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/src/session-jsonl.ts

@@ -0,0 +1,36 @@
+import { appendFile } from 'node:fs/promises'
+import { join } from 'node:path'
+import type { Context } from 'cordis'
+import type { Session, SessionEvent } from '@deepseek-ai/dsh-session'
+
+export const name = 'session-jsonl'
+export const inject = ['sessions']
+
+/**
+ * Minimal persistence plugin: buffers session events (write-behind) and
+ * drains to a JSONL file at every `session/flush` checkpoint — the pattern a
+ * real JSONL/sqlite persistence plugin would follow.
+ */
+export function apply(ctx: Context) {
+  const buffers = new Map<Session, SessionEvent[]>()
+  const path = (session: Session) => join(import.meta.dirname, '..', `${session.id}.jsonl`)
+
+  ctx.on('session/event', (session, event) => {
+    let buffer = buffers.get(session)
+    if (!buffer) buffers.set(session, buffer = [])
+    buffer.push(event)
+  })
+
+  const flush = async (session: Session) => {
+    const buffer = buffers.get(session)
+    if (!buffer?.length) return
+    const lines = buffer.splice(0).map(event => JSON.stringify(event) + '\n').join('')
+    await appendFile(path(session), lines)
+  }
+
+  ctx.on('session/flush', flush)
+  ctx.effect(() => () => {
+    // drain remaining buffers on dispose
+    for (const session of buffers.keys()) void flush(session)
+  }, 'session-jsonl')
+}