[codex] Add agent permissions and controls plan (#6386)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies by keeping
task ownership, approvals, and operator control inside one control
plane.
> - Agent permissions and plugin-hosted company settings sit on the
boundary between autonomy and governance.
> - V1 needs scoped task assignment rules, plugin extension points, and
clearer company access surfaces without weakening company boundaries.
> - The branch builds the core authorization service, plugin SDK/host
APIs, and UI simplifications needed to support those controls.
> - Paperclip EE plugin surfaces were intentionally moved out of this
core PR per review direction, so this PR now carries only the public
core/plugin infrastructure work.
> - The latest updates preserve the PAP-9937 branch changes that belong
in this PR, remove the `design/` artifacts, and exclude the experimental
`plugin-briefs` package.
> - Greptile feedback was applied through the authorization/audit paths
and the final cleanup commit was re-reviewed at 5/5 with no unresolved
Greptile threads.
> - The benefit is safer assignment control with extension hooks for
richer permission products while preserving simple defaults for normal
operators.

## What Changed

- Added scoped task-assignment authorization decisions and routed
issue/agent assignment mutations through the authorization service.
- Added plugin SDK and host APIs for company settings slots,
authorization policy/grant management, assignment previews, and bridge
invocation scope propagation.
- Simplified core company access UI and moved advanced controls behind
plugin-provided settings surfaces.
- Added retry-now affordances for blocked issue next-step notices.
- Added protected-assignment enforcement for persisted
agent/project/issue policies, including explicit-grant fallback
behavior.
- Added incremental principal-access compatibility backfill for active
agent memberships and role-default human permission grants.
- Added the Markdown code block wrap action fix from the latest branch
changes.
- Removed `design/` artifacts from the PR and removed
`packages/plugins/plugin-briefs` from the final diff.
- Addressed Greptile feedback for plugin actor sanitization, legacy
membership handling, audit pagination, unknown grant-scope metadata, and
startup test mocks.

## Verification

- `pnpm exec vitest run server/src/__tests__/access-service.test.ts
server/src/__tests__/company-portability.test.ts` -> 2 files passed, 54
tests passed.
- `pnpm exec vitest run
server/src/__tests__/server-startup-feedback-export.test.ts
server/src/__tests__/access-service.test.ts
server/src/__tests__/company-portability.test.ts` -> 3 files passed, 62
tests passed.
- `pnpm exec vitest run
server/src/__tests__/authorization-service.test.ts
server/src/__tests__/plugin-access-authorization-host-services.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts` -> 3 files
passed, 28 tests passed.
- `pnpm --filter @paperclipai/server typecheck` -> passed.
- `git diff --check` -> passed.
- `node ./scripts/check-docker-deps-stage.mjs` -> passed.
- `CI=true pnpm install --frozen-lockfile --ignore-scripts` -> passed
with no lockfile update.
- `pnpm exec vitest run
ui/src/components/MarkdownBody.interaction.test.tsx` -> 1 test passed.
- `git ls-files design packages/plugins/plugin-briefs | wc -l` -> 0.
- GitHub CI on `40cd83b53` -> all checks passed, merge state `CLEAN`.
- Greptile on `40cd83b53` -> 5/5, 102 files reviewed, 0
comments/annotations added, 0 unresolved review threads.
- Confirmed the PR diff contains no `design/`,
`packages/plugins/plugin-briefs`, `pnpm-lock.yaml`, or
`.github/workflows` changes.

## Risks

- Medium: task assignment authorization paths are behaviorally stricter
for protected/private policy data, so existing plugin-authored policies
may block assignment until explicit grants or approval flows are
configured.
- Medium: plugin-host authorization APIs expand the surface area
available to trusted plugins and need careful review for company
scoping.
- Low: startup now performs a principal-access compatibility backfill,
but the migration and runtime backfill use conflict-tolerant inserts.

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex, GPT-5 coding agent, tool-enabled workflow with shell,
git, and GitHub CLI access.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

packages/db/src/migrations/0087_backfill_environment_manage_human_defaults.sql

@@ -0,0 +1,29 @@
+INSERT INTO "principal_permission_grants" (
+  "company_id",
+  "principal_type",
+  "principal_id",
+  "permission_key",
+  "scope",
+  "granted_by_user_id",
+  "created_at",
+  "updated_at"
+)
+SELECT
+  "company_id",
+  'user',
+  "principal_id",
+  'environments:manage',
+  NULL,
+  NULL,
+  now(),
+  now()
+FROM "company_memberships"
+WHERE "principal_type" = 'user'
+  AND "status" = 'active'
+  AND "membership_role" IN ('owner', 'admin')
+ON CONFLICT (
+  "company_id",
+  "principal_type",
+  "principal_id",
+  "permission_key"
+) DO NOTHING;

packages/db/src/migrations/0088_backfill_principal_access_compatibility.sql

@@ -0,0 +1,75 @@
+INSERT INTO "company_memberships" (
+  "company_id",
+  "principal_type",
+  "principal_id",
+  "status",
+  "membership_role",
+  "created_at",
+  "updated_at"
+)
+SELECT
+  "company_id",
+  'agent',
+  "id",
+  'active',
+  'member',
+  now(),
+  now()
+FROM "agents"
+WHERE "status" NOT IN ('pending_approval', 'terminated')
+ON CONFLICT (
+  "company_id",
+  "principal_type",
+  "principal_id"
+) DO NOTHING;
+
+INSERT INTO "principal_permission_grants" (
+  "company_id",
+  "principal_type",
+  "principal_id",
+  "permission_key",
+  "scope",
+  "granted_by_user_id",
+  "created_at",
+  "updated_at"
+)
+SELECT
+  memberships."company_id",
+  'user',
+  memberships."principal_id",
+  role_defaults."permission_key",
+  NULL,
+  NULL,
+  now(),
+  now()
+FROM "company_memberships" memberships
+JOIN (
+  VALUES
+    ('owner', 'agents:create'),
+    ('owner', 'environments:manage'),
+    ('owner', 'users:invite'),
+    ('owner', 'users:manage_permissions'),
+    ('owner', 'tasks:assign'),
+    ('owner', 'joins:approve'),
+    ('admin', 'agents:create'),
+    ('admin', 'environments:manage'),
+    ('admin', 'users:invite'),
+    ('admin', 'tasks:assign'),
+    ('admin', 'joins:approve'),
+    ('operator', 'tasks:assign')
+) AS role_defaults("membership_role", "permission_key")
+  ON role_defaults."membership_role" = CASE
+    WHEN memberships."membership_role" = 'owner' THEN 'owner'
+    WHEN memberships."membership_role" = 'admin' THEN 'admin'
+    WHEN memberships."membership_role" = 'viewer' THEN 'viewer'
+    WHEN memberships."membership_role" = 'member' THEN 'operator'
+    ELSE 'operator'
+  END
+WHERE memberships."principal_type" = 'user'
+  AND memberships."status" = 'active'
+ON CONFLICT (
+  "company_id",
+  "principal_type",
+  "principal_id",
+  "permission_key"
+) DO NOTHING;

packages/db/src/migrations/meta/_journal.json

@@ -610,6 +610,20 @@
       "when": 1778976000000,
       "tag": "0086_routine_env_runtime_contract",
       "breakpoints": true
+    },
+    {
+      "idx": 87,
+      "version": "7",
+      "when": 1779360000000,
+      "tag": "0087_backfill_environment_manage_human_defaults",
+      "breakpoints": true
+    },
+    {
+      "idx": 88,
+      "version": "7",
+      "when": 1779446400000,
+      "tag": "0088_backfill_principal_access_compatibility",
+      "breakpoints": true
     }
   ]
 }