[codex] Add resource membership controls (#6677)

## 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>

doc/DATABASE.md

@@ -143,6 +143,17 @@ The database mode is controlled by `DATABASE_URL`:
 
 Your Drizzle schema (`packages/db/src/schema/`) stays the same regardless of mode.
 
+## Resource membership tables
+
+Paperclip stores current-user sidebar membership state in:
+
+- `project_memberships`
+- `agent_memberships`
+
+These rows are company-scoped and user-scoped. A missing row means the user is joined, so existing users keep seeing projects and agents in the sidebar until they explicitly leave them. Rows only control sidebar visibility; they do not affect project/agent detail access, all-pages, selectors, assignment flows, or existing company permissions.
+
+Both tables use a unique key on `(company_id, user_id, resource_id)` and keep `state` as `joined` or `left`. Join/leave mutations are idempotent board-user `/me` operations and write activity entries when the effective state changes.
+
 ## Plugin database namespaces
 
 The plugin runtime tracks plugin-owned database namespaces and migrations in `plugin_database_namespaces` and `plugin_migrations`. Hosted deployments that separate runtime and migration connections should set `DATABASE_MIGRATION_URL`; plugin namespace migration work uses the migration connection when present.

doc/SPEC-implementation.md

@@ -311,7 +311,32 @@ Invariant: each event must attach to agent and company; rollups are aggregation,
 - `details` jsonb null
 - `created_at` timestamptz not null default now()
 
-## 7.12 `company_secrets` + `company_secret_versions`
+## 7.12 `project_memberships` + `agent_memberships`
+
+Per-user project/agent membership is personal visibility state for board users. It only controls whether a resource appears in the current user's sidebar; it must not grant or revoke access to all-pages, detail pages, selectors, assignment flows, search, or existing permissions.
+
+`project_memberships`:
+
+- `id` uuid pk
+- `company_id` uuid fk `companies.id` not null
+- `project_id` uuid fk `projects.id` not null
+- `user_id` text not null
+- `state` enum-like text: `joined | left`
+- `created_at` timestamptz not null default now()
+- `updated_at` timestamptz not null default now()
+- unique `(company_id, user_id, project_id)`
+
+`agent_memberships` mirrors the same shape with `agent_id` instead of `project_id` and unique `(company_id, user_id, agent_id)`.
+
+Invariants:
+
+- Missing membership rows mean `joined` for backward compatibility.
+- Mutations are board-user-only `/me` operations; agent API keys are rejected.
+- Viewer-role board users may update only their own membership rows through the narrow self-service helper.
+- Target project/agent ownership is checked against the path company before mutation.
+- Successful state changes write `resource_membership.joined` or `resource_membership.left` activity entries.
+
+## 7.13 `company_secrets` + `company_secret_versions`
 
 - Secret values are not stored inline in `agents.adapter_config.env`.
 - Agent env entries should use secret refs for sensitive values.
@@ -325,7 +350,7 @@ Operational policy:
 - Activity and approval payloads must not persist raw sensitive values.
 - Config revisions may include redacted placeholders; such revisions are non-restorable for redacted fields.
 
-## 7.13 Required Indexes
+## 7.14 Required Indexes
 
 - `agents(company_id, status)`
 - `agents(company_id, reports_to)`
@@ -343,8 +368,12 @@ Operational policy:
 - `issue_attachments(company_id, issue_id)`
 - `company_secrets(company_id, name)` unique
 - `company_secret_versions(secret_id, version)` unique
+- `project_memberships(company_id, user_id)`
+- `project_memberships(company_id, user_id, project_id)` unique
+- `agent_memberships(company_id, user_id)`
+- `agent_memberships(company_id, user_id, agent_id)` unique
 
-## 7.14 `assets` + `issue_attachments`
+## 7.15 `assets` + `issue_attachments`
 
 - `assets` stores provider-backed object metadata (not inline bytes):
   - `id` uuid pk
@@ -623,14 +652,28 @@ Server behavior:
 - `GET /projects/:projectId`
 - `PATCH /projects/:projectId`
 
-## 10.6 Approvals
+## 10.6 Current-user Resource Memberships
+
+- `GET /companies/:companyId/resource-memberships/me`
+- `PUT /companies/:companyId/resource-memberships/me/projects/:projectId`
+- `PUT /companies/:companyId/resource-memberships/me/agents/:agentId`
+
+Request payload:
+
+```json
+{ "state": "joined" }
+```
+
+Allowed states are `joined` and `left`. Endpoints require a concrete board user and active company membership, reject agent API keys, and only mutate the caller's own sidebar visibility state. Joining/leaving is idempotent; missing rows read as `joined`.
+
+## 10.7 Approvals
 
 - `GET /companies/:companyId/approvals?status=pending`
 - `POST /companies/:companyId/approvals`
 - `POST /approvals/:approvalId/approve`
 - `POST /approvals/:approvalId/reject`
 
-## 10.7 Cost and Budgets
+## 10.8 Cost and Budgets
 
 - `POST /companies/:companyId/cost-events`
 - `GET /companies/:companyId/costs/summary`
@@ -639,7 +682,7 @@ Server behavior:
 - `PATCH /companies/:companyId/budgets`
 - `PATCH /agents/:agentId/budgets`
 
-## 10.8 Activity and Dashboard
+## 10.9 Activity and Dashboard
 
 - `GET /companies/:companyId/activity`
 - `GET /companies/:companyId/dashboard`
@@ -651,7 +694,7 @@ Dashboard payload must include:
 - month-to-date spend and budget utilization
 - pending approvals count
 
-## 10.9 Error Semantics
+## 10.10 Error Semantics
 
 - `400` validation error
 - `401` unauthenticated
@@ -661,7 +704,7 @@ Dashboard payload must include:
 - `422` semantic rule violation
 - `500` server error
 
-## 10.10 Current Implementation API Addenda
+## 10.11 Current Implementation API Addenda
 
 The current app also exposes V1-supporting surfaces for: