[codex] Add built-in agents and Reflection Coach bundle (#9206)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Operators need first-party agent capabilities for repeatable company
work, not just manually created one-off agents.
> - Built-in agents need to behave like normal company-scoped agents
while preserving approval gates, permissions, budgets, and audit trails.
> - Reflection and coaching work also needs bundled instructions, skill
content, and a routine so the feature can be installed and reset
predictably.
> - The API, database, UI, portability, and tests all need to agree on
the built-in lifecycle from not provisioned through setup, approval,
ready, paused, and reset.
> - This pull request adds built-in agent provisioning and the
Reflection Coach bundle end-to-end.
> - The benefit is a safer first-party path for Paperclip-managed agents
without bypassing the same governance model used for operator-created
agents.

## Linked Issues or Issue Description

No public GitHub issue was found for this exact built-in agent and
Reflection Coach bundle work.

Problem/motivation:
- Paperclip did not have a first-party built-in agent lifecycle for
product-owned agents.
- Bundled agent resources such as default instructions, skills, and
routines needed managed ownership and reset semantics.
- Approval-gated companies needed built-in setup to preserve requested
adapter, budget, manager, and permission state through board approval.
- The board UI needed clear built-in badges, setup affordances,
readiness state, and bundle status without exposing secrets.

Proposed solution:
- Add a company-scoped built-in agent registry,
provisioning/reset/reconcile/status APIs, and Reflection Coach bundled
resources.
- Track bundled managed resources in the database with idempotent
migration behavior.
- Reuse existing agent approval, authorization, budget, and activity-log
paths instead of creating a bypass.
- Add UI setup, badges, gates, bundle panels, and route coverage for
built-in agents.

Duplicate search:
- Searched GitHub PRs for `built-in agents Reflection Coach
repo:paperclipai/paperclip`; only this PR was returned.
- Searched GitHub issues for the same query; no public issues were
returned.

## What Changed

- Added built-in agent definitions, lifecycle state derivation,
provisioning, reset, reconcile, status, and routine-control routes.
- Added the `built_in_managed_resources` migration and schema exports
for bundled instructions, skill, and routine ownership.
- Added the Reflection Coach built-in bundle with default instructions,
skill catalog content, routine template, default permissions, and
managed-resource drift handling.
- Added approval-aware provisioning behavior that preserves requested
adapter config, budgets, manager assignment, and built-in permissions
through hire approval.
- Added authorization and mutation gates for built-in agent and skill
changes, including consented Reflection Coach change paths.
- Added UI surfaces for built-in agent setup, roster/detail badges,
readiness gates, bundle status, routine controls, and route filtering.
- Added company import/export and validator coverage for built-in
managed resources and low-trust/red-team presets.
- Addressed Greptile follow-ups for pending approval reconciliation,
consent-gate error propagation, config-read authorization fallback,
approval-path manager preservation, and non-model adapter provisioning.

## Verification

Local verification:
- `git diff --check public/master..HEAD` passed.
- `pnpm check:token-gates` passed with all gates clean.
- `pnpm exec vitest run
ui/src/components/ConfigureBuiltInAgentModal.test.tsx` passed: 1 file, 4
tests.
- `pnpm exec vitest run ui/src/components/EntityRow.test.tsx
ui/src/pages/Agents.test.tsx ui/src/components/BuiltInAgentGate.test.tsx
ui/src/components/ConfigureBuiltInAgentModal.test.tsx
ui/src/components/BuiltInBundlePanel.test.tsx
ui/src/pages/InstanceExperimentalSettings.test.tsx
ui/src/pages/Routines.test.tsx` passed: 7 files, 64 tests.
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/built-in-agents.test.ts
src/__tests__/authorization-service.test.ts
src/__tests__/company-skills-routes.test.ts` passed: 3 files, 91 tests.
- `pnpm --filter @paperclipai/db check:migrations` passed.
- `pnpm -r typecheck` passed after the rebase; `pnpm --filter ui
typecheck` passed after the final UI review fix.

Remote verification on latest head
`1c61f693a4ec881d739022b0e75a8ca8bf8c2cd8`:
- Merge state: `CLEAN`.
- Greptile: `5/5`, zero unresolved Greptile threads.
- PR check rollup: all checks successful, neutral, or skipped as
expected.
- Passing gates include Build, Typecheck + Release Registry, all server
shards, all workspace shards, all serialized server suites, e2e, Canary
Dry Run, policy, review, verify, Socket, Superagent, and Snyk.

## Risks

- This adds a new managed-resource table and migration; the migration
uses idempotent create/add/index guards and passed migration safety
checks.
- Built-in agent provisioning touches approval and authorization paths;
tests cover pending approval preservation, stale retry rejection,
consent gates, and config-read fallback behavior.
- Reflection Coach creates managed instructions, skill, and routine
resources; drift/reset behavior is covered by service tests and redacted
API responses.
- Non-model adapter setup now provisions a `needs_setup` built-in row
before command/endpoint fields are complete; this matches the server
lifecycle and is covered by the setup modal regression test.

## Model Used

OpenAI Codex coding agent based on GPT-5. Exact hosted model ID,
context-window size, and reasoning-mode labels are not exposed in this
runtime; tool use, shell execution, GitHub CLI/API access, and local
code editing were 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)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

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

cli/src/__tests__/company-import-export-e2e.test.ts

@@ -208,6 +208,11 @@ async function api<T>(baseUrl: string, pathname: string, init?: RequestInit): Pr
   return text ? JSON.parse(text) as T : (null as T);
 }
 
+function isPortableAgent(agent: { metadata?: Record<string, unknown> | null }) {
+  const marker = agent.metadata?.paperclipBuiltInAgent;
+  return typeof marker !== "object" || marker === null;
+}
+
 async function runCliJson<T>(
   args: string[],
   opts: TestPaperclipEnv & { apiBase?: string; includeConfigArg?: boolean },
@@ -560,7 +565,7 @@ describeEmbeddedPostgres("paperclipai company import/export e2e", () => {
     expect(importedExisting.company.action).toBe("unchanged");
     expect(importedExisting.agents.some((agent) => agent.action === "created")).toBe(true);
 
-    const twiceImportedAgents = await api<Array<{ id: string; name: string }>>(
+    const twiceImportedAgents = await api<Array<{ id: string; name: string; metadata?: Record<string, unknown> | null }>>(
       apiBase,
       `/api/companies/${importedNew.company.id}/agents`,
     );
@@ -573,9 +578,10 @@ describeEmbeddedPostgres("paperclipai company import/export e2e", () => {
       `/api/companies/${importedNew.company.id}/issues`,
     );
     const twiceImportedMatchingIssues = twiceImportedIssues.filter((issue) => issue.title === sourceIssue.title);
+    const twiceImportedPortableAgents = twiceImportedAgents.filter(isPortableAgent);
 
-    expect(twiceImportedAgents).toHaveLength(2);
-    expect(new Set(twiceImportedAgents.map((agent) => agent.name)).size).toBe(2);
+    expect(twiceImportedPortableAgents).toHaveLength(2);
+    expect(new Set(twiceImportedPortableAgents.map((agent) => agent.name)).size).toBe(2);
     expect(twiceImportedProjects).toHaveLength(2);
     expect(twiceImportedMatchingIssues).toHaveLength(2);
     expect(new Set(twiceImportedMatchingIssues.map((issue) => issue.identifier)).size).toBe(2);

cli/src/__tests__/company.test.ts

@@ -377,6 +377,7 @@ describe("renderCompanyImportPreview", () => {
             adapterConfig: {},
             runtimeConfig: {},
             permissions: {},
+            permissionGrants: [],
             budgetMonthlyCents: 0,
             metadata: null,
           },
@@ -597,6 +598,7 @@ describe("import selection catalog", () => {
             adapterConfig: {},
             runtimeConfig: {},
             permissions: {},
+            permissionGrants: [],
             budgetMonthlyCents: 0,
             metadata: null,
           },
@@ -757,6 +759,7 @@ describe("default adapter overrides", () => {
             adapterConfig: {},
             runtimeConfig: {},
             permissions: {},
+            permissionGrants: [],
             budgetMonthlyCents: 0,
             metadata: null,
           },
@@ -776,6 +779,7 @@ describe("default adapter overrides", () => {
             adapterConfig: {},
             runtimeConfig: {},
             permissions: {},
+            permissionGrants: [],
             budgetMonthlyCents: 0,
             metadata: null,
           },