## 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 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 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-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 is the control plane for autonomous AI companies.
> - Routines are the scheduled/recurring work surface that keeps a
company operating without manual kicks.
> - Operators need routine edits to be auditable and recoverable,
especially when routines control assignments, prompts, triggers, and
webhook secrets.
> - Documents already have revision-style safety, but routines did not
have equivalent history or restore semantics.
> - This pull request adds append-only routine revisions across the
database, shared contracts, server routes, and board UI.
> - The benefit is safer routine iteration: users can inspect history,
compare changes, restore older definitions, and avoid overwriting newer
edits.
## What Changed
- Added `routine_revisions` storage, latest revision pointers on
routines, shared types, validators, and API docs for routine revision
history.
- Added server service/route support for listing routine revisions,
conflict-aware routine saves, and append-only restore operations.
- Added a History tab on routine detail with revision preview,
structured change summaries, description line diffs, dirty-edit
blocking, restore confirmation, and restored webhook secret surfacing.
- Extracted the line diff helper from `DocumentDiffModal` into
`ui/src/lib/line-diff.ts` for reuse.
- Rebased the branch onto current `public-gh/master` and renumbered the
routine revision migration to `0077_unusual_karnak` after upstream
`0076_useful_elektra`.
- Made the `0077` routine revision migration idempotent so installs that
already applied the branch-local `0076_unusual_karnak` can safely
advance.
- Updated the plugin SDK test harness routine fixture with the new
revision fields required by the shared `Routine` contract.
## Verification
- `pnpm --filter @paperclipai/db run check:migrations` passed.
- `pnpm exec vitest run --project @paperclipai/shared
packages/shared/src/validators/routine.test.ts` passed.
- `pnpm exec vitest run --project @paperclipai/ui
ui/src/lib/line-diff.test.ts
ui/src/components/RoutineHistoryTab.test.tsx
ui/src/lib/workspace-routines.test.ts ui/src/pages/Routines.test.tsx`
passed.
- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/routines-service.test.ts --pool=forks
--poolOptions.forks.isolate=true` passed.
- `pnpm exec vitest run --project @paperclipai/server
server/src/__tests__/routines-routes.test.ts --pool=forks
--poolOptions.forks.isolate=true` passed.
- `pnpm --filter @paperclipai/plugin-sdk typecheck` passed after
updating the SDK test harness fixture.
- `pnpm --filter @paperclipai/plugin-sdk build` passed; this refreshed
local generated SDK output needed by plugin example typechecks.
- `pnpm -r typecheck` passed.
## Risks
- Medium migration risk: this adds routine revision storage and
backfills existing routines. The migration is ordered after upstream
`0076` and uses `IF NOT EXISTS` / duplicate-object guards to tolerate
earlier branch-local migration application.
- Restore behavior intentionally appends a new revision instead of
mutating history; callers expecting an in-place rollback need to follow
the new latest revision pointer.
- Restoring webhook triggers recreates webhook secret material, so users
must copy newly surfaced secrets after restore.
- Conflict-aware saves now reject stale routine edits when the client
sends an older `baseRevisionId`.
> 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 shell/tool use in a local
git worktree. 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
Screenshots: not attached in this draft PR; the new UI flow is covered
by component tests listed above.
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies
> - The plugin system is the extension boundary for optional product
capabilities
> - Rich plugins need more than a worker entrypoint: they need scoped
database storage, local project folders, managed agents/routines, host
navigation, and reusable UI components
> - The LLM Wiki work exposed those missing host surfaces while keeping
plugin code outside the core control plane
> - This pull request expands the core plugin host, SDK, server APIs,
and UI bridge so plugins can declare and use those surfaces
> - The benefit is that future plugins can integrate with Paperclip
through documented, validated contracts instead of bespoke server or UI
imports
## What Changed
- Added plugin-managed database namespaces and migration tracking,
including Drizzle schema/migration files and SQL validation for
namespace isolation.
- Added server support for plugin local folders, managed agents, managed
routines, scoped plugin APIs, and plugin operation visibility.
- Expanded shared plugin manifest/types/validators and SDK
host/testing/UI exports for richer plugin surfaces.
- Added reusable UI pieces for file trees, managed routines, resizable
sidebars, route sidebars, and plugin bridge initialization.
- Updated plugin docs and example plugins to use the expanded host and
SDK surface.
## Verification
- `pnpm install --frozen-lockfile`
- `pnpm run preflight:workspace-links && pnpm exec vitest run
packages/shared/src/validators/plugin.test.ts
server/src/__tests__/plugin-database.test.ts
server/src/__tests__/plugin-local-folders.test.ts
server/src/__tests__/plugin-managed-agents.test.ts
server/src/__tests__/plugin-managed-routines.test.ts
server/src/__tests__/plugin-orchestration-apis.test.ts
ui/src/api/plugins.test.ts ui/src/components/FileTree.test.tsx
ui/src/components/ResizableSidebarPane.test.tsx
ui/src/pages/PluginPage.test.tsx ui/src/plugins/bridge.test.ts` passed:
11 files, 67 tests.
- Confirmed this PR changes 89 files and does not include
`pnpm-lock.yaml` or `.github/workflows/*`.
## Risks
- Medium: this expands plugin host contracts across db/shared/server/ui
and includes a new core migration (`0076_useful_elektra.sql`).
- The plugin database namespace validator is intentionally restrictive;
plugin authors may need follow-up affordances for SQL patterns that
remain blocked.
- Merge this before the LLM Wiki plugin PR so the plugin can resolve the
new SDK and host APIs.
> 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/git/GitHub
workflow. 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
- [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.
> - This branch extends the issue control-plane so board operators can
pause, cancel, and later restore whole issue subtrees while keeping
descendant execution and wake behavior coherent.
> - That required new hold state in the database, shared contracts,
server routes/services, and issue detail UI controls so subtree actions
are durable and auditable instead of ad hoc.
> - While this branch was in flight, `master` advanced with new
environment lifecycle work, including a new `0065_environments`
migration.
> - Before opening the PR, this branch had to be rebased onto
`paperclipai/paperclip:master` without losing the existing
subtree-control work or leaving conflicting migration numbering behind.
> - This pull request rebases the subtree pause/cancel/restore feature
cleanly onto current `master`, renumbers the hold migration to
`0066_issue_tree_holds`, and preserves the full branch diff in a single
PR.
> - The benefit is that reviewers get one clean, mergeable PR for the
subtree-control feature instead of stale branch history with migration
conflicts.
## What Changed
- Added durable issue subtree hold data structures, shared
API/types/validators, server routes/services, and UI flows for subtree
pause, cancel, and restore operations.
- Added server and UI coverage for subtree previewing, hold
creation/release, dependency-aware scheduling under holds, and issue
detail subtree controls.
- Rebased the branch onto current `paperclipai/paperclip:master` and
renumbered the branch migration from `0065_issue_tree_holds` to
`0066_issue_tree_holds` so it no longer conflicts with upstream
`0065_environments`.
- Added a small follow-up commit that makes restore requests return `200
OK` explicitly while keeping pause/cancel hold creation at `201
Created`, and updated the route test to match that contract.
## Verification
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm --filter @paperclipai/shared typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm --filter @paperclipai/ui typecheck`
- `cd server && pnpm exec vitest run
src/__tests__/issue-tree-control-routes.test.ts
src/__tests__/issue-tree-control-service.test.ts
src/__tests__/issue-tree-control-service-unit.test.ts
src/__tests__/heartbeat-dependency-scheduling.test.ts`
- `cd ui && pnpm exec vitest run src/components/IssueChatThread.test.tsx
src/pages/IssueDetail.test.tsx`
## Risks
- This is a broad cross-layer change touching DB/schema, shared
contracts, server orchestration, and UI; regressions are most likely
around subtree status restoration or wake suppression/resume edge cases.
- The migration was renumbered during PR prep to avoid the new upstream
`0065_environments` conflict. Reviewers should confirm the final
`0066_issue_tree_holds` ordering is the only hold-related migration that
lands.
- The issue-tree restore endpoint now responds with `200` instead of
relying on implicit behavior, which is semantically better for a restore
operation but still changes an API detail that clients or tests could
have assumed.
> 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 in the Paperclip Codex runtime (GPT-5-class
tool-using coding model; exact deployment ID/context window is not
exposed inside this session).
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have 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
- [ ] 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.
> - Every heartbeat run needs a concrete place where the agent's adapter
process executes.
> - Today that execution location is implicitly the local machine, which
makes it hard to track, audit, and manage as a first-class runtime
concern.
> - The first step is to represent the current local execution path
explicitly without changing how users experience agent runs.
> - This pull request adds core Environment and Environment Lease
records, then routes existing local heartbeat execution through a
default `Local` environment.
> - The benefit is that local runs remain behavior-preserving while the
system now has durable environment identity, lease lifecycle tracking,
and activity records for execution placement.
## What Changed
- Added `environments` and `environment_leases` database tables, schema
exports, and migration `0065_environments.sql`.
- Added shared environment constants, TypeScript types, and validators
for environment drivers, statuses, lease policies, lease statuses, and
cleanup states.
- Added `environmentService` for listing, reading, creating, updating,
and ensuring company-scoped environments.
- Added environment lease lifecycle operations for acquire, metadata
update, single-lease release, and run-wide release.
- Updated heartbeat execution to lazily ensure a company-scoped default
`Local` environment before adapter execution.
- Updated heartbeat execution to acquire an ephemeral local environment
lease, write `paperclipEnvironment` into the run context snapshot, and
release active leases during run finalization.
- Added activity log events for environment lease acquisition and
release.
- Added tests for environment service behavior and the local heartbeat
environment lifecycle.
- Added a CI-follow-up heartbeat guard so deferred issue comment wakes
are promoted before automatic missing-comment retries, with focused
batching test coverage.
## Verification
Local verification run for this branch:
- `pnpm -r typecheck`
- `pnpm build`
- `pnpm exec vitest run server/src/__tests__/environment-service.test.ts
server/src/__tests__/heartbeat-local-environment.test.ts --pool=forks`
Additional reviewer/CI verification:
- Confirm `pnpm-lock.yaml` is not modified.
- Confirm `pnpm test:run` passes in CI.
- Confirm `PAPERCLIP_E2E_SKIP_LLM=true pnpm run test:e2e` passes in CI.
- Confirm a local heartbeat run creates one active `Local` environment
when needed, records one lease for the run, releases the lease when the
run finishes, and includes `paperclipEnvironment` in the run context
snapshot.
Screenshots: not applicable; this PR has no UI changes.
## Risks
- Migration risk: introduces two new tables and a new migration journal
entry. Review should verify company scoping, indexes, foreign keys, and
enum defaults are correct.
- Lifecycle risk: heartbeat finalization now releases environment leases
in addition to existing runtime cleanup. A finalization bug could leave
stale active leases or mark a failed run's lease incorrectly.
- Behavior-preservation risk: local adapter execution should remain
unchanged apart from environment bookkeeping. Review should pay
attention to the heartbeat path around context snapshot updates and
final cleanup ordering.
- Activity volume risk: each heartbeat run now logs lease acquisition
and release events, increasing activity log volume by two records per
run.
## Model Used
OpenAI GPT-5.4 via Codex CLI. Capabilities used: repository inspection,
TypeScript implementation review, local test/build execution, and
PR-description drafting.
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [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: no UI changes)
- [x] I have updated relevant documentation to reflect my changes (N/A:
no user-facing docs or commands changed)
- [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.
> - Operators supervise that work through issues, comments, approvals,
and the board UI.
> - Some agent proposals need structured board/user decisions, not
hidden markdown conventions or heavyweight governed approvals.
> - Issue-thread interactions already provide a natural thread-native
surface for proposed tasks and questions.
> - This pull request extends that surface with request confirmations,
richer interaction cards, and agent/plugin/MCP helpers.
> - The benefit is that plan approvals and yes/no decisions become
explicit, auditable, and resumable without losing the single-issue
workflow.
## What Changed
- Added persisted issue-thread interactions for suggested tasks,
structured questions, and request confirmations.
- Added board UI cards for interaction review, selection, question
answers, and accept/reject confirmation flows.
- Added MCP and plugin SDK helpers for creating interaction cards from
agents/plugins.
- Updated agent wake instructions, onboarding assets, Paperclip skill
docs, and public docs to prefer structured confirmations for
issue-scoped decisions.
- Rebased the branch onto `public-gh/master` and renumbered branch
migrations to `0063` and `0064`; the idempotency migration uses `ADD
COLUMN IF NOT EXISTS` for old branch users.
## Verification
- `git diff --check public-gh/master..HEAD`
- `pnpm exec vitest run packages/adapter-utils/src/server-utils.test.ts
packages/mcp-server/src/tools.test.ts
packages/shared/src/issue-thread-interactions.test.ts
ui/src/lib/issue-thread-interactions.test.ts
ui/src/lib/issue-chat-messages.test.ts
ui/src/components/IssueThreadInteractionCard.test.tsx
ui/src/components/IssueChatThread.test.tsx
server/src/__tests__/issue-thread-interaction-routes.test.ts
server/src/__tests__/issue-thread-interactions-service.test.ts
server/src/services/issue-thread-interactions.test.ts` -> 9 files / 79
tests passed
- `pnpm -r typecheck` -> passed, including `packages/db` migration
numbering check
## Risks
- Medium: this adds a new issue-thread interaction model across
db/shared/server/ui/plugin surfaces.
- Migration risk is reduced by placing this branch after current master
migrations (`0063`, `0064`) and making the idempotency column add
idempotent for users who applied the old branch numbering.
- UI interaction behavior is covered by component tests, but this PR
does not include browser 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-class coding agent runtime. Exact model ID and
context window are not exposed in this Paperclip run; tool use and local
shell/code execution were enabled.
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have 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 orchestrates AI agents for zero-human companies.
> - Operators and agents coordinate through company-scoped issues,
comments, documents, and task relationships.
> - Issue text can mention other tickets, but those references were
previously plain markdown/text without durable relationship data.
> - That made it harder to understand related work, surface backlinks,
and keep cross-ticket context visible in the board.
> - This pull request adds first-class issue reference extraction,
storage, API responses, and UI surfaces.
> - The benefit is that issue references become queryable, navigable,
and visible without relying on ad hoc text scanning.
## What Changed
- Added shared issue-reference parsing utilities and exported
reference-related types/constants.
- Added an `issue_reference_mentions` table, idempotent migration DDL,
schema exports, and database documentation.
- Added server-side issue reference services, route integration,
activity summaries, and a backfill command for existing issue content.
- Added UI reference pills, related-work panels, markdown/editor mention
handling, and issue detail/property rendering updates.
- Added focused shared, server, and UI tests for parsing, persistence,
display, and related-work behavior.
- Rebased `PAP-735-first-class-task-references` cleanly onto
`public-gh/master`; no `pnpm-lock.yaml` changes are included.
## Verification
- `pnpm -r typecheck`
- `pnpm test:run packages/shared/src/issue-references.test.ts
server/src/__tests__/issue-references-service.test.ts
ui/src/components/IssueRelatedWorkPanel.test.tsx
ui/src/components/IssueProperties.test.tsx
ui/src/components/MarkdownBody.test.tsx`
## Risks
- Medium risk because this adds a new issue-reference persistence path
that touches shared parsing, database schema, server routes, and UI
rendering.
- Migration risk is mitigated by `CREATE TABLE IF NOT EXISTS`, guarded
foreign-key creation, and `CREATE INDEX IF NOT EXISTS` statements so
users who have applied an older local version of the numbered migration
can re-run safely.
- UI risk is limited by focused component coverage, but reviewers should
still manually inspect issue detail pages containing ticket references
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 Codex, GPT-5-based coding agent, tool-using shell workflow with
repository inspection, git rebase/push, typecheck, and focused Vitest
verification.
## 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: dotta <dotta@example.com>
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system is the extension path for optional capabilities
that should not require core product changes for every integration.
> - Plugins need scoped host APIs for issue orchestration, documents,
wakeups, summaries, activity attribution, and isolated database state.
> - Without those host APIs, richer plugins either cannot coordinate
Paperclip work safely or need privileged core-side special cases.
> - This pull request adds the plugin orchestration host surface, scoped
route dispatch, a database namespace layer, and a smoke plugin that
exercises the contract.
> - The benefit is a broader plugin API that remains company-scoped,
auditable, and covered by tests.
## What Changed
- Added plugin orchestration host APIs for issue creation, document
access, wakeups, summaries, plugin-origin activity, and scoped API route
dispatch.
- Added plugin database namespace tables, schema exports, migration
checks, and idempotent replay coverage under migration
`0059_plugin_database_namespaces`.
- Added shared plugin route/API types and validators used by server and
SDK boundaries.
- Expanded plugin SDK types, protocol helpers, worker RPC host behavior,
and testing utilities for orchestration flows.
- Added the `plugin-orchestration-smoke-example` package to exercise
scoped routes, restricted database namespaces, issue orchestration,
documents, wakeups, summaries, and UI status surfaces.
- Kept the new orchestration smoke fixture out of the root pnpm
workspace importer so this PR preserves the repository policy of not
committing `pnpm-lock.yaml`.
- Updated plugin docs and database docs for the new orchestration and
database namespace surfaces.
- Rebased the branch onto `public-gh/master`, resolved conflicts, and
removed `pnpm-lock.yaml` from the final PR diff.
## Verification
- `pnpm install --frozen-lockfile`
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm exec vitest run packages/db/src/client.test.ts`
- `pnpm exec vitest run server/src/__tests__/plugin-database.test.ts
server/src/__tests__/plugin-orchestration-apis.test.ts
server/src/__tests__/plugin-routes-authz.test.ts
server/src/__tests__/plugin-scoped-api-routes.test.ts
server/src/__tests__/plugin-sdk-orchestration-contract.test.ts`
- From `packages/plugins/examples/plugin-orchestration-smoke-example`:
`pnpm exec vitest run --config ./vitest.config.ts`
- `pnpm --dir
packages/plugins/examples/plugin-orchestration-smoke-example run
typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- PR CI on latest head `293fc67c`: `policy`, `verify`, `e2e`, and
`security/snyk` all passed.
## Risks
- Medium risk: this expands plugin host authority, so route auth,
company scoping, and plugin-origin activity attribution need careful
review.
- Medium risk: database namespace migration behavior must remain
idempotent for environments that may have seen earlier branch versions.
- Medium risk: the orchestration smoke fixture is intentionally excluded
from the root workspace importer to avoid a `pnpm-lock.yaml` PR diff;
direct fixture verification remains listed above.
- Low operational risk from the PR setup itself: the branch is rebased
onto current `master`, the migration is ordered after upstream
`0057`/`0058`, and `pnpm-lock.yaml` is not in the final diff.
> 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`.
Roadmap checked: this work aligns with the completed Plugin system
milestone and extends the plugin surface rather than duplicating an
unrelated planned core feature.
## Model Used
- OpenAI Codex, GPT-5-based coding agent in a tool-enabled CLI
environment. Exact hosted model build and context-window size are not
exposed by the runtime; reasoning/tool use were enabled for repository
inspection, editing, testing, git operations, and PR creation.
## 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 (N/A: no core UI screen change; example plugin UI contract
is covered by tests)
- [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
> - That operator experience depends not just on issue chat, but also on
how workspaces, inbox groups, and navigation state behave over
long-running sessions
> - The current branch included a separate cluster of workspace-runtime
controls, inbox grouping, sidebar ordering, and worktree lifecycle fixes
> - Those changes cross server, shared contracts, database state, and UI
navigation, but they still form one coherent operator workflow area
> - This pull request isolates the workspace/runtime and navigation
ergonomics work into one standalone branch
> - The benefit is better workspace recovery and navigation persistence
without forcing reviewers through the unrelated issue-detail/chat work
## What Changed
- Improved execution workspace and project workspace controls, request
wiring, layout, and JSON editor ergonomics
- Hardened linked worktree reuse/startup behavior and documented the
`worktree repair` flow for recovering linked worktrees safely
- Added inbox workspace grouping, mobile collapse, archive undo,
keyboard navigation, shared group-header styling, and persisted
collapsed-group behavior
- Added persistent sidebar order preferences with the supporting DB
migration, shared/server contracts, routes, services, hooks, and UI
integration
- Scoped issue-list preferences by context and added targeted UI/server
tests for workspace controls, inbox behavior, sidebar preferences, and
worktree validation
## Verification
- `pnpm vitest run
server/src/__tests__/sidebar-preferences-routes.test.ts
ui/src/pages/Inbox.test.tsx
ui/src/components/ProjectWorkspaceSummaryCard.test.tsx
ui/src/components/WorkspaceRuntimeControls.test.tsx
ui/src/api/workspace-runtime-control.test.ts`
- `server/src/__tests__/workspace-runtime.test.ts` was attempted, but
the embedded Postgres suite self-skipped/hung on this host after
reporting an init-script issue, so it is not counted as a local pass
here
## Risks
- Medium: this branch includes migration-backed preference storage plus
worktree/runtime behavior, so merge review should pay attention to state
persistence and worktree recovery semantics
- The sidebar preference migration is standalone, but it should still be
watched for conflicts if another migration lands first
## Model Used
- OpenAI Codex coding agent (GPT-5-class runtime in Codex CLI; exact
deployed model ID is not exposed in this environment), reasoning
enabled, tool use and local code execution 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)
- [ ] 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>
Introduce a singleton instance_settings store and experimental settings API, add the Experimental instance settings page, and gate execution workspace behavior behind the new enableIsolatedWorkspaces flag.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
* public-gh/master: (51 commits)
Use attachment-size limit for company logos
Address Greptile company logo feedback
Drop lockfile from PR branch
Use asset-backed company logos
fix: use appType "custom" for Vite dev server so worktree branding is applied
docs: fix documentation drift — adapters, plugins, tech stack
docs: update documentation for accuracy after plugin system launch
chore: ignore superset artifacts
Dark theme for CodeMirror code blocks in MDXEditor
Remove duplicate @paperclipai/adapter-openclaw-gateway in server/package.json
Fix code block styles with robust prose overrides
Add Docker setup for untrusted PR review in isolated containers
Fix org chart canvas height to fit viewport without scrolling
Add doc-maintenance skill for periodic documentation accuracy audits
Fix sidebar scrollbar: hide track background when not hovering
Restyle markdown code blocks: dark background, smaller font, compact padding
Add archive project button and filter archived projects from selectors
fix: address review feedback — subscription cleanup, filter nullability, stale diagram
fix: wire plugin event subscriptions from worker to host
fix(ui): hide scrollbar track background when sidebar is not hovered
...
# Conflicts:
# packages/db/src/migrations/meta/0030_snapshot.json
# packages/db/src/migrations/meta/_journal.json
* public-gh/master:
Drop lockfile from watcher change
Tighten plugin dev file watching
Fix plugin smoke example typecheck
Fix plugin dev watcher and migration snapshot
Clarify plugin authoring and external dev workflow
Expand kitchen sink plugin demos
fix: set AGENT_HOME env var for agent processes
Add kitchen sink plugin example
Simplify plugin runtime and cleanup lifecycle
Add plugin framework and settings UI
# Conflicts:
# packages/db/src/migrations/meta/0029_snapshot.json
# packages/db/src/migrations/meta/_journal.json
New labels and issue_labels tables with cascade deletes, unique
per-company name constraint. CRUD routes for labels, label filtering
on issue list, and label sync on issue create/update. All issue
responses now include labels array.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add Better Auth, drizzle-orm, @dnd-kit, and remark-gfm dependencies.
Introduce DB schema for auth tables (user, session, account, verification),
company memberships, instance user roles, permission grants, invites, and
join requests. Add assigneeUserId to issues. Extend shared config schema
with deployment mode/exposure/auth settings, add access types and validators,
and wire up new API path constants.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Create project_goals join table with composite PK (project_id, goal_id),
backfill from existing projects.goal_id, and update the project service
to read/write through the join table. Shared types now include goalIds
and goals arrays on Project. Legacy goalId column is kept in sync.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Introduces a provider-agnostic storage subsystem for file attachments.
Includes local disk and S3 backends, asset/attachment DB schemas, issue
attachment CRUD routes with multer upload, CLI configure/doctor/env
integration, and enriched issue ancestors with project/goal resolution.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Introduce company_secrets and company_secret_versions tables for
encrypted secret storage. Add EnvBinding discriminated union (plain vs
secret_ref) to replace raw string env values in adapter configs. Add
hiddenAt column to issues for soft-hiding. Improve migration system
with journal-ordered application and manual fallback when Drizzle
migrator can't reconcile history.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add agent_task_sessions table for per-task session state keyed by
(agent, adapter, taskKey). Add AgentTaskSession type, resetAgentSessionSchema
validator, and sessionDisplayId/sessionParamsJson to AgentRuntimeState.
Rework migration hash-resolution fallback ordering to prefer hash-based
matching over timestamp-based journal matching. Move backup-db.sh logic
into packages/db/src/backup.ts for programmatic use and simplify the shell
script to call the TypeScript implementation.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add agent_config_revisions table for tracking agent configuration changes with
rollback support. Add issue_approvals junction table linking issues to approvals.
New migrations (0005, 0006) for permissions column and new tables. Rework migration
client with statement-level idempotency checks (table/column/index/constraint
existence) so migrations can be safely retried against partially-migrated databases.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add pending_approval agent status, permissions jsonb column, and AgentPermissions
type with canCreateAgents flag. Add approval_comments table and ApprovalComment
type. Extend approval statuses with revision_requested. Add validators for
permission updates, approval revision requests, resubmission, and approval
comments. Add requireBoardApprovalForNewAgents to company update schema.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
New schemas: agent_runtime_state, agent_wakeup_requests,
heartbeat_run_events. New migrations for runtime tables. Expand
heartbeat types with run events, wakeup reasons, and adapter state.
Add live event types. Update agent schema and shared constants.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add new DB schemas: companies, agent_api_keys, approvals, cost_events,
heartbeat_runs, issue_comments. Add corresponding shared types and
validators. Update existing schemas (agents, goals, issues, projects)
with new fields for company association, budgets, and richer metadata.
Generate initial Drizzle migration. Update seed data.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Devin Foley
