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

@@ -0,0 +1,51 @@
+# 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`.