trust.sql`
to avoid collisions with existing `0091` through `0096` migrations.
> - Greptile feedback was addressed by tightening low-trust detection,
preserving project-level trust policy checks, fixing issue-kind
promotion lookup, removing duplicate post-lease isolation assertion,
documenting fail-closed source-trust behavior, bounding ancestry checks,
enforcing runtime issue context for CEOs, awaiting accepted-plan monitor
authorization, and making low-trust issue source-trust tagging atomic.
> - The benefit is a first production slice of deny-by-default review
containment with regression coverage for the main control-plane pivot
surfaces.
Fixes#7531.
## What Changed
- Added shared trust-policy types and validators, plus
database/source-trust fields for issues, comments, documents, and work
products.
- Implemented server enforcement for low-trust issue scope, agent
self-view redaction, secret/plugin/runtime denial paths, promotion
checks, and quarantined continuation/wake context.
- Added focused low-trust regression tests for resolver behavior, source
trust, route authorization, heartbeat preflight ordering, runtime
containment, and quarantine redaction.
- Added board UI affordances for selecting/reviewing the low-trust
preset and surfacing source-trust badges in relevant issue views.
- Added `doc/LOW-TRUST-PRESETS.md`, updated
`doc/SPEC-implementation.md`, and committed the low-trust review
contract plan under `doc/plans/`.
- Rebasing note: the original `0097_low_trust_source_trust.sql`
migration was renamed to `0097_low_trust_source_trust.sql`; the SQL uses
`ADD COLUMN IF NOT EXISTS` so users who already applied the old-numbered
migration are not broken by the renumbered migration.
## Verification
- Rebased branch onto current `origin/master` and force-pushed with
lease to `origin/PAP-10211-low-trust-agent` at head `2719f31e3`.
- Confirmed the PR diff does not include `pnpm-lock.yaml` or
`.github/workflows` changes.
- Resolved upstream UI/comment conflicts by preserving deleted-comment
tombstone behavior and low-trust source-trust badges/metadata.
- Renumbered the low-trust source-trust migration to
`0097_low_trust_source_trust.sql`; the SQL uses `ADD COLUMN IF NOT
EXISTS` so users who already applied an old-numbered copy are not
broken.
- `pnpm exec vitest run ui/src/lib/issue-chat-messages.test.ts
server/src/__tests__/heartbeat-workspace-session.test.ts`
- `pnpm exec vitest run server/src/__tests__/source-trust.test.ts
server/src/__tests__/workspace-runtime-service-authz.test.ts
ui/src/lib/trust-policy-ui.test.ts
ui/src/components/TrustPresetSection.test.tsx`
- `pnpm run typecheck:build-gaps`
- `git diff --check`
- GitHub checks pass on head `2719f31e3`: build, typecheck/release
registry, general tests, serialized server suites, e2e, canary, verify,
policy/review, Socket, and Snyk.
- Greptile Review passes with Confidence Score 5/5 and zero unresolved
Greptile review threads.
- No design screenshots/images were added because the task explicitly
says not to add them unless they are specifically part of the work.
## Risks
- Medium risk: this touches shared trust-policy contracts, server
authorization paths, heartbeat context generation, migration metadata,
and UI preset controls.
- Low-trust containment is intentionally deny-by-default; legitimate
future review workflows may need explicit allowlisted exceptions.
- Plugin/runtime/security surfaces are broad, so regression tests cover
the current known routes but future integrations must route through the
same containment layer.
- The PR is ready for review; GitHub checks are green and Greptile is
5/5.
> 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 coding agent, tool-enabled shell and GitHub CLI
workflow.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] UI changes are covered by focused tests; no screenshots were added
per task instruction not to add design images unless specifically
required
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies
> - Each agent has a heartbeat scheduler that wakes it on timers and on
events; every wake spawns an adapter (Claude / Codex / …) run that bills
the operator's subscription
> - When an operator archives a company, the agents inside it remain in
invokable states — the heartbeat scheduler never consults company status
— so timers keep firing and event-driven wakes (comments, mentions,
blockers-resolved, etc.) keep cascading
> - On real deployments this silently drains the operator's
subscription: idle archived companies wake their CEOs hourly, plus any
cross-company event cascade
> - This pull request enforces "archived ⇒ never spawns a run" as a
structural invariant by guarding the wake path AND cascading agent state
on archive/reactivate
> - The benefit is that archived companies stop billing the operator,
and the UI/queue stays consistent with the invariant
## What Changed
- `server/src/services/heartbeat.ts`:
- `enqueueWakeup()` loads the company and short-circuits when status is
not `active`. Background sources (timer, automation, events) write a
`company.inactive` skipped wake and return `null`; explicit user invokes
throw a `conflict` so the UI surfaces the real reason.
- `tickTimers()` joins agents to active companies so the scheduler does
not iterate archived-company agents at all (no skip-row noise).
- `server/src/services/companies.ts`:
- `archive(id, actor?)` pauses runnable agents with `pauseReason =
"company_archived"` inside the transaction (preserving
`pending_approval`, `terminated`, and agents paused for unrelated
reasons), then cancels `queued`/`running` heartbeat runs after the
transaction commits.
- `update(id, data, actor?)` reverses the cascade only for agents whose
`pauseReason === "company_archived"` on the `archived → active`
transition; manually-paused agents stay paused.
- Both methods emit activity-log entries (`company.archived` with
`agentsPaused` + `runsCancelled`, `company.reactivated` with
`agentsRestored`) so the audit trail fires regardless of caller.
- `packages/shared/src/constants.ts` + `server/src/services/budgets.ts`:
add `company_archived` to the legal `PauseReason` union so the
restorable marker is a first-class value.
-
`packages/db/src/migrations/0094_backfill_archived_company_agent_pauses.sql`:
backfill so existing archived-company agents become `paused /
company_archived` (excludes `pending_approval`).
- `ui/src/lib/activity-format.ts`: add the `company.reactivated` label.
## Verification
- `npx vitest run src/__tests__/companies-service.test.ts` — archive
cascade, reactivate cascade, and activity-log entries (with counts) all
pass.
- `npx vitest run
src/__tests__/heartbeat-archived-company-guard.test.ts` — timer +
on-demand + event-wake paths all blocked for archived companies;
`company.inactive` skipped-wake row written; user-initiated wakes throw
`conflict`.
- `pnpm typecheck` — clean.
- Manual repro from the bug description: archive a company, wait an
interval / post a comment on one of its issues, observe zero new
heartbeat runs.
## Risks
- Migration `0094` is a single bulk UPDATE on `agents` joined to
archived `companies`. On large deployments it briefly holds row locks on
archived-company agent rows; should be quick because the predicate is
narrow (`status NOT IN (paused, terminated, pending_approval)` and
`companies.status = 'archived'`).
- New `pauseReason` value (`company_archived`) is opaque to older
clients that only know the previous union. Acceptable because the union
is read as plain text and the contract is sync'd in the same change.
- Behavior change for users: invoking an agent in an archived company
now fails with a conflict instead of silently spawning a run. Intended.
## Model Used
- Claude (Anthropic) — model `claude-opus-4-7` ("Opus 4.7"), Claude Code
CLI, with tool use (Read/Edit/Bash/Grep). No extended thinking mode.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots — N/A, no UI changes beyond an activity-log label string
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
## Related Work
Fixes#1348 (`[Bug] Archived companies still running heartbeats and
consuming tokens`).
Prior attempts and parallel work in this area:
- #1365 and #1429 by @hungdqdesign (March 2026) — both closed without
merging. Same three-layer shape (`tickTimers` / `enqueueWakeup` /
`resumeQueuedRuns` + archive-route cancellation) targeting #1348. Credit
for first publicly proposing the wake-path-guard approach.
- #5865 by @stubbi (May 2026, open) — adds the same `companies.status !=
'archived'` joins to `tickTimers`, `enqueueWakeup`, `resumeQueuedRuns`,
**and** routines `tickScheduledTriggers`, bundled with plugin-table
tenant isolation (`plugin_entities` / `plugin_job_runs` / `plugin_logs`
/ `plugin_webhook_deliveries` get a `companyId` FK with `ON DELETE
CASCADE`). This PR is narrower — it does not touch routines or plugin
tables — but adds the **archive cascade** (pause agents with
`pauseReason = "company_archived"`), the **reactivate reverse**
(un-pause only that subset), the **`company_archived` pause-reason
marker**, and a **backfill migration** for pre-existing archived
companies, which #5865 does not include. Happy to coordinate sequencing
or rebase if #5865 lands first.
## Thinking Path
> - Paperclip orchestrates AI agents across isolated execution
workspaces; the local cwd is the only persistence boundary between runs.
> - Workspace lifecycle (worktree_prepare → execute →
workspace_finalize) and the wake/accept flow are what guarantee that
dependent issues see a consistent worktree.
> - PAPA-380 / PAPA-431 / PAPA-432 / PAPA-440 surfaced three holes in
that contract: silent env reuse across assignees, dependent wakes firing
before finalize, and `issue.interaction.accept` advancing before
finalize landed.
> - PAPA-441 / PAPA-442 then needed to document the "no remote git"
contract and prevent future adapter/runtime code from quietly
reintroducing `git push` as a backdoor sync.
> - This pull request lands those server fixes, the static
`check-no-git-push` enforcement, the AUTHORING.md cross-link, and the
Cody-review follow-ups on the PAPA-430 thread.
> - The benefit is that finalize is a real barrier — board accepts,
dependent wakes, and operator-set env all respect it — and adapter code
can't bypass it via raw `git push`.
## What Changed
- **server (PAPA-380, PAPA-431):** `execution-workspace-policy` refuses
silent env reuse when the assignee's resolved env disagrees with the
workspace it would inherit. The inheritance protection is now scoped to
the actual inheritance signal — explicit issue-level `environmentId` is
honored even when the agent's default env is `null`.
- **server (PAPA-432):** `heartbeat.ts` gates dependent wakes on
`listUnfinalizedExecutionWorkspaceIds`, and writes a
`workspace_finalize` row on the succeeded path. Write failures now
surface instead of being swallowed so dependents aren't silently
stranded behind a missing row.
- **server (PAPA-440):** `issue-thread-interactions.acceptInteraction`
adds a workspace_finalize precondition for `request_confirmation` (not
`suggest_tasks`). Accept returns 409 if finalize hasn't succeeded for
the latest workspace operation.
- **ci (PAPA-442):** new `scripts/check-no-git-push.mjs` static check
scans `packages/adapters/`, `packages/adapter-utils/`, `server/src/`,
and `cli/src/` for any `git push` invocation (string or args-array).
Wired into the `policy` PR job and `test:release-registry`. Operators
can opt in per-call with `// paperclip:allow-git-push: <reason>`.
Release scripts are out of scope by design.
- **docs (PAPA-441):** `AUTHORING.md` documents the no-remote-git
contract and cross-links the static check so adapter authors learn the
rule and the enforcement together.
- **review follow-up (PAPA-430, Cody):** three fixes — env resolver bug,
accept-gate scope (request_confirmation only), and finalize record write
on the succeeded path.
## Verification
- `pnpm exec vitest run
server/src/__tests__/execution-workspace-policy.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts` → 33/33
pass
- `node scripts/check-no-git-push.test.mjs` → check covers string form,
args-array form, comment exclusions, and per-line allow-comment.
- Manual: server compiles; the policy job runs the check in <1s before
heavier jobs.
## Risks
- **Behavioral shift in accept:** boards accepting
`request_confirmation` while finalize is in-flight now get 409s. This is
intentional — they can retry — but it changes timing on a hot path.
`suggest_tasks` is unaffected.
- **Workspace policy:** the env-reuse refusal is a new error path.
Issues that previously silently reused an env from a different-assignee
workspace will now fail-loud; the resolver still honors explicit
issue-level `executionWorkspaceSettings.environmentId`.
- **CI rule:** any future legitimate `git push` in scoped dirs must be
marked with the allow-comment, which is the intended ergonomic.
## Model Used
- Claude Opus 4.7 (`claude-opus-4-7`, extended thinking), via Claude
Code in the Paperclip executor adapter.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots (N/A — server/CI/docs only)
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
Closes related issues: PAPA-430, PAPA-380, PAPA-431, PAPA-432, PAPA-440,
PAPA-441, PAPA-442
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies, so
planning approvals and child-issue fan-out are part of the core
control-plane loop.
> - Accepted plans are supposed to be a safe bridge from planning into
execution, especially when agents wake from review decisions and reuse
isolated workspaces.
> - The duplicate-subtask incident showed that an accepted plan revision
could be interpreted more than once across overlapping runs, which broke
the single-source-of-truth model for issue decomposition.
> - Fixing that required tightening the backend contract first:
accepted-plan decomposition needs an exact-once fingerprint, durable
claim state, and retry-safe child creation.
> - Once that backend behavior existed, the board still needed
visibility into what happened, so the issue detail view needed a
dedicated decomposition section instead of forcing operators to
reconstruct child creation from raw activity.
> - This pull request adds the exact-once decomposition primitive,
hardens wake routing and regressions around the incident, and surfaces
decomposition state in the UI so future incidents are both prevented and
easier to inspect.
## What Changed
- Added accepted-plan decomposition semantics to
`doc/execution-semantics.md`, including the exact-once fingerprint,
durable claim/result expectations, and retry/resume behavior.
- Added persistent accepted-plan decomposition claims in the backend,
including schema, shared types/validators, service logic, and issue
routes for creating and listing decomposition state.
- Hardened heartbeat routing so an accepted-plan continuation stays
scoped to the relevant planning issue instead of opportunistically
re-decomposing another accepted issue on the same assignee.
- Added regression coverage for the original failure modes: concurrent
same-parent retries, cross-issue accepted-plan isolation, and partial
child recreation under the same fingerprint.
- Added the `Plan decomposition` issue-detail section plus supporting
API/query-key/activity formatting updates so operators can see revision
status, owner, child counts, and the linked child issues directly in the
UI.
- Included the small follow-up UI fix so the decomposition section still
renders when the issue work mode is no longer `planning`.
## Verification
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm --filter @paperclipai/ui typecheck`
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm exec vitest run server/src/__tests__/issues-service.test.ts`
- `pnpm exec vitest run server/src/__tests__/issues-service.test.ts -t
"lists persisted decompositions with child issue summaries"`
- `pnpm exec vitest run server/src/__tests__/issues-service.test.ts -t
"accepted plan decomposition"
server/src/__tests__/heartbeat-accepted-plan-workspace-refresh.test.ts
server/src/__tests__/heartbeat-context-summary.test.ts`
- Manual UI path: create a planning issue without an isolated execution
workspace, add a `plan` document, accept the `request_confirmation`, let
Paperclip create child issues, then reopen the parent issue detail page
and confirm the `Plan decomposition` section shows the accepted
revision, status, idempotent-claim badge, and child links.
- Separate follow-up bug noted during manual UI validation: accepting a
plan on an issue whose run never records `workspace_finalize` is tracked
in `PAPA-445` and is not part of this PR’s fix scope.
## Risks
- This adds a new migration and a large Drizzle snapshot update;
reviewers should confirm the schema shape and generated metadata match
the intended decomposition table.
- The exact-once claim changes sit on the accepted-plan fan-out path, so
regressions there could block legitimate child creation or mis-handle
retries if the claim state machine is wrong.
- The new UI only appears when decomposition records exist; reviewers
should use the manual verification path above rather than expecting
existing issues on a stale local instance to show the section
automatically.
- `PAPA-445` remains an open follow-up for the `workspace_finalize`
accept gate when a planning handoff never records finalize; that bug can
interfere with reproducing the UI flow on isolated workspaces but does
not change the correctness of the exact-once decomposition feature
itself.
> Checked `ROADMAP.md`: this PR is a bug fix / control-plane hardening
change for accepted-plan decomposition, not a new uncoordinated roadmap
feature.
## Model Used
- OpenAI Codex via Paperclip `codex_local` (GPT-5-based coding agent;
exact backend model ID/context window not exposed in the run context),
with repository tool use, shell execution, and code-editing
capabilities.
<img width="806" height="1069" alt="Screenshot 2026-05-27 at 11 05
48 PM"
src="https://github.com/user-attachments/assets/5b00b670-96cd-4470-b0a3-581743bcae28"
/>
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI-agent companies through issues, documents,
runs, and durable company-scoped state.
> - Issue documents are where agents and operators capture plans,
handoffs, and work products.
> - Before this change, document collaboration could only happen through
whole-document edits and detached issue comments.
> - Inline document annotations need stable anchors, revision-aware
persistence, and UI affordances that do not break existing document
editing.
> - This pull request adds company-scoped document annotation threads,
comments, anchor snapshots, API routes, and board UI.
> - The benefit is that operators and agents can discuss specific
document passages without losing context as documents evolve.
## What Changed
- Added document annotation tables, schema exports, shared types,
validators, anchor hashing, and text-anchor helpers.
- Added server-side document annotation services and issue routes for
listing, creating, commenting, resolving, and reopening annotation
threads.
- Included annotation summaries in relevant issue document reads and
backup/recovery document workspace behavior.
- Added React UI for inline document highlights, comment panels, mobile
sheet behavior, deep-link focus, and resolved/open filtering.
- Added annotation design artifacts, Storybook coverage, screenshots,
and a screenshot helper script.
- Rebased the branch onto current `paperclipai/paperclip` `master` and
renumbered the annotation migration from `0085_old_swarm` to
`0091_old_swarm`; the SQL uses `IF NOT EXISTS` guards so environments
that previously applied the old migration number can safely apply the
new one.
- Adjusted the new annotation UI tests to use a local async flush helper
because this workspace's React 19.2.4 export does not expose
`React.act`.
## Verification
- `pnpm run preflight:workspace-links && pnpm exec vitest run
packages/shared/src/document-anchors.test.ts
server/src/__tests__/document-annotation-routes.test.ts
server/src/__tests__/document-annotations-service.test.ts
ui/src/components/DocumentAnnotationLayer.test.tsx
ui/src/components/IssueDocumentAnnotations.test.tsx
ui/src/lib/document-annotation-hash.test.ts
ui/src/lib/document-annotation-selection.test.ts`
- Confirmed `git diff --check` passes.
- Confirmed no `pnpm-lock.yaml` or `.github/workflows/*` files are
included in the PR diff.
## Risks
- Medium risk: this adds new persisted annotation tables and routes
across db/shared/server/ui.
- Migration risk is reduced by moving the branch migration to
`0091_old_swarm` after upstream `0090_resource_memberships` and keeping
the SQL idempotent for old `0085_old_swarm` adopters.
- UI risk is mostly around text range anchoring and panel positioning
across long documents, folded content, and mobile layouts; the PR
includes focused unit coverage and design screenshots.
> 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 coding agent, tool-using software engineering
mode. Context window size is not exposed in this Paperclip runtime.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI-agent companies through company-scoped
issues, projects, agents, and board-visible workflows.
> - The board sidebar and project list are the daily navigation surface
for that control plane.
> - Users need to keep all projects and agents accessible while hiding
resources they have intentionally left from their own sidebar.
> - That requires user-scoped resource membership state backed by
company-scoped API and database contracts.
> - The branch also needed to preserve HTTP worktree login sessions and
keep the project list easier to scan after membership grouping.
> - This pull request adds resource membership controls, sidebar leave
actions, grouped/sortable project listings, and focused tests.
> - The benefit is a cleaner personal workspace view without weakening
company-scoped access to the underlying project or agent detail pages.
## What Changed
- Added `project_memberships` and `agent_memberships` tables with
API/shared/server contracts for current-user join/leave state.
- Renumbered the membership migration to `0090_resource_memberships`
after rebasing onto current `master`, and made it idempotent for anyone
who had applied the old branch-local `0087` migration.
- Added project and agent sidebar leave actions, plus list filtering
that waits for membership state before hiding resources.
- Added grouped project listing, project sorting controls, and reserved
row subtitle height for cleaner scanning.
- Fixed HTTP auth cookie security handling so HTTP worktree sessions can
persist.
- Updated focused server and UI tests for the new membership, sidebar,
project list, and auth behavior.
## Verification
- `pnpm exec vitest run server/src/__tests__/better-auth.test.ts
server/src/__tests__/resource-memberships-routes.test.ts
ui/src/pages/Projects.test.tsx
ui/src/components/SidebarProjects.test.tsx
ui/src/components/SidebarAgents.test.tsx
ui/src/components/MembershipAction.test.tsx
ui/src/components/EntityRow.test.tsx`
- Confirmed the branch is rebased on current `origin/master`.
- Confirmed the PR diff does not include `pnpm-lock.yaml` or
`.github/workflows` changes.
## Risks
- Migration safety: low to medium. The migration now uses `IF NOT
EXISTS` / guarded constraints and is numbered after current master
migrations, but it should still get CI coverage against fresh databases.
- UI behavior: low. Left resources are hidden from sidebar only after
membership state loads; direct detail access remains available.
- Auth behavior: low. Cookie security is relaxed only for HTTP/private
local-style origins where secure cookies would prevent login
persistence.
> 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 coding agent, tool-enabled shell/git workflow,
context window not exposed by runtime.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
Screenshot note: no browser screenshots were captured in this heartbeat;
the UI changes are covered by focused component tests above.
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip coordinates autonomous company work through local and
hosted runtime surfaces.
> - Local embedded Postgres and tenant import/export paths are
foundational reliability pieces.
> - A runtime failure in either path can stop agents or imports before
useful work begins.
> - The branch included remaining fixes for embedded native library
bootstrap and async tenant import handling.
> - This pull request groups those runtime/import reliability changes
into one standalone PR.
> - The benefit is a more robust local runtime and safer cloud tenant
import behavior.
## What Changed
- Prepared embedded Postgres native runtime before startup in
CLI/server/test entrypoints.
- Added embedded Postgres native bootstrap coverage.
- Added async tenant import job handling and deferred validation
coverage.
- Kept the runtime/import changes based directly on current
`origin/master` after related upstream PRs had already merged.
## Verification
- `pnpm --filter @paperclipai/plugin-sdk build`
- `NODE_ENV=test pnpm exec vitest run
packages/db/src/embedded-postgres-native.test.ts
server/src/__tests__/company-portability-routes.test.ts`
## Risks
- Medium-low: this touches startup/import paths, but the branch is small
and covered by targeted tests.
- The embedded Postgres change depends on platform-specific
native-library behavior, so CI and follow-up checks should still verify
supported runners.
> 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 via `codex_local`, tool-enabled coding session;
exact context window not exposed by this runtime.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
## Thinking Path
> - Paperclip is the control plane for AI-agent companies.
> - Operators need a path to move local company state toward Paperclip
Cloud without losing local-first control.
> - The Cloud Upstream flow needs API, persistence, CLI, and board UI
surfaces that agree on the same manifest/run model.
> - The existing branch had the feature work plus UX and error-handling
follow-ups.
> - This pull request packages the remaining Cloud Upstream sync work
into one standalone branch.
> - The benefit is an inspectable local-to-cloud sync workflow with
preview, conflicts, activation, and captured UX review states.
## What Changed
- Added Cloud Upstream shared types, server routes/services, and
persisted run schema/migration.
- Added Paperclip Cloud CLI sync helpers and local connection storage.
- Added the Cloud Upstream board UI, settings entry points, query keys,
and UX lab page.
- Added preview/activation checklist behavior, redirect handling,
manifest-only preview support, friendly errors, in-flight hints, and
entity count summaries.
## Verification
- `pnpm --filter @paperclipai/plugin-sdk build`
- `NODE_ENV=test pnpm exec vitest run cli/src/__tests__/cloud.test.ts
server/src/__tests__/instance-settings-routes.test.ts
server/src/__tests__/instance-settings-service.test.ts
ui/src/pages/CloudUpstream.test.tsx
ui/src/components/CompanySettingsSidebar.test.tsx`
- `NODE_ENV=test pnpm exec vitest run
server/src/__tests__/cloud-upstreams.test.ts`
Worktree setup note: the isolated worktree install skipped native sqlite
build scripts, so I copied the already-built local sqlite binding from
the main checkout before running
`server/src/__tests__/cloud-upstreams.test.ts`. The test then passed.
## Risks
- Medium: this adds a database migration and a broad feature path across
CLI/server/UI.
- Merge order: this is the only PR in this split with a DB migration;
merge it before any future Cloud Upstream migration follow-up.
- Mitigation: the PR is based directly on current `origin/master`, has
targeted route/service/UI tests, and keeps the feature behind existing
experimental Cloud Sync settings.
> 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 via `codex_local`, tool-enabled coding session;
exact context window not exposed by this runtime.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, screenshot artifacts are
intentionally omitted per reviewer request
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies by keeping
task ownership, approvals, and operator control inside one control
plane.
> - Agent permissions and plugin-hosted company settings sit on the
boundary between autonomy and governance.
> - V1 needs scoped task assignment rules, plugin extension points, and
clearer company access surfaces without weakening company boundaries.
> - The branch builds the core authorization service, plugin SDK/host
APIs, and UI simplifications needed to support those controls.
> - Paperclip EE plugin surfaces were intentionally moved out of this
core PR per review direction, so this PR now carries only the public
core/plugin infrastructure work.
> - The latest updates preserve the PAP-9937 branch changes that belong
in this PR, remove the `design/` artifacts, and exclude the experimental
`plugin-briefs` package.
> - Greptile feedback was applied through the authorization/audit paths
and the final cleanup commit was re-reviewed at 5/5 with no unresolved
Greptile threads.
> - The benefit is safer assignment control with extension hooks for
richer permission products while preserving simple defaults for normal
operators.
## What Changed
- Added scoped task-assignment authorization decisions and routed
issue/agent assignment mutations through the authorization service.
- Added plugin SDK and host APIs for company settings slots,
authorization policy/grant management, assignment previews, and bridge
invocation scope propagation.
- Simplified core company access UI and moved advanced controls behind
plugin-provided settings surfaces.
- Added retry-now affordances for blocked issue next-step notices.
- Added protected-assignment enforcement for persisted
agent/project/issue policies, including explicit-grant fallback
behavior.
- Added incremental principal-access compatibility backfill for active
agent memberships and role-default human permission grants.
- Added the Markdown code block wrap action fix from the latest branch
changes.
- Removed `design/` artifacts from the PR and removed
`packages/plugins/plugin-briefs` from the final diff.
- Addressed Greptile feedback for plugin actor sanitization, legacy
membership handling, audit pagination, unknown grant-scope metadata, and
startup test mocks.
## Verification
- `pnpm exec vitest run server/src/__tests__/access-service.test.ts
server/src/__tests__/company-portability.test.ts` -> 2 files passed, 54
tests passed.
- `pnpm exec vitest run
server/src/__tests__/server-startup-feedback-export.test.ts
server/src/__tests__/access-service.test.ts
server/src/__tests__/company-portability.test.ts` -> 3 files passed, 62
tests passed.
- `pnpm exec vitest run
server/src/__tests__/authorization-service.test.ts
server/src/__tests__/plugin-access-authorization-host-services.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts` -> 3 files
passed, 28 tests passed.
- `pnpm --filter @paperclipai/server typecheck` -> passed.
- `git diff --check` -> passed.
- `node ./scripts/check-docker-deps-stage.mjs` -> passed.
- `CI=true pnpm install --frozen-lockfile --ignore-scripts` -> passed
with no lockfile update.
- `pnpm exec vitest run
ui/src/components/MarkdownBody.interaction.test.tsx` -> 1 test passed.
- `git ls-files design packages/plugins/plugin-briefs | wc -l` -> 0.
- GitHub CI on `40cd83b53` -> all checks passed, merge state `CLEAN`.
- Greptile on `40cd83b53` -> 5/5, 102 files reviewed, 0
comments/annotations added, 0 unresolved review threads.
- Confirmed the PR diff contains no `design/`,
`packages/plugins/plugin-briefs`, `pnpm-lock.yaml`, or
`.github/workflows` changes.
## Risks
- Medium: task assignment authorization paths are behaviorally stricter
for protected/private policy data, so existing plugin-authored policies
may block assignment until explicit grants or approval flows are
configured.
- Medium: plugin-host authorization APIs expand the surface area
available to trusted plugins and need careful review for company
scoping.
- Low: startup now performs a principal-access compatibility backfill,
but the migration and runtime backfill use conflict-tolerant inserts.
> 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 coding agent, tool-enabled workflow with shell,
git, and GitHub CLI access.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents through a server-side control plane
> - That control plane depends on reliable issue state transitions,
plugin lifecycle behavior, import limits, and startup/shutdown handling
> - Several small runtime fixes had accumulated on the working branch
and were mixed with larger feature work
> - Keeping them separate makes the correctness fixes reviewable and
mergeable without waiting for cloud-sync UI work
> - This pull request groups the server/runtime control-plane fixes into
one standalone branch
> - The benefit is a tighter, safer runtime baseline for retries,
imports, plugin migrations, feedback flushing, and trusted cloud import
handling
## What Changed
- Fixed updated issue list pagination sorting and scheduled retry
comment handling.
- Re-applied pending plugin migrations during hot reload and fixed
plugin-schema worktree seed restore.
- Hardened public tenant DB startup, portable import body limits,
trusted cloud import errors, and trusted cloud tenant import mutation
access.
- Expired stale request confirmations after user comments.
- Added feedback export shutdown hardening so database-unavailable flush
loops stop cleanly.
- Guarded plugin worker `error` event emission when no listener is
registered.
## Verification
- `pnpm install --frozen-lockfile --ignore-scripts`
- `pnpm --filter @paperclipai/plugin-sdk build`
- `npm run install --prefix
node_modules/.pnpm/sqlite3@5.1.7/node_modules/sqlite3`
- `pnpm exec vitest run server/src/__tests__/issues-service.test.ts
server/src/__tests__/plugin-lifecycle-restart.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts
server/src/__tests__/issue-comment-reopen-routes.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts
server/src/__tests__/issue-thread-interaction-routes.test.ts
server/src/__tests__/body-limits.test.ts
server/src/__tests__/feedback-flush-controller.test.ts
server/src/__tests__/error-handler.test.ts
server/src/__tests__/board-mutation-guard.test.ts
packages/db/src/backup-lib.test.ts` initially exposed local setup issues
and two 5s test timeouts.
- Rerun after local prereq build: `pnpm exec vitest run --testTimeout
15000 server/src/__tests__/issue-comment-reopen-routes.test.ts
server/src/__tests__/issue-thread-interaction-routes.test.ts
server/src/__tests__/feedback-flush-controller.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts` passed.
- Some embedded Postgres-backed tests skipped on this host because local
Postgres init was unavailable.
## Risks
- Runtime-touching branch: startup/shutdown and issue interaction
behavior should be reviewed carefully.
- The feedback export change disables repeated flush attempts only for
database connection-refused failures; other upload failures still log
normally.
- The plugin worker error guard avoids process crashes from unhandled
EventEmitter errors but may hide errors from code paths that expected an
emitted listener.
> 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 with local shell/git/tool use.
Exact hosted model ID and context-window size are not exposed by the
local Paperclip adapter runtime.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - Scheduled routines are the control-plane path for recurring agent
work.
> - Routines already had dispatch/history, but their runtime environment
did not carry routine-owned secret bindings through execution.
> - Operators need routine-specific secrets that can override
project/agent env without exposing secret values in history, logs, or
access events.
> - This pull request adds the routine env runtime contract, wires it
into execution, and makes the routine UI/history surfaces show safe
secret metadata.
> - The benefit is that routine executions can use scoped secret refs
predictably while preserving company boundaries and auditability.
## What Changed
- Added routine env persistence/runtime support, including
`routines.env`, `routine_runs.routine_revision_id`, revision snapshots,
and idempotent migration `0086_routine_env_runtime_contract`.
- Resolved routine env during heartbeat adapter config assembly with
precedence `agent < project < routine` and secret access events recorded
against the routine consumer.
- Added secret binding synchronization for routine create/update/restore
flows and guarded cross-company, missing, disabled, and deleted secret
cases.
- Added a Secrets tab to routine detail, env/secret history diff
rendering, and Storybook coverage for the new UI states.
- Added server/UI regression tests, including an embedded-Postgres QA
path for routine secret execution and restore behavior.
- Updated implementation/database docs for routine env and
secret-binding behavior.
## Verification
- `pnpm install --frozen-lockfile` after rebasing onto
`public-gh/master` to refresh workspace links for the newly-added
upstream Grok adapter package.
- `pnpm exec vitest run
server/src/__tests__/heartbeat-project-env.test.ts
server/src/__tests__/routines-service.test.ts
server/src/__tests__/secrets-service.test.ts
server/src/__tests__/qa-routine-secrets-e2e.test.ts
ui/src/components/RoutineHistoryTab.test.tsx` passed: 5 files, 92 tests.
- `pnpm -r typecheck` passed across the workspace.
- `pnpm build` passed. Vite emitted the existing
large-chunk/dynamic-import warnings.
- UI screenshots were captured locally during QA in
`artifacts/pap-9521/` and `artifacts/pap-9522/`; generated screenshots
are not committed to avoid adding binary artifacts to the repo.
## Risks
- Migration risk is limited by `IF NOT EXISTS` guards for the new
columns, FK, and index, and the migration is ordered as `0086`
immediately after upstream `0085`.
- Runtime behavior changes env precedence for routine executions by
adding routine env as the highest-precedence layer; tests cover
agent/project/routine precedence.
- Secret handling is security-sensitive; tests cover value-free
manifests/events/errors, disabled/missing/deleted secrets, and
cross-company rejection.
- UI history now renders routine env/secret diffs; tests and Storybook
stories cover the main rendering 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 coding agent based on GPT-5, with shell/tool use and
medium reasoning effort.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI-agent companies through company-scoped
issues, comments, and issue documents.
> - Issue documents are the durable place where plans, handoffs, and
other work artifacts are revised over time.
> - Some documents need to be preserved as operator-approved snapshots
while agents continue working on the same issue.
> - Without document locking, a later board or agent write can overwrite
the document key that reviewers expected to remain stable.
> - This pull request adds board-managed issue document locks and makes
agent writes to locked keys create a derived document instead of
mutating the locked document.
> - The benefit is safer document handoffs: approved or frozen issue
documents stay immutable until the board explicitly unlocks them.
## What Changed
- Added `locked_at`, `locked_by_agent_id`, and `locked_by_user_id`
document fields plus migration `0085_tranquil_the_executioner.sql`.
- Added document lock/unlock service behavior, route endpoints, activity
events, and locked-document write protections.
- Made agent document writes to locked keys create a new derived key
such as `plan-2` rather than overwriting the locked document.
- Surfaced lock state through shared issue document types, UI API
methods, document header lock controls, and activity formatting.
- Added server and UI tests for lock/unlock behavior, locked document
immutability, and UI action visibility.
- Updated `doc/SPEC-implementation.md` with the V1 document lock
contract and endpoints.
## Verification
- `git rebase public-gh/master` completed cleanly after committing the
branch changes.
- `git diff --check` passed before commit.
- `pnpm run preflight:workspace-links && pnpm exec vitest run
server/src/__tests__/documents-service.test.ts
server/src/__tests__/issue-agent-mutation-ownership-routes.test.ts
ui/src/components/IssueDocumentsSection.test.tsx
ui/src/components/IssueContinuationHandoff.test.tsx
ui/src/lib/document-revisions.test.ts` passed: 5 files, 32 tests.
## Risks
- Medium risk because this changes the document persistence contract and
adds a migration.
- The migration uses `ADD COLUMN IF NOT EXISTS` and guarded foreign-key
creation so it remains safe for users who may have already applied an
earlier copy of the migration.
- Locked documents intentionally reject board edits/deletes/restores
until unlocked; any existing workflows that expected direct overwrite
need to unlock first.
- Agent writes to locked keys now create derived documents, which may
create extra issue documents when agents retry locked writes.
## Model Used
- OpenAI Codex coding agent based on GPT-5, with tool use and local code
execution in the Paperclip worktree.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is a control plane for autonomous AI companies, where work
must end with a clear disposition rather than ambiguous agent liveness.
> - Recovery currently detects stalled or missing-next-step issues, but
source issue recovery can become split across child recovery issues,
blockers, and comments.
> - That makes it harder for operators and agents to see who owns
recovery and what exact action is needed on the original issue.
> - Source-scoped recovery actions give the original issue a first-class
active recovery state with owner, evidence, wake policy, and resolution
outcome.
> - This pull request adds the recovery-action data model, backend
reconciliation and resolution APIs, and board UI indicators/actions.
> - The benefit is clearer stalled-work recovery without losing source
issue context or relying on comments as the liveness path.
## What Changed
- Added the `issue_recovery_actions` schema, shared
types/constants/validators, and an idempotent
`0084_issue_recovery_actions` migration ordered after current `master`
migrations.
- Updated stranded/missing-disposition recovery to create source-scoped
recovery actions, wake the recovery owner on the source issue, and avoid
locking the source issue for recovery-action wakes.
- Added API support for reading active recovery actions on issue
detail/list surfaces and resolving them with restored, blocked,
cancelled, or false-positive outcomes.
- Require blocked recovery resolutions to have an unresolved first-class
blocker, and removed the UI shortcut that could mark recovery blocked
without a blocker selection path.
- Surfaced recovery indicators/actions in the issue UI, blocker notices,
active run panels, issue rows, and Storybook coverage.
- Updated docs and focused tests for recovery semantics, ownership,
races, stale comments, and UI behavior.
## Verification
- `pnpm exec vitest run
server/src/__tests__/issue-recovery-actions.test.ts
server/src/__tests__/heartbeat-process-recovery.test.ts
ui/src/components/IssueRecoveryActionCard.test.tsx
ui/src/components/IssueBlockedNotice.test.tsx ui/src/api/issues.test.ts`
— 5 files, 72 tests passed.
- `pnpm --filter @paperclipai/shared typecheck` — passed.
- `pnpm --filter @paperclipai/db typecheck` — passed, including
migration numbering check.
- `pnpm --filter @paperclipai/server typecheck` — passed.
- `pnpm --filter @paperclipai/ui typecheck` — passed.
- Follow-up verification after blocker-resolution guard: `pnpm exec
vitest run server/src/__tests__/issue-recovery-actions.test.ts
ui/src/components/IssueRecoveryActionCard.test.tsx
ui/src/api/issues.test.ts` — 3 files, 27 tests passed.
- Follow-up `pnpm --filter @paperclipai/server typecheck` — passed.
- Follow-up `pnpm --filter @paperclipai/ui typecheck` — passed.
- UI states are available in
`ui/storybook/stories/source-issue-recovery.stories.tsx`; screenshot
capture helper is `scripts/screenshot-recovery-card.cjs`.
## Risks
- Medium: recovery behavior changes from child recovery issue ownership
toward source-scoped actions, so operators may see stalled-work state in
new places.
- Migration risk is mitigated by using the next migration slot after
`master` and making the table/constraints/index creation idempotent for
anyone who previously applied the old branch-local
`0082_dizzy_master_mold` migration.
- Existing child recovery issue paths are still guarded for
already-created recovery issues, but new source-scoped flows should be
watched in CI and Greptile review.
> 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 coding agent, tool use enabled for shell, Git,
GitHub, and local test execution. Context window not exposed by the
runtime.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system needs host contracts and runtime support before
large plugins can integrate cleanly.
> - The source branch mixed the LLM Wiki package with supporting
host/runtime work, managed plugin skills, root-level storage spaces, and
a bookmarks reference plugin.
> - [PAP-9173](/PAP/issues/PAP-9173) asked for the current branch to be
split by file boundary: plugin package separately from everything else.
> - [PAP-9188](/PAP/issues/PAP-9188) clarified that LLM Wiki may have
plugin-local spaces, but Paperclip core should not reorganize top-level
local storage into spaces.
> - Follow-up review clarified that the bookmarks example should not
ship in this PR either.
> - This pull request contains the
non-`packages/plugins/plugin-llm-wiki/` host/runtime work, keeps runtime
state under the selected Paperclip instance root, and no longer includes
the bookmarks example.
## What Changed
- Added/updated plugin host contracts, SDK types, worker RPC plumbing,
managed plugin skill support, and related server tests.
- Removed the bookmarks example plugin package and its
bundled-example/workspace references.
- Removed the root-level local spaces CLI/migration surface and restored
instance-root runtime defaults for config, db, logs, storage, secrets,
workspaces, projects, and adapter homes.
- Replaced shared root `space-paths` helpers with `home-paths` helpers
for core runtime storage.
- Tightened stranded recovery unique-conflict detection so concurrent
recovery scans reuse the raced recovery issue when Postgres errors are
wrapped.
- Kept `packages/plugins/plugin-llm-wiki/` out of this PR diff;
plugin-local spaces remain in the stacked plugin-only PR.
## Verification
- `pnpm exec vitest run cli/src/__tests__/data-dir.test.ts
cli/src/__tests__/home-paths.test.ts cli/src/__tests__/onboard.test.ts
packages/shared/src/home-paths.test.ts
packages/db/src/runtime-config.test.ts
server/src/__tests__/agent-instructions-service.test.ts
server/src/__tests__/claude-local-execute.test.ts
server/src/__tests__/codex-local-execute.test.ts`
- `pnpm exec vitest run packages/db/src/runtime-config.test.ts`
- `pnpm exec vitest run
server/src/__tests__/plugin-routes-authz.test.ts`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "reuses the
raced stranded recovery issue"` skipped locally because embedded
Postgres did not initialize on this macOS temp host; the code path was
typechecked and is covered by Linux CI.
- Boundary check: no core references remain for `PAPERCLIP_SPACE_ID`,
`spaces migrate-default`, `@paperclipai/shared/space-paths`,
`registerSpacesCommands`, or the removed bookmarks example.
- Previous PR head `4f23e034` had green GitHub checks: `verify`, all
four serialized server shards, `e2e`, `Canary Dry Run`, `policy`, Snyk,
and `Greptile Review`. Current head `582f466d` is re-running checks
after the bookmarks deletion.
## Risks
- Plugin host changes touch shared runtime paths, so regressions would
most likely appear in adapter startup, plugin loading, or local dev path
defaults.
- Removing the bookmarks example also removes one demonstration of
plugin database namespaces plus local-folder persistence; remaining
plugin examples still cover bundled example discovery and plugin host
flows.
- The plugin package itself is intentionally deferred to the stacked
plugin-only PR, where LLM Wiki plugin-local spaces live.
- Existing installs that tested the transient root-level spaces CLI
should stop using it; this PR intentionally removes that unsupported
migration surface before merge.
> 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 via Codex CLI, tool use and local code execution
enabled; context window 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 run tests locally and they pass, except where noted above
for host-specific embedded Postgres initialization
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
Stacked follow-up: PR #5592 contains only
`packages/plugins/plugin-llm-wiki/` and targets this branch.
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The server, DB package, and CLI all rely on the shared Drizzle ORM
dependency for core persistence flows.
> - A published install was still resolving nested `drizzle-orm@0.38.4`,
which left the production package graph behind the intended security
update.
> - The repo’s documented dependency policy says GitHub Actions owns
`pnpm-lock.yaml`, so the correct maintainer workflow is to update
dependency manifests in the feature PR and let the lockfile refresh
happen separately after merge.
> - This pull request therefore keeps the Drizzle upgrade to the package
manifests only and leaves lockfile regeneration to the existing `Refresh
Lockfile` automation.
## What Changed
- Updated `drizzle-orm` dependency declarations in `cli/package.json`,
`packages/db/package.json`, and `server/package.json` from `0.38.4` /
`^0.38.4` to `0.45.2` / `^0.45.2`.
- Re-verified the packed `@paperclipai/db` and `@paperclipai/server`
publish payloads to confirm their generated `package.json` files
advertise `drizzle-orm ^0.45.2`.
- Removed the temporary lockfile/CI follow-up commits so the branch now
matches the intended manifest-only protocol.
## Verification
- `pnpm list drizzle-orm -r --depth 0`
- `pnpm exec vitest run packages/db/src/client.test.ts
server/src/__tests__/issues-service.test.ts`
- `pnpm run test:release-registry`
- Packed `@paperclipai/db` and `@paperclipai/server` locally and
inspected the tarball `package.json` files to confirm they advertise
`drizzle-orm ^0.45.2`.
## Risks
- Low to moderate risk: the runtime code paths are unchanged, but
downstream lockfile refresh now depends on the existing post-merge
GitHub automation working as documented.
- A separate packaging/versioning issue around unpublished
`@paperclipai/plugin-sdk@1.0.0` showed up during a raw local tarball
install experiment; that is called out for reviewers but is not part of
this Drizzle bump.
## Model Used
- OpenAI Codex via the `codex_local` adapter, using a GPT-5-based coding
agent with terminal tool use and code execution. The adapter does not
expose a public exact model ID or context-window value in this
environment.
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
## Thinking Path
> - Paperclip orchestrates AI-agent companies and needs secrets handling
to work across local development, hosted operators, and governed agent
execution.
> - The affected subsystem is the company-scoped secrets control plane:
database schema, server services/routes, CLI workflows, and the Secrets
settings UI.
> - The gap was that secrets were local-only and operators could not
manage provider vaults or import existing remote references without
exposing plaintext.
> - This branch adds provider vault configuration plus an AWS Secrets
Manager remote-import path while preserving company boundaries, binding
context, and audit trails.
> - I kept the PR to a single branch PR, removed unrelated
lockfile/package drift, rebased the full branch onto the current
`public-gh/master`, and addressed fresh Greptile findings.
> - The benefit is a reviewable implementation of provider-backed
secrets with focused tests covering provider selection, import
conflicts, deleted secret reuse, rotation guards, and AWS signing
behavior.
## What Changed
- Added provider vault support for company secrets, including provider
config storage, default vault handling, health checks, binding usage,
access events, and remote import preview/commit.
- Added an AWS Secrets Manager provider using SigV4 request signing,
bounded request timeouts, namespace guardrails, cached runtime
credential resolution, and external-reference linking without plaintext
reads.
- Added Secrets UI surfaces for vault management and remote import, plus
CLI/API documentation for setup and operations.
- Stabilized routine webhook secret binding paths and SSH
environment-driver fixture bindings discovered during verification.
- Addressed Greptile and CI findings: no lockfile/package drift,
monotonic migration metadata, disabled-vault default races, soft-deleted
secret hiding/recreate behavior, remove behavior with disabled vaults,
soft-deleted external-reference re-import, non-active rotation guards,
managed-secret soft deletion through PATCH, and per-call AWS SDK
credential client churn.
- Rebased this branch onto `public-gh/master` at `0e1a5828` and
force-pushed with lease to keep this as the single PR for the branch.
## Verification
- `git fetch public-gh master`
- `git rebase public-gh/master`
- `git diff --name-only public-gh/master...HEAD | grep
'^pnpm-lock\.yaml$' || true` confirmed `pnpm-lock.yaml` is not in the PR
diff.
- Confirmed migration ordering: master ends at `0081_optimal_dormammu`;
this PR adds `0082_dry_vision` and
`0083_company_secret_provider_configs`.
- Inspected migrations for repeat safety: new tables/indexes use `IF NOT
EXISTS`; foreign keys are guarded by `DO $$ ... IF NOT EXISTS`; column
additions use `ADD COLUMN IF NOT EXISTS`.
- `pnpm -r typecheck` passed before the Greptile follow-up commits.
- `pnpm test:run` ran the full stable Vitest path before the Greptile
follow-up commits; it completed with 3 timing-related failures under
parallel load: `codex-local-execute.test.ts`,
`cursor-local-execute.test.ts`, and `environment-service.test.ts`.
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/codex-local-execute.test.ts
src/__tests__/cursor-local-execute.test.ts
src/__tests__/environment-service.test.ts` passed on targeted rerun
(`24/24`).
- `pnpm build` passed before the Greptile follow-up commits. Vite
reported existing chunk-size/dynamic-import warnings.
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
exec vitest run src/__tests__/secrets-service.test.ts` passed (`26/26`).
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
exec vitest run src/__tests__/aws-secrets-manager-provider.test.ts
src/__tests__/secrets-service.test.ts` passed (`39/39`).
- After Greptile follow-up commits: `pnpm --filter @paperclipai/server
typecheck` passed.
- Captured Storybook screenshots from `ui/storybook-static` for visual
review.
- Latest PR checks on `5ca3a5cf`: `policy`, serialized server suites
1/4-4/4, `Canary Dry Run`, `e2e`, `security/snyk`, and `Greptile Review`
pass; aggregate `verify` is still registering the completed child
checks.
- Greptile review loop continued through the latest requested pass; all
Greptile review threads are resolved and the latest `Greptile Review`
check on `5ca3a5cf` passed with 0 comments added.
## Screenshots
Before: the provider-vault and remote-import surfaces did not exist on
`master`; these are after-state screenshots from the Storybook fixtures.
## Risks
- Migration risk: this adds new secret provider tables and extends
existing secret rows. The migrations were checked for monotonic ordering
and idempotent guards, but reviewers should still inspect upgrade
behavior carefully.
- Provider risk: AWS support uses direct SigV4 requests. Automated tests
cover signing, request timeouts, vault-config selection, namespace
guardrails, pending-version archival, sanitized provider errors, and
service-level cleanup paths. A real-vault AWS smoke test remains
deployment validation for an operator with AWS credentials rather than
an unverified merge blocker in this local branch.
- UI risk: the Secrets page and import dialog are large new surfaces;
screenshots are included above for reviewer inspection.
- Verification risk: the full local stable test command hit
parallel-load timing failures, although the exact failed files passed
when rerun directly.
- Operational risk: remote import intentionally avoids plaintext reads;
operators must understand that imported external references resolve at
runtime and may fail if AWS permissions 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
- OpenAI Codex, GPT-5 coding agent with local shell/tool use in the
Paperclip worktree. Exact context-window size was not exposed by the
runtime.
## 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 have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies
> - The issue thread is the operator's durable audit trail for what
changed and why
> - Workspace changes and stale disposition notices need to be visible
in that same timeline without noisy or misleading rendering
> - The local branch already contained backend activity details,
timeline conversion, and UI rendering work for those events
> - This pull request isolates the issue-thread activity work into a
standalone branch against `origin/master`
> - The benefit is a focused audit-trail PR that can merge independently
of the sidebar/operator UI polish branch
## What Changed
- Adds readable workspace-change activity details to issue update
activity events.
- Surfaces workspace-change events in issue chat/timeline rendering.
- Makes the existing issue comment migration idempotent.
- Folds and renders stale disposition notices inline so they match
activity-log styling and spacing.
- Adds focused route, timeline, and issue-thread system notice coverage.
## Verification
- `pnpm install --frozen-lockfile`
- `pnpm exec vitest run
server/src/__tests__/issue-activity-events-routes.test.ts
ui/src/lib/issue-timeline-events.test.ts
ui/src/components/IssueChatThreadSystemNotice.test.tsx` — 3 files
passed, 22 tests passed.
- Confirmed the PR changes 9 files and does not include `pnpm-lock.yaml`
or `.github/workflows/*`.
- `pnpm exec vitest run
server/src/__tests__/issue-closed-workspace-routes.test.ts` — 1 file
passed, 4 tests passed.
- `pnpm exec vitest run
server/src/__tests__/issue-activity-events-routes.test.ts
ui/src/lib/issue-timeline-events.test.ts
ui/src/components/IssueChatThreadSystemNotice.test.tsx
server/src/services/recovery/successful-run-handoff.test.ts
packages/shared/src/validators/issue.test.ts` — 5 files passed, 54 tests
passed.
- `pnpm --filter @paperclipai/shared typecheck && pnpm --filter
@paperclipai/server typecheck && pnpm --filter @paperclipai/ui
typecheck`.
- `pnpm --filter @paperclipai/ui typecheck` after adding the Storybook
screenshot fixture.
- Captured Storybook screenshots for the new UI rendering paths:
- Collapsed stale notice + workspace-change row:
`docs/pr-screenshots/pr-5356/issue-thread-notices-collapsed.png`
- Expanded stale notice details:
`docs/pr-screenshots/pr-5356/issue-thread-notices-expanded.png`
### Screenshots
Collapsed stale notice with workspace-change row:
Expanded stale notice details:
## Risks
- Moderate risk: this touches issue activity serialization and
issue-thread rendering, both of which are central operator surfaces.
- Migration risk is low: the only migration change makes an existing
migration idempotent.
- No new migrations are introduced, so there is no cross-PR migration
ordering requirement.
> 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 coding agent, shell/tool-use enabled, used to
split the existing branch, verify the isolated PR branch, and create
this 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is a control plane for autonomous AI companies.
> - Issues are the core unit of work, and issue comments are how board
users and agents coordinate execution.
> - Some issue conversations need to produce plans and approvals instead
of immediate implementation work.
> - The existing issue contract did not distinguish standard execution
comments from planning-oriented issue work.
> - This pull request adds an issue work-mode contract and board UI
affordances for standard vs planning mode.
> - The benefit is that planning-mode issues can be created, displayed,
discussed, and carried through agent heartbeat context without losing
the normal issue workflow.
## What Changed
- Added `standard` / `planning` issue work-mode contracts across DB,
shared validators/types, server issue flows, plugin protocol, and
adapter heartbeat payloads.
- Added an idempotent `0081_optimal_dormammu` migration for
`issues.work_mode`, ordered after current `public-gh/master` migrations.
- Updated heartbeat/context summaries and issue-thread interaction
behavior so planning work mode is preserved when creating suggested
follow-up issues.
- Added UI support for planning-mode issue creation, issue rows, detail
composer styling, and composer work-mode toggles.
- Added focused server/shared/UI tests plus a Playwright visual
verification spec for planning-mode surfaces.
- Rebased the branch onto current `public-gh/master` and added durable
planning-mode screenshots under `doc/assets/pap-3368/`.
## Verification
- `pnpm --filter @paperclipai/db run check:migrations`
- `pnpm exec vitest run --project @paperclipai/shared
packages/shared/src/validators/issue.test.ts`
- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/heartbeat-context-summary.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts
server/src/__tests__/issues-goal-context-routes.test.ts --pool=forks
--poolOptions.forks.isolate=true`
- `pnpm exec vitest run --project @paperclipai/ui
ui/src/components/IssueChatThread.test.tsx
ui/src/components/NewIssueDialog.test.tsx
ui/src/components/IssueRow.test.tsx ui/src/pages/IssueDetail.test.tsx`
- `pnpm exec vitest run --project @paperclipai/adapter-utils
packages/adapter-utils/src/server-utils.test.ts`
- `PAPERCLIP_E2E_SKIP_LLM=true npx playwright test --config
tests/e2e/playwright.config.ts
tests/e2e/planning-mode-visual-verification.spec.ts`
## Screenshots
Desktop planning detail:
Desktop planning row:
Desktop staged standard toggle:
Mobile planning detail:
Mobile planning row:
## Risks
- Medium migration risk: this adds a non-null issue column. The
migration uses `ADD COLUMN IF NOT EXISTS` so installations that applied
an older branch-local migration number can still apply the final
numbered migration safely.
- Medium contract risk: issue payloads, plugin payloads, and adapter
heartbeat payloads now include work mode; compatibility is handled by
defaulting missing values to `standard`.
- UI risk is moderate because composer controls changed; focused
component tests and visual e2e coverage exercise standard vs planning
display and toggle behavior.
> 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 coding agent in a local Paperclip worktree, with
shell/tool use. Exact context-window size is not exposed in this
runtime.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - Operators need to find work, documents, agents, projects, comments,
and activity across a company without jumping through separate surfaces.
> - The existing Command-K flow was useful for fast navigation but not
enough for deeper company-wide discovery.
> - Search also needs company-scoped backend contracts, query cost
controls, and indexed document matching so it stays safe as company data
grows.
> - This pull request adds a full company search API and a dedicated
board search page that Command-K can hand off to.
> - The benefit is a single searchable control-plane surface with richer
result context, recents, highlights, and test coverage across server and
UI behavior.
## What Changed
- Added a company-scoped search endpoint/service with query validation,
rate limiting, text matching, fuzzy title matching, and result typing
shared through `@paperclipai/shared`.
- Added idempotent search migrations for document search indexes and
fuzzy matching support.
- Added the full `/companies/:companyKey/search` UI, search result row
components, highlighted snippets, recent searches, and sidebar/Command-K
handoff.
- Added Storybook coverage for search surfaces and Vitest coverage for
server search behavior, rate limiting, route generation, Command-K
behavior, and the search page.
- Addressed Greptile findings by renaming the no-match SQL helper,
applying search pagination after cross-type merge sorting, and
lazy-initializing the default search service so unrelated route-test
mocks do not need to know about it.
- Merged current `public-gh/master` and renumbered the search migrations
behind upstream `0078_white_darwin`: search indexes are now
`0079_company_search_document_indexes` and fuzzy matching is
`0080_company_search_fuzzystrmatch`.
## Verification
- `git fetch public-gh master`
- `git diff --check public-gh/master...HEAD`
- `git diff --name-only public-gh/master...HEAD | rg '^pnpm-lock\.yaml$'
|| true` produced no output before opening the PR.
- `pnpm run preflight:workspace-links && pnpm exec vitest run
server/src/__tests__/company-search-service.test.ts
server/src/__tests__/company-search-rate-limit-routes.test.ts
ui/src/pages/Search.test.tsx ui/src/components/CommandPalette.test.tsx
ui/src/lib/company-routes.test.ts` passed: 5 files, 25 tests.
- `pnpm --filter @paperclipai/shared typecheck && pnpm --filter
@paperclipai/db typecheck && pnpm --filter @paperclipai/server typecheck
&& pnpm --filter @paperclipai/ui typecheck` passed.
- `pnpm exec vitest run
server/src/__tests__/company-search-service.test.ts
server/src/__tests__/company-search-rate-limit-routes.test.ts && pnpm
--filter @paperclipai/server typecheck` passed after Greptile pagination
fixes.
- `pnpm exec vitest run
server/src/__tests__/issue-agent-mutation-ownership-routes.test.ts
server/src/__tests__/company-search-rate-limit-routes.test.ts
server/src/__tests__/company-search-service.test.ts && pnpm --filter
@paperclipai/server typecheck` passed after the CI mock fix.
- After resolving the migration conflict with current
`public-gh/master`: `pnpm --filter @paperclipai/db typecheck && pnpm
exec vitest run server/src/__tests__/company-search-service.test.ts
server/src/__tests__/company-search-rate-limit-routes.test.ts && pnpm
--filter @paperclipai/server typecheck` passed.
- DB migration numbering check passed as part of `@paperclipai/db`
typecheck.
- UI states are covered by the added Storybook stories in
`ui/storybook/stories/search.stories.tsx`.
- GitHub reports the PR merge state as `CLEAN` on head `18e54fa8`.
- GitHub PR checks are green on head `18e54fa8`: policy, verify,
serialized server shards 1/4 through 4/4, e2e, canary dry run, Snyk, and
Greptile Review.
## Risks
- Search ranking and snippets are new user-facing behavior, so reviewers
should check whether result ordering feels right on real company data.
- Search touches broad company data, so company scoping and query
cost/rate-limit behavior should be reviewed carefully.
- The migrations add search indexes/extensions; they are idempotent with
`IF NOT EXISTS` for users who may have applied an earlier branch
migration number.
> ROADMAP.md checked. This PR adds a focused board search surface and
does not duplicate an open roadmap item.
## Model Used
- OpenAI Codex, GPT-5 coding agent, tool-enabled shell/git/GitHub CLI
session with medium reasoning effort. Existing branch commits were
produced across prior agent sessions; this packaging pass verified,
opened the PR, addressed Greptile findings, resolved migration conflicts
after upstream PRs landed, and got PR checks green.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
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