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/harness.ts

@@ -0,0 +1,55 @@
+import { Context } from 'cordis'
+import LlmService from '@deepseek-ai/dsh-llm'
+import SessionStore from '@deepseek-ai/dsh-session'
+import type { SessionEvent } from '@deepseek-ai/dsh-session'
+import SystemPrompt from '@deepseek-ai/dsh-system-prompt'
+import ToolRegistry from '@deepseek-ai/dsh-tools'
+import AgentRegistry from '@deepseek-ai/dsh-agent'
+import AgentLoop, { LoopAgent } from '@deepseek-ai/dsh-agent-loop'
+import { LocalBashExecutor } from '@deepseek-ai/dsh-bash-local'
+import * as ToolBash from '@deepseek-ai/dsh-tool-bash'
+import * as LlmDeepSeek from '@deepseek-ai/dsh-llm-deepseek'
+
+/**
+ * Shared harness for the coding-agent e2e suites: the full plugin stack
+ * with the real DeepSeek adapter and the real bash tool. Lives outside the
+ * *.e2e.ts pattern so importing it never re-registers another file's tests.
+ */
+
+export const SYSTEM_PROMPT = 'You are a coding agent. Your only tool is bash; '
+  + 'do file operations with cat/grep/heredocs, check [exit code: N] markers, '
+  + 'and report results briefly.'
+
+export async function codingHarness(workdir: string): Promise<Context> {
+  const ctx = new Context()
+  await ctx.plugin(LlmService)
+  await ctx.plugin(SessionStore)
+  await ctx.plugin(SystemPrompt)
+  await ctx.plugin(ToolRegistry)
+  await ctx.plugin(AgentRegistry)
+  await ctx.plugin(AgentLoop, { agents: [] })
+  await ctx.plugin(LlmDeepSeek, { models: ['deepseek-v4-flash'] })
+  await ctx.plugin(LocalBashExecutor, { cwd: workdir, timeoutMs: 30_000 })
+  await ctx.plugin(ToolBash)
+  return ctx
+}
+
+export function waitForIdle(ctx: Context, agent: LoopAgent): Promise<void> {
+  return new Promise((resolve) => {
+    const dispose = ctx.on('agent/status', (subject, status) => {
+      if (subject === agent && status === 'idle') {
+        dispose()
+        resolve()
+      }
+    })
+  })
+}
+
+export function finalText(events: SessionEvent[]): string {
+  const message = events.findLast(event => event.type === 'assistant/message')
+  if (message?.type !== 'assistant/message') return ''
+  return message.data.content
+    .filter(block => block.type === 'text')
+    .map(block => block.text)
+    .join('')
+}