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/README.md

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+# coding-agent
+
+The first REAL agent wiring: DeepSeek V4 + the bash tool suite + stdio chat
++ JSONL persistence, loaded from `cordis.yml`. Where echo-agent proves the
+skeleton with mocks, this example is a usable coding assistant.
+
+## Run it
+
+```sh
+# repo root .env (gitignored) or exported env:
+#   DEEPSEEK_API_KEY=sk-…
+#   DEEPSEEK_BASE_URL=https://…   # optional; defaults to the public API
+yarn demo:coding
+```
+
+Type a coding task. The agent's only tools are `bash` (+ `bash_output` /
+`bash_kill` for background tasks): file reads, writes, searches, and test
+runs all happen through shell commands, each in a fresh `bash -c` (the
+system prompt tells the model to pass `workdir` instead of `cd`). Reasoning
+streams dimmed; tool calls/results render inline.
+
+```
+> fix the failing test in /path/to/project
+[main turn 1] (reasoning…)
+  [tool call] bash({"command": "node --test", "workdir": "/path/to/project"})
+  [tool result] … [exit code: 1]
+  …
+```
+
+## What each plugin demonstrates
+
+| Entry | Demonstrates |
+|---|---|
+| `llm-deepseek` | real `LlmAdapter` via config (`!!js process.env.…` secrets); swap one line to `@deepseek-ai/dsh-llm-pi-ai` for the library-backed twin |
+| `bash` (`dsh-bash-local`) + `tool-bash` | the executor seam + tool schemas as separate plugins |
+| `agent-loop` | agent created from config with a coding system prompt |
+| `src/session-jsonl.ts` | write-behind persistence on `session/event` + `session/flush` (copied from echo-agent) |
+| `src/stdio-chat.ts` | UI as a plugin; copied from echo-agent with reasoning-dimming and an exit-on-idle close handler for piped stdin. Example-local on purpose — extract a shared UI package when a third example needs it |
+
+## End-to-end tests (`yarn test:e2e`, key-gated)
+
+- `tests/full-loop.e2e.ts` — the canary: real model runs `echo e2e-ok`
+  through the real bash tool; asserts `tool/call`/`tool/result` session
+  events and the final answer.
+- `tests/coding-task.e2e.ts` — the swebench-style smoke: a temp dir holds
+  `add.js` (with `a - b` where `a + b` belongs) and a failing
+  `add.test.js`; the agent must fix the bug and verify. The test re-runs
+  `node add.test.js` ITSELF and inspects the files — agent claims are not
+  trusted.
+
+Both self-skip without `DEEPSEEK_API_KEY`.

examples/coding-agent/cordis.yml

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+# The coding-agent plugin tree, loaded via @cordisjs/plugin-include.
+# Core services first, then the real adapters/tools, then the agent itself.
+#
+# Requires DEEPSEEK_API_KEY (and optionally DEEPSEEK_BASE_URL) in the
+# environment — start.ts loads the gitignored repo-root .env first.
+
+- id: logger
+  name: '@cordisjs/plugin-logger-console'
+
+- id: timer
+  name: '@cordisjs/plugin-timer'
+
+- id: hmr
+  name: '@cordisjs/plugin-hmr'
+  config:
+    root: ['.']
+
+- id: llm
+  name: '@deepseek-ai/dsh-llm'
+
+- id: sessions
+  name: '@deepseek-ai/dsh-session'
+
+- id: system-prompt
+  name: '@deepseek-ai/dsh-system-prompt'
+
+- id: tools
+  name: '@deepseek-ai/dsh-tools'
+
+- id: agents
+  name: '@deepseek-ai/dsh-agent'
+
+# The DeepSeek adapter. Swap to '@deepseek-ai/dsh-llm-pi-ai' for the
+# pi-ai-backed twin (same config shape; `reasoning: high` replaces
+# thinking/reasoningEffort).
+- id: llm-deepseek
+  name: '@deepseek-ai/dsh-llm-deepseek'
+  config:
+    apiKey: !!js process.env.DEEPSEEK_API_KEY
+    baseURL: !!js process.env.DEEPSEEK_BASE_URL
+    models:
+      - deepseek-v4-flash
+      - deepseek-v4-pro
+
+# Bash execution: the local executor implementation + the tool schemas.
+- id: bash
+  name: '@deepseek-ai/dsh-bash-local'
+  config:
+    timeoutMs: 60000
+
+- id: tool-bash
+  name: '@deepseek-ai/dsh-tool-bash'
+
+- id: agent-loop
+  name: '@deepseek-ai/dsh-agent-loop'
+  config:
+    agents:
+      - id: main
+        model: deepseek-v4-flash
+        systemPrompt: |
+          You are coding-agent, a CLI coding assistant.
+
+          Your only tools are bash (plus bash_output/bash_kill for background
+          tasks). Do ALL file operations through bash: read with cat/sed/head,
+          search with grep, write with heredocs (cat <<'EOF' > file), edit
+          with sed or a rewrite. Each bash call runs in a fresh shell — pass
+          workdir instead of cd, and never rely on shell state between calls.
+
+          Check the [exit code: N] marker on every command; investigate
+          failures before moving on. Verify your work by running the code or
+          tests. Keep answers brief and factual.
+
+- id: session-jsonl
+  name: './src/session-jsonl.ts'
+
+- id: stdio-chat
+  name: './src/stdio-chat.ts'

examples/coding-agent/package.json

@@ -0,0 +1,7 @@
+{
+  "name": "coding-agent-example",
+  "private": true,
+  "version": "0.0.1",
+  "type": "module",
+  "description": "Runnable demo: a real coding agent — DeepSeek V4 + the bash tool suite"
+}

examples/coding-agent/src/session-jsonl.ts

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+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

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+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')
+}

examples/coding-agent/start.ts

@@ -0,0 +1,25 @@
+import { pathToFileURL } from 'node:url'
+import { Context } from 'cordis'
+import Loader from '@cordisjs/plugin-loader'
+
+// Load DEEPSEEK_API_KEY / DEEPSEEK_BASE_URL from a gitignored repo-root .env
+// (Node >= 21.7 native). Absent file is fine — the environment may already
+// carry the variables; cordis.yml reads them via the `!!js` tag.
+try {
+  process.loadEnvFile(new URL('../../.env', import.meta.url).pathname)
+} catch {
+  // no .env — rely on the ambient environment
+}
+
+// Boot a Cordis app from this example's cordis.yml — the same shape as the
+// upstream `cordis` bin, pinned to this directory.
+const ctx = new Context()
+ctx.baseUrl = pathToFileURL(import.meta.dirname).href + '/'
+
+await ctx.plugin(Loader)
+await ctx.loader.create({
+  name: '@cordisjs/plugin-include',
+  config: {
+    path: './cordis.yml',
+  },
+})

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)
+})

examples/coding-agent/tests/full-loop.e2e.ts

@@ -0,0 +1,43 @@
+import { afterEach, describe, expect, it } from 'vitest'
+import type { Context } from 'cordis'
+import { codingHarness, finalText, SYSTEM_PROMPT, waitForIdle } from './harness.ts'
+
+/**
+ * The first place a REAL model meets the REAL bash tool: the cheap canary
+ * before the coding-task e2e. Key-gated (see vitest.e2e.config.ts).
+ */
+
+let ctx: Context | undefined
+
+afterEach(async () => {
+  // Always dispose the harness, even on failure/retry/timeout: agent-loop
+  // teardown stops the loop and LocalBashExecutor teardown kills any
+  // process the model left behind.
+  await ctx?.fiber.dispose()
+  ctx = undefined
+})
+
+describe.skipIf(!process.env.DEEPSEEK_API_KEY)('full loop: real model + real bash tool', () => {
+  it('runs a bash command on request and reports its output', async () => {
+    ctx = await codingHarness(process.cwd())
+    const agent = ctx.agentLoop.create('e2e-loop', {
+      model: 'deepseek-v4-flash',
+      systemPrompt: SYSTEM_PROMPT,
+    })
+
+    agent.send([{ type: 'text', text: 'Run `echo e2e-ok` with the bash tool and tell me its exact output.' }])
+    await waitForIdle(ctx, agent)
+
+    const events = [...agent.session.events]
+    const calls = events.filter(event => event.type === 'tool/call')
+    expect(calls.length).toBeGreaterThan(0)
+    expect(calls.some(event => event.data.name === 'bash')).toBe(true)
+
+    const results = events.filter(event => event.type === 'tool/result')
+    const resultTexts = results.flatMap(event =>
+      event.data.content.filter(block => block.type === 'text').map(block => block.text))
+    expect(resultTexts.some(text => text.includes('e2e-ok'))).toBe(true)
+
+    expect(finalText(events)).toContain('e2e-ok')
+  }, 120_000)
+})

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('')
+}