Add examples/coding-agent and the docs cookbook

The first real agent wiring: DeepSeek V4 + the bash tool suite + stdio
chat + JSONL persistence, runnable via yarn demo:coding (reads the
gitignored repo-root .env through process.loadEnvFile).

- examples/coding-agent: cordis.yml wiring both real plugin families
  (llm-deepseek with !!js env secrets; bash-local + tool-bash), a
  bash-only coding system prompt, a max-steps-guard plugin (bounds
  runaway turns via the agent/turn-continuation waterfall — abort()
  from step-end is a no-op by then), and a stdio UI with dimmed
  reasoning and exit-on-idle for piped stdin.
- e2e (yarn test:e2e, key-gated): full-loop.e2e.ts runs a real model
  against the real bash tool; coding-task.e2e.ts is the swebench-style
  smoke — the model fixes a buggy add.js in a temp dir and the test
  re-runs node add.test.js itself rather than trusting the agent.
- docs/cookbook: adding-a-package (the verified checklist),
  adding-a-tool (execute() contract, background pattern, seams),
  adding-an-llm-adapter (protocol obligations, mock-server testing,
  e2e policy). AGENTS.md layout/commands/secrets sections updated;
  architecture.md points at both examples and the cookbook.
- vitest.e2e.config.ts: serialize test files + retry twice — parallel
  e2e files trip the shared internal key's concurrency quota.
- fix: the !js YAML tag spelling in docs/JSDoc is actually !!js
  (js-yaml resolves custom tags under tag:yaml.org,2002:js).

examples/coding-agent/tests/coding-task.e2e.ts

@@ -0,0 +1,86 @@
+import { spawnSync } from 'node:child_process'
+import { mkdtemp, readFile, rm, writeFile } from 'node:fs/promises'
+import { tmpdir } from 'node:os'
+import { join } from 'node:path'
+import { afterEach, describe, expect, it } from 'vitest'
+import type { Context } from 'cordis'
+import { codingHarness, finalText, SYSTEM_PROMPT, waitForIdle } from './harness.ts'
+
+/**
+ * The swebench-style smoke test: a real model fixes a real bug in a temp
+ * directory using only the bash tool, and the fix is verified OUTSIDE the
+ * agent by re-running the test script. Key-gated.
+ */
+
+const TEST_FILE = [
+  "const assert = require('node:assert');",
+  "const { add } = require('./add.js');",
+  'assert.strictEqual(add(2, 3), 5);',
+  'assert.strictEqual(add(-1, 1), 0);',
+  "console.log('PASS');",
+  '',
+].join('\n')
+
+const BUGGY_ADD = [
+  '// A tiny module with an obvious bug.',
+  'function add(a, b) {',
+  '  return a - b;',
+  '}',
+  'module.exports = { add };',
+  '',
+].join('\n')
+
+let workdir: string | undefined
+let ctx: Context | undefined
+
+afterEach(async () => {
+  // Dispose the harness even on failure/retry: agent-loop teardown stops the
+  // loop and LocalBashExecutor teardown kills anything the model left running.
+  await ctx?.fiber.dispose()
+  ctx = undefined
+  if (workdir !== undefined) await rm(workdir, { recursive: true, force: true })
+  workdir = undefined
+})
+
+describe.skipIf(!process.env.DEEPSEEK_API_KEY)('coding task: fix a failing test via bash', () => {
+  it('repairs add.js so node add.test.js passes', async () => {
+    workdir = await mkdtemp(join(tmpdir(), 'dsh-coding-task-'))
+    await writeFile(join(workdir, 'add.js'), BUGGY_ADD)
+    await writeFile(join(workdir, 'add.test.js'), TEST_FILE)
+
+    // Confirm the fixture actually fails before the agent touches it.
+    const before = spawnSync('node', ['add.test.js'], { cwd: workdir })
+    expect(before.status).not.toBe(0)
+
+    ctx = await codingHarness(workdir)
+    const agent = ctx.agentLoop.create('e2e-task', {
+      model: 'deepseek-v4-flash',
+      systemPrompt: SYSTEM_PROMPT,
+    })
+
+    agent.send([{
+      type: 'text',
+      text: 'In the current directory, `node add.test.js` fails because add.js has a bug. '
+        + 'Fix add.js so the test passes, run `node add.test.js` to verify, and report the result. '
+        + 'Do not modify add.test.js.',
+    }])
+    await waitForIdle(ctx, agent)
+
+    // The agent claims success…
+    const summary = finalText([...agent.session.events]).toLowerCase()
+    expect(summary.length).toBeGreaterThan(0)
+
+    // …and the world agrees: the test passes when WE run it, and the test
+    // file is byte-identical (an agent that neutered the test instead of
+    // fixing the bug fails here, not just on a keyword probe).
+    const untouchedTest = await readFile(join(workdir, 'add.test.js'), 'utf8')
+    expect(untouchedTest).toBe(TEST_FILE)
+
+    const after = spawnSync('node', ['add.test.js'], { cwd: workdir, encoding: 'utf8' })
+    expect(after.stdout).toContain('PASS')
+    expect(after.status).toBe(0)
+
+    const fixed = await readFile(join(workdir, 'add.js'), 'utf8')
+    expect(fixed).not.toMatch(/a\s*-\s*b/)
+  }, 180_000)
+})