## 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 is a local-first control plane for AI-agent companies.
> - Operators need predictable local dev behavior, recoverable instance
data, and scripts that do not churn the running app.
> - Several accumulated changes improve backup streaming, dev-server
health, static UI caching/logging, diagnostic-file ignores, and instance
isolation.
> - These are operational improvements that can land independently from
product UI work.
> - This pull request groups the dev-infra and backup changes from the
split branch into one standalone branch.
> - The benefit is safer local operation, easier manual backups, less
noisy dev output, and less cross-instance auth leakage.
## What Changed
- Added a manual instance database backup endpoint and route tests.
- Streamed backup/restore handling to avoid materializing large payloads
at once.
- Reduced dev static UI log/cache churn and ignored Node diagnostic
report captures.
- Added guarded dev auto-restart health polling coverage.
- Preserved worktree config during provisioning and scoped auth cookies
by instance.
- Added a Discord daily digest helper script and environment
documentation.
- Hardened adapter-route and startup feedback export tests around the
changed infrastructure.
## Verification
- `pnpm install --frozen-lockfile`
- `pnpm exec vitest run packages/db/src/backup-lib.test.ts
server/src/__tests__/instance-database-backups-routes.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts
server/src/__tests__/adapter-routes.test.ts
server/src/__tests__/dev-runner-paths.test.ts
server/src/__tests__/health-dev-server-token.test.ts
server/src/__tests__/http-log-policy.test.ts
server/src/__tests__/vite-html-renderer.test.ts
server/src/__tests__/workspace-runtime.test.ts
server/src/__tests__/better-auth.test.ts`
- Split integration check: merged after the runtime/governance branch
and before UI branches with no merge conflicts.
- Confirmed this branch does not include `pnpm-lock.yaml`.
## Risks
- Medium risk: touches server startup, backup streaming, auth cookie
naming, dev health checks, and worktree provisioning.
- Backup endpoint behavior depends on existing board/admin access
controls and database backup helpers.
- No database migrations are included.
> 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-5.4 tool-enabled coding model, agentic
code-editing/runtime with local shell and GitHub CLI access; exact
context window and reasoning mode are not exposed by the Paperclip
harness.
## 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
> - 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>
Wire up Better Auth for session-based authentication. Add actor middleware
that resolves local_trusted mode to an implicit board actor and authenticated
mode to Better Auth sessions. Add access service with membership, permission,
invite, and join-request management. Register access routes for member/invite/
join-request CRUD. Update health endpoint to report deployment mode and
bootstrap status. Enforce tasks:assign and agents:create permissions in issue
and agent routes. Add deployment mode validation at startup with guardrails
(loopback-only for local_trusted, auth config required for authenticated).
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add AES-256-GCM local encrypted secrets provider with auto-generated
master key, stub providers for AWS/GCP/Vault, and a secrets service
that normalizes adapter configs (converting sensitive inline values to
secret refs in strict mode) and resolves secret refs back to plain
values at runtime. Extract redaction utilities from agent routes into
shared module. Redact sensitive values in activity logs, config
revisions, and approval payloads. Block rollback of revisions
containing redacted secrets. Filter hidden issues from list queries.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Agent management: hire endpoint with permission gates and pending_approval status,
config revision tracking with rollback, agent duplicate route, permission CRUD.
Block pending_approval agents from auth, heartbeat, and assignments.
Approvals: revision request/resubmit flow, approval comments CRUD, issue-approval
linking, auto-wake agents on approval decisions with context snapshot.
Costs: per-agent breakdown, period filtering (month/week/day/all), cost by agent
list endpoint.
Adapters: agentConfigurationDoc on all adapters, /llms/agent-configuration.txt
reflection routes. Inject PAPERCLIP_APPROVAL_ID, PAPERCLIP_APPROVAL_STATUS,
PAPERCLIP_LINKED_ISSUE_IDS into adapter environments.
Sidebar badges endpoint for pending approval/inbox counts. Dashboard and company
settings extensions.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
New routes: companies, approvals, costs, dashboard, authz. New
services: companies, approvals, costs, dashboard, heartbeat,
activity-log. Add auth middleware and structured error handling.
Expand existing agent and issue routes with richer CRUD operations.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Express server with CRUD routes for agents, goals, issues, projects,
and activity log. Includes validation middleware, structured error
handling, request logging, and health check endpoint with tests.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
