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')
+}

examples/coding-agent/src/stdio-chat.ts

@@ -0,0 +1,119 @@
+import { createInterface } from 'node:readline'
+import type { Context } from 'cordis'
+import type {} from '@deepseek-ai/dsh-agent'
+
+export const name = 'stdio-chat'
+export const inject = ['agents']
+
+// Copied from examples/echo-agent (welcome text + reasoning rendering
+// adjusted). Deliberately example-local rather than a shared package — two
+// examples don't justify the abstraction yet; revisit at the third.
+
+/**
+ * Minimal UI plugin: reads lines from stdin → agent.send(); renders the
+ * agent's stream chunks and tool activity to stdout. Demonstrates that a UI
+ * is "just a plugin" — it only consumes the agent/* event taxonomy.
+ */
+export function apply(ctx: Context) {
+  let inReasoning = false
+  ctx.on('agent/stream-chunk', (_agent, _turn, _step, chunk) => {
+    if (chunk.type === 'reasoning-delta') {
+      // Dim the chain-of-thought so the answer stands out.
+      if (!inReasoning) process.stdout.write('\x1B[2m')
+      inReasoning = true
+      process.stdout.write(chunk.text)
+    } else if (chunk.type === 'text-delta') {
+      if (inReasoning) process.stdout.write('\x1B[0m\n')
+      inReasoning = false
+      process.stdout.write(chunk.text)
+    }
+  })
+
+  ctx.on('agent/turn-start', (agent, turn) => {
+    process.stdout.write(`\n[${agent.id} turn ${turn}] `)
+  })
+
+  ctx.on('agent/turn-end', () => {
+    if (inReasoning) process.stdout.write('\x1B[0m')
+    inReasoning = false
+    process.stdout.write('\n> ')
+  })
+
+  ctx.on('session/event', (_session, event) => {
+    if (event.type === 'tool/call') {
+      const { name: toolName, arguments: args } = event.data
+      if (inReasoning) process.stdout.write('\x1B[0m')
+      inReasoning = false
+      process.stdout.write(`\n  [tool call] ${toolName}(${args})`)
+    } else if (event.type === 'tool/result') {
+      const { content } = event.data
+      const text = content.filter(b => b.type === 'text').map(b => b.text).join('')
+      process.stdout.write(`\n  [tool result] ${text}\n  `)
+    }
+  })
+
+  ctx.effect(() => {
+    const reader = createInterface({ input: process.stdin })
+    // Piped-input exit, once stdin reaches EOF:
+    //  - If no line ever submitted work (empty stdin, blank-only lines), exit
+    //    immediately — no turn will ever start, so there is nothing to wait
+    //    for. (Gating on an observed 'running' here would hang forever.)
+    //  - If work WAS submitted, exit the next time the agent settles to idle
+    //    AFTER having run. Two subtleties this handles: the loop batches
+    //    several queued messages into ONE turn (one idle), so we don't count
+    //    sends; and agent.send() does NOT synchronously flip status to
+    //    'running', so requiring an observed 'running' first (`sawRunning`)
+    //    avoids exiting in the gap before the turn starts and dropping work.
+    let stdinClosed = false
+    let disposed = false
+    let submittedWork = false
+    let sawRunning = false
+
+    const maybeExit = (): void => {
+      if (disposed || !stdinClosed) return
+      // No work submitted: nothing will ever run, exit straight away.
+      // Work submitted: wait until a turn has run and the agent is idle.
+      if (submittedWork) {
+        if (!sawRunning) return
+        const agent = ctx.agents.get('main')
+        if (agent && agent.status !== 'idle') return // a turn is still running
+      }
+      // Let any final output flush, then exit.
+      setTimeout(() => process.exit(0), 200)
+    }
+
+    const disposeStatusListener = ctx.on('agent/status', (subject, status) => {
+      if (subject.id !== 'main') return
+      if (status === 'running') sawRunning = true
+      if (status === 'idle') maybeExit()
+    })
+
+    reader.on('line', (line) => {
+      const text = line.trim()
+      if (!text) return
+      const agent = ctx.agents.get('main')
+      if (!agent) {
+        console.error('agent "main" is not running')
+        return
+      }
+      submittedWork = true
+      if (agent.status === 'running') {
+        agent.steer([{ type: 'text', text }])
+      } else {
+        agent.send([{ type: 'text', text }])
+      }
+    })
+    reader.on('close', () => {
+      // Fires for BOTH stdin EOF and plugin disposal (reader.close() below);
+      // `disposed` guards teardown so HMR/dispose never exits the process.
+      stdinClosed = true
+      maybeExit()
+    })
+    process.stdout.write('coding-agent ready. Give it a coding task (bash is its only tool).\n> ')
+    return () => {
+      disposed = true
+      disposeStatusListener()
+      reader.close()
+    }
+  }, 'stdio-chat')
+}