[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/adapters/codex-local/src/server/codex-home.test.ts

@@ -0,0 +1,57 @@
+import fs from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it, vi } from "vitest";
+import { prepareManagedCodexHome } from "./codex-home.js";
+
+describe("codex managed home", () => {
+  afterEach(() => {
+    vi.restoreAllMocks();
+  });
+
+  it("treats a concurrently-created expected auth symlink as success", async () => {
+    const root = await fs.mkdtemp(path.join(os.tmpdir(), "paperclip-codex-home-"));
+    const sharedCodexHome = path.join(root, "shared-codex-home");
+    const paperclipHome = path.join(root, "paperclip-home");
+    const managedCodexHome = path.join(
+      paperclipHome,
+      "instances",
+      "default",
+      "companies",
+      "company-1",
+      "codex-home",
+    );
+    const sharedAuth = path.join(sharedCodexHome, "auth.json");
+    const managedAuth = path.join(managedCodexHome, "auth.json");
+
+    await fs.mkdir(sharedCodexHome, { recursive: true });
+    await fs.writeFile(sharedAuth, '{"token":"shared"}\n', "utf8");
+
+    const originalSymlink = fs.symlink.bind(fs);
+    vi.spyOn(fs, "symlink").mockImplementationOnce(async (source, target, type) => {
+      await originalSymlink(source, target, type);
+      const error = new Error("file already exists") as NodeJS.ErrnoException;
+      error.code = "EEXIST";
+      throw error;
+    });
+
+    try {
+      await expect(
+        prepareManagedCodexHome(
+          {
+            CODEX_HOME: sharedCodexHome,
+            PAPERCLIP_HOME: paperclipHome,
+            PAPERCLIP_INSTANCE_ID: "default",
+          },
+          async () => {},
+          "company-1",
+        ),
+      ).resolves.toBe(managedCodexHome);
+
+      expect((await fs.lstat(managedAuth)).isSymbolicLink()).toBe(true);
+      expect(await fs.realpath(managedAuth)).toBe(await fs.realpath(sharedAuth));
+    } finally {
+      await fs.rm(root, { recursive: true, force: true });
+    }
+  });
+});

packages/adapters/codex-local/src/server/codex-home.ts

@@ -45,11 +45,31 @@ async function ensureParentDir(target: string): Promise<void> {
   await fs.mkdir(path.dirname(target), { recursive: true });
 }
 
+async function isExpectedSymlink(target: string, source: string): Promise<boolean> {
+  const existing = await fs.lstat(target).catch(() => null);
+  if (!existing?.isSymbolicLink()) return false;
+
+  const linkedPath = await fs.readlink(target).catch(() => null);
+  if (!linkedPath) return false;
+
+  return path.resolve(path.dirname(target), linkedPath) === path.resolve(source);
+}
+
+async function createExpectedSymlink(target: string, source: string): Promise<void> {
+  try {
+    await fs.symlink(source, target);
+  } catch (error) {
+    const code = (error as NodeJS.ErrnoException).code;
+    if (code === "EEXIST" && await isExpectedSymlink(target, source)) return;
+    throw error;
+  }
+}
+
 async function ensureSymlink(target: string, source: string): Promise<void> {
   const existing = await fs.lstat(target).catch(() => null);
   if (!existing) {
     await ensureParentDir(target);
-    await fs.symlink(source, target);
+    await createExpectedSymlink(target, source);
     return;
   }
 
@@ -57,14 +77,10 @@ async function ensureSymlink(target: string, source: string): Promise<void> {
     return;
   }
 
-  const linkedPath = await fs.readlink(target).catch(() => null);
-  if (!linkedPath) return;
-
-  const resolvedLinkedPath = path.resolve(path.dirname(target), linkedPath);
-  if (resolvedLinkedPath === source) return;
+  if (await isExpectedSymlink(target, source)) return;
 
   await fs.unlink(target);
-  await fs.symlink(source, target);
+  await createExpectedSymlink(target, source);
 }
 
 async function ensureCopiedFile(target: string, source: string): Promise<void> {