fix(pending): allow suggest-tier 'upsert' drafts; make dependency wiring owner-only

The pending_changes.action CHECK only permitted create/update/delete, so a
suggest-tier agent hitting POST /api/refs/upsert (or the resource dependency
routes) 500'd on the INSERT (docs/security-followups.md HIGH finding).

- migration 009: widen CHECK to include 'upsert'
- applyPendingChange: dispatch 'upsert' -> refsRepo.upsertByExternal on approve
- resources.js: add_dependency/remove_dependency are now owner-only (requireOwner),
  infra wiring is never diverted to pending_changes
- tests/api/pending_extended_actions.test.js: regression coverage

Full suite green (278 pass / 1 skip).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

docs/security-followups.md

@@ -39,6 +39,13 @@ defensible for the alpha. (a) is the right long-term answer.
 
 ## Migration 006 (audit + pending_changes) — Plan 2 finding
 
+> **✅ RESOLVED 2026-06-01** (migration `009_pending_upsert_action.sql`). Applied the
+> recommended fix: (1) `upsert` is now a valid `pending_changes.action` with an
+> approval dispatch arm (`applyPendingChange` → `refsRepo.upsertByExternal`); (3)
+> `add_dependency` / `remove_dependency` routes are now **owner-only** (`requireOwner`)
+> and never divert to `pending_changes`. Regression coverage in
+> `tests/api/pending_extended_actions.test.js`. Original finding kept below for context.
+
 **[HIGH] `pending_changes.action` CHECK constraint blocks extended actions emitted
 by some routes.** The table's CHECK accepts only `('create','update','delete')`,
 but the following routes call `divertToPending` with actions outside that set:

lib/api/routes/pending_changes.js

@@ -22,10 +22,10 @@ const REPOS = {
   source_doc: sourceDocsRepo
 };
 
-// Action dispatch only supports the three CHECK-allowed actions on
-// pending_changes. Extended actions like 'upsert' / 'add_dependency' /
-// 'remove_dependency' are surfaced from a few routes but are blocked at
-// the DB level today — see docs/security-followups.md.
+// Action dispatch for approving a pending_change. 'create'/'update'/'delete'
+// plus 'upsert' (the suggestion path from POST /api/refs/upsert). Dependency
+// mutations are owner-only and never reach pending_changes — see
+// docs/security-followups.md.
 export async function applyPendingChange(row, actor) {
   const repo = REPOS[row.entity_type];
   if (!repo) throw new ValidationError(`unsupported entity_type for approval: ${row.entity_type}`);
@@ -34,6 +34,10 @@ export async function applyPendingChange(row, actor) {
       const created = await repo.create(row.payload, actor);
       return created.id;
     }
+    case 'upsert': {
+      const row_ = await repo.upsertByExternal(row.payload, actor);
+      return row_.id;
+    }
     case 'update': {
       await repo.update(row.entity_id, row.payload, actor);
       return row.entity_id;

lib/api/routes/resources.js

@@ -5,7 +5,7 @@ import * as sourceDocs from '../../db/repos/source_docs.js';
 import * as audit from '../../db/repos/audit.js';
 import { validate } from '../validate.js';
 import { NotFoundError, ValidationError, ConflictError, asyncWrap } from '../errors.js';
-import { requireWrite, divertToPending } from '../cap.js';
+import { requireWrite, requireOwner, divertToPending } from '../cap.js';
 
 const RUNTIME = ['lxc', 'vm', 'docker', 'bare-metal'];
 const STATUSES = ['running', 'stopped', 'down', 'unknown'];
@@ -103,18 +103,14 @@ router.delete('/:id',
   })
 );
 
+// Dependency wiring is infra-level: owner-only, never diverted to pending_changes.
 router.post('/:id/dependencies',
-  requireWrite('resource'),
+  requireOwner,
   validate({ params: idParams, body: depBody }),
   asyncWrap(async (req, res) => {
     if (req.params.id === req.body.depends_on) {
       throw new ValidationError('resource cannot depend on itself');
     }
-    if (req.capTier === 'suggest') {
-      return divertToPending(req, res, {
-        entity_type: 'resource', entity_id: req.params.id, action: 'add_dependency', payload: req.body
-      });
-    }
     try {
       await repo.addDependency(req.params.id, req.body.depends_on, req.body.kind);
       res.status(201).json({ resource_id: req.params.id, depends_on: req.body.depends_on });
@@ -135,15 +131,9 @@ router.get('/:id/dependencies',
 );
 
 router.delete('/:id/dependencies/:dep_id',
-  requireWrite('resource'),
+  requireOwner,
   validate({ params: depParams }),
   asyncWrap(async (req, res) => {
-    if (req.capTier === 'suggest') {
-      return divertToPending(req, res, {
-        entity_type: 'resource', entity_id: req.params.id, action: 'remove_dependency',
-        payload: { depends_on: req.params.dep_id }
-      });
-    }
     await repo.removeDependency(req.params.id, req.params.dep_id);
     res.status(204).end();
   })

lib/db/migrations/009_pending_upsert_action.sql

@@ -0,0 +1,9 @@
+-- Allow the legitimate suggestion action 'upsert' on pending_changes.
+-- A suggest-tier agent hitting POST /api/refs/upsert previously 500'd because
+-- the inline CHECK only permitted create/update/delete (docs/security-followups.md).
+-- 'add_dependency' / 'remove_dependency' are intentionally NOT added here:
+-- those routes become owner-only and never divert to pending_changes.
+ALTER TABLE pending_changes DROP CONSTRAINT IF EXISTS pending_changes_action_check;
+ALTER TABLE pending_changes
+  ADD CONSTRAINT pending_changes_action_check
+  CHECK (action IN ('create','update','delete','upsert'));

tests/api/pending_extended_actions.test.js

@@ -0,0 +1,105 @@
+import { describe, it, expect, beforeAll, beforeEach } from 'vitest';
+import request from 'supertest';
+import { setup } from './helpers.js';
+import * as spacesRepo from '../../lib/db/repos/spaces.js';
+import * as agentsRepo from '../../lib/db/repos/agents.js';
+import * as refsRepo from '../../lib/db/repos/refs.js';
+import * as pendingChanges from '../../lib/db/repos/pending_changes.js';
+
+// Regression coverage for docs/security-followups.md:
+// the pending_changes.action CHECK previously rejected the extended actions
+// 'upsert' / 'add_dependency' / 'remove_dependency', so a suggest-tier agent
+// hitting those routes 500'd on the INSERT. Fix: 'upsert' is a legitimate
+// suggestion path (widen CHECK + add an approval dispatch arm); dependency
+// mutations are infra wiring and become owner-only.
+
+let app, ownerHeaders, space;
+const owner = { kind: 'user', id: null };
+
+async function mintAgent(slug, caps, scopes = {}) {
+  const a = await agentsRepo.create({
+    slug, name: slug, kind: 'claude', model: 'sonnet',
+    capabilities: caps, scopes
+  }, owner);
+  const { token } = await agentsRepo.createToken(a.id, 'test');
+  return { agent: a, headers: { Authorization: `Bearer ${token}` } };
+}
+
+async function makeResource(spaceId, slug) {
+  const res = await request(app).post(`/api/spaces/${spaceId}/resources`).set(ownerHeaders)
+    .send({ slug, name: slug, runtime_type: 'lxc' });
+  return res.body;
+}
+
+beforeAll(async () => { ({ app, ownerHeaders } = await setup()); });
+beforeEach(async () => {
+  space = await spacesRepo.create({ slug: `s-${Date.now()}-${Math.random().toString(36).slice(2,5)}`, name: 'S' }, owner);
+});
+
+describe('ref upsert as a suggest-tier draft', () => {
+  it('suggest-tier upsert diverts to a pending_change with action=upsert (not 500)', async () => {
+    const { agent, headers } = await mintAgent(`sug-up-${Date.now()}`, { read: true, suggest: true });
+    const res = await request(app).post('/api/refs/upsert').set(headers).send({
+      space_id: space.id, kind: 'url', source_url: 'https://x', title: 'X',
+      source_kind: 'karakeep', external_id: 'ext-1'
+    });
+    expect(res.status).toBe(202);
+    expect(res.body.pending).toBe(true);
+    const change = await pendingChanges.getById(res.body.change_id);
+    expect(change.agent_id).toBe(agent.id);
+    expect(change.entity_type).toBe('ref');
+    expect(change.action).toBe('upsert');
+    expect(change.payload.external_id).toBe('ext-1');
+  });
+
+  it('approving an upsert pending_change creates the ref via upsertByExternal', async () => {
+    const { headers } = await mintAgent(`sug-up2-${Date.now()}`, { read: true, suggest: true });
+    const draft = await request(app).post('/api/refs/upsert').set(headers).send({
+      space_id: space.id, kind: 'url', source_url: 'https://y', title: 'Y',
+      source_kind: 'karakeep', external_id: 'ext-2'
+    });
+    expect(draft.status).toBe(202);
+
+    const approve = await request(app)
+      .post(`/api/pending-changes/${draft.body.change_id}/approve`).set(ownerHeaders);
+    expect(approve.status).toBe(200);
+
+    const list = await refsRepo.list({ space_id: space.id, kind: 'url', limit: 50, offset: 0 });
+    const created = list.find(r => r.external_id === 'ext-2');
+    expect(created).toBeTruthy();
+    expect(created.title).toBe('Y');
+  });
+});
+
+describe('resource dependency mutations are owner-only', () => {
+  it('owner can add and remove a dependency', async () => {
+    const a = await makeResource(space.id, 'dep-a');
+    const b = await makeResource(space.id, 'dep-b');
+    const add = await request(app).post(`/api/resources/${a.id}/dependencies`).set(ownerHeaders)
+      .send({ depends_on: b.id });
+    expect(add.status).toBe(201);
+    const del = await request(app).delete(`/api/resources/${a.id}/dependencies/${b.id}`).set(ownerHeaders);
+    expect(del.status).toBe(204);
+  });
+
+  it('an agent (even suggest tier) cannot add a dependency → 403, no pending_change', async () => {
+    const a = await makeResource(space.id, 'dep-c');
+    const b = await makeResource(space.id, 'dep-d');
+    const { headers } = await mintAgent(`sug-dep-${Date.now()}`, { read: true, suggest: true });
+    const res = await request(app).post(`/api/resources/${a.id}/dependencies`).set(headers)
+      .send({ depends_on: b.id });
+    expect(res.status).toBe(403);
+    const pending = await pendingChanges.listPending({ limit: 50 });
+    expect(pending.some(p => p.action === 'add_dependency')).toBe(false);
+  });
+
+  it('an agent cannot remove a dependency → 403', async () => {
+    const a = await makeResource(space.id, 'dep-e');
+    const b = await makeResource(space.id, 'dep-f');
+    await request(app).post(`/api/resources/${a.id}/dependencies`).set(ownerHeaders)
+      .send({ depends_on: b.id });
+    const { headers } = await mintAgent(`sug-dep2-${Date.now()}`, { read: true, suggest: true });
+    const res = await request(app).delete(`/api/resources/${a.id}/dependencies/${b.id}`).set(headers);
+    expect(res.status).toBe(403);
+  });
+});