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).

docs/architecture.md

@@ -371,14 +371,22 @@ export function apply(ctx: Context) {
 }
 ```
 
-A complete runnable wiring lives in [`examples/echo-agent`](../examples/echo-agent)
-(mock model + echo tool + stdio UI + JSONL persistence, loaded from
-`cordis.yml` with HMR).
+Two complete runnable wirings exist: [`examples/echo-agent`](../examples/echo-agent)
+(mock model + echo tool — the all-mock skeleton check) and
+[`examples/coding-agent`](../examples/coding-agent) (DeepSeek V4 + the bash
+tool suite — the real thing; `yarn demo:coding`). Both load from `cordis.yml`
+with HMR.
+
+Step-by-step guides live in [`docs/cookbook`](./cookbook): adding a package,
+adding a tool, adding an LLM adapter.
 
 ## Deferred work (TODO)
 
 Tracked here deliberately — each is designed-for but not implemented:
 
+- **Restructure this document** — it has grown long; split it into focused
+  sections (or per-area files) so readers can navigate it without scrolling
+  the whole thing.
 - **Sub-agent spawn/fork semantics** (seam: `AgentLoop.create()`); inter-agent
   channels beyond `send`/`steer`/events.
 - **Persistence backends** (JSONL session dirs, sqlite) on the