fix(runner): enable API tools by default (#14186)

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The native runner exposes tools for company tasks.
> - API search and call tools cover operations without a dedicated tool.
> - The current default hides these tools unless an operator sets an
environment variable.
> - This pull request enables the tools when that variable is absent.
> - Operators can still disable the tools or restrict them to selected
companies.

## Linked Issues or Issue Description

Refs #13003, which added the guarded API tools.

**What happened?**
The native runner does not advertise `search_api` or `call_api` with the
default server configuration.

**Expected behavior**
The tools are available without a special environment variable. Existing
authorization checks still apply.

**Steps to reproduce**
Remove `PAPERCLIP_RUNNER_API_TOOLS_ENABLED` and
`PAPERCLIP_RUNNER_API_TOOLS_COMPANY_IDS`. Create a normal runner
authority. Inspect its tool definitions.

**Paperclip version or commit**
a6c4e7a.

## What Changed

- Enable API tools when the server flag is absent.
- Keep explicit disable, invalid-value rejection, company restrictions,
and binding restrictions.
- Test default tool definitions and run HTTP integration tests without
the enabling flag.
- Update operator and hiring documentation. The existing shared gate
also controls `hire_agent`.
- Use the same policy in the E2E evidence summary so an unset flag is
not reported as disabled.
- Isolate default-availability tests from operator environment
variables.

## Verification

- Red test: two new rollout policy assertions failed before the fix.
- Focused policy, authority, and HTTP tests: 3 files passed; 41 tests
passed, 2 skipped. The two runnerd transport cases require a Rust-built
binary absent from this workspace.
- Command: `pnpm exec vitest run
server/src/services/native-runtime/runner-api-rollout.test.ts
server/src/services/native-runtime/paperclip-runner-tool-authority.test.ts
server/src/services/native-runtime/runner-api.integration.test.ts`.
- Attempted `pnpm -r typecheck`: blocked by missing `cargo` in this
workspace.
- Attempted `pnpm build`: terminated at the 4 GiB memory limit.
- Attempted `pnpm test:run`: stopped after memory pressure to run
focused tests alone.
- Repeated the 41 passing focused tests with an inherited disabled flag
and a foreign-company restriction; test isolation passed.
- `pnpm test:e2e:runner:unit`: 44 files and 543 tests passed.
- `pnpm test:e2e:runner:typecheck` exceeded the workspace memory limit,
including a retry with bounded Go memory settings.
- CI results will be recorded before handoff.

## Risks

- More native runs can discover API tools and the existing `hire_agent`
tool by default.
- The change does not remove company, run, mode, credential, lifecycle,
or approval checks.
- Explicit operator restrictions still take precedence. No database
migration is required.

## Model Used

OpenAI Codex agent. The runtime does not expose the exact model ID or
context-window size. Used reasoning, repository tools, shell execution,
and tests.

## 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
- [ ] All Paperclip CI gates are green
- [ ] 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>

server/src/services/native-runtime/runner-api.integration.test.ts

@@ -4,7 +4,7 @@ import { chmod, writeFile, symlink } from "node:fs/promises";
 import { join } from "node:path";
 import { eq } from "drizzle-orm";
 import { documents, heartbeatRuns, issues, routineDocuments, routines } from "@paperclipai/db";
-import { beforeAll, afterAll, describe, expect, it, vi } from "vitest";
+import { beforeAll, afterAll, beforeEach, afterEach, describe, expect, it, vi } from "vitest";
 import { startRunnerApiTestServer } from "../../__tests__/helpers/runner-api-server.js";
 import { createRunnerdCodexTransport, defaultCapabilityRunnerdBinary } from "../../vendor/paperclip-runner/index.js";
 import { runnerApiCatalog } from "./runner-api-catalog.js";
@@ -13,18 +13,19 @@ import { registerRunnerPrpAuthority } from "../../realtime/runner-prp-ws.js";
 describe("runner API against real HTTP routes", () => {
   let server: Awaited<ReturnType<typeof startRunnerApiTestServer>>;
   const oldSecret = process.env.PAPERCLIP_AGENT_JWT_SECRET;
-  const oldEnabled = process.env.PAPERCLIP_RUNNER_API_TOOLS_ENABLED;
+  beforeEach(() => {
+    vi.stubEnv("PAPERCLIP_RUNNER_API_TOOLS_ENABLED", undefined);
+    vi.stubEnv("PAPERCLIP_RUNNER_API_TOOLS_COMPANY_IDS", undefined);
+  });
+  afterEach(() => vi.unstubAllEnvs());
   beforeAll(async () => {
     process.env.PAPERCLIP_AGENT_JWT_SECRET = randomUUID();
-    process.env.PAPERCLIP_RUNNER_API_TOOLS_ENABLED = "true";
     server = await startRunnerApiTestServer();
   }, 60_000);
   afterAll(async () => {
     await server?.close();
     if (oldSecret === undefined) delete process.env.PAPERCLIP_AGENT_JWT_SECRET;
     else process.env.PAPERCLIP_AGENT_JWT_SECRET = oldSecret;
-    if (oldEnabled === undefined) delete process.env.PAPERCLIP_RUNNER_API_TOOLS_ENABLED;
-    else process.env.PAPERCLIP_RUNNER_API_TOOLS_ENABLED = oldEnabled;
   });
 
   it.skipIf(!process.env.PAPERCLIP_REQUIRE_RUNNER_API_INTEGRATION && !existsSync(defaultCapabilityRunnerdBinary())).each(["current", "legacy_http"])("runs runnerd → PRP → authority → actual authenticated HTTP (%s receipt)", async (receiptFormat) => {
@@ -92,16 +93,16 @@ else if(m.id!==undefined) send({id:m.id,result:{}});
     } finally { await bundle.transport.close(); }
   }, 30_000);
 
-  it("cannot opt into API tools through a binding when the operator flag is absent", async () => {
+  it("cannot opt into API tools through a binding when the operator flag is false", async () => {
     const fixture = await server.fixture({ apiToolsEnabled: true });
-    delete process.env.PAPERCLIP_RUNNER_API_TOOLS_ENABLED;
+    process.env.PAPERCLIP_RUNNER_API_TOOLS_ENABLED = "false";
     try {
       const names = (await fixture.authority.definitions()).map(tool => tool.name);
       expect(names).toContain("get_task_context");
       expect(names).not.toContain("search_api");
       expect(names).not.toContain("call_api");
       await expect(fixture.authority.execute({ tool: "call_api", callId: "disabled", arguments: { operationId: "GET /api/companies/{companyId}/projects" } })).rejects.toThrow("not_advertised");
-    } finally { process.env.PAPERCLIP_RUNNER_API_TOOLS_ENABLED = "true"; }
+    } finally { delete process.env.PAPERCLIP_RUNNER_API_TOOLS_ENABLED; }
   });
 
   it("rejects credential calls before any durable receipt or secret result exists", async () => {