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).

vitest.e2e.config.ts

@@ -25,10 +25,15 @@ export default defineConfig({
   plugins: [tsconfigPaths({ projects: ['./tsconfig.test.json'] })],
   test: {
     include: ['packages/*/tests/**/*.e2e.ts', 'examples/*/tests/**/*.e2e.ts'],
-    // Real model calls: generous timeouts, one retry for transient flakes,
-    // no coverage (unit suites own the coverage gate).
+    // Real model calls: generous timeouts, and retries for transient flakes
+    // (the shared internal key hits concurrency quotas). No coverage — the
+    // unit suites own the coverage gate.
     testTimeout: 120_000,
     hookTimeout: 30_000,
-    retry: 1,
+    retry: 2,
+    // Run e2e files one at a time: the shared internal API key has a small
+    // concurrency quota, and parallel files issue enough simultaneous requests
+    // to trip it (manifesting as flaky rate-limit errors).
+    fileParallelism: false,
   },
 })