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).

package.json

@@ -23,6 +23,7 @@
     "publint": "tsx scripts/publint-all.ts",
     "hygiene": "yarn knip && yarn publint && yarn constraints",
     "demo": "node --expose-internals --import tsx examples/echo-agent/start.ts",
+    "demo:coding": "node --expose-internals --import tsx examples/coding-agent/start.ts",
     "postinstall": "lefthook install"
   },
   "devDependencies": {