## 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>
