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docs: sync implementation docs and doc gates

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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.
The real stdio coding-agent wiring: DeepSeek V4 + the bash tool suite + subagent delegation + `todo_write` + 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
@@ -34,7 +33,7 @@ The id is wired through `cordis.yml` (`resumeSessionId: !!js process.env.RESUME_
## What each leaf entry demonstrates
This example is a thin leaf `cordis.yml`: it picks the swappable backends and loads one app package. The spine (sessions, system-prompt, tools, agents, invariants, `agent-loop`) and the front-door cluster (console logger, JSONL persistence, readline UI, the pre-created `main` agent) all live inside the [`@deepseek-ai/dsh-stdio-agent`](../../packages/ui/stdio-agent) app and the [`@deepseek-ai/dsh-agent-core`](../../packages/core/agent-core) bundle it loads — so the leaf has only four entries:
This example is a thin leaf `cordis.yml`: it picks the swappable backends, loads one app package, and adds product tools that are intentionally outside the shared spine. The spine (sessions, system-prompt, tools, agents, invariants, `agent-loop`) and the front-door cluster (console logger, JSONL persistence, readline UI, the pre-created `main` agent) live inside the [`@deepseek-ai/dsh-stdio-agent`](../../packages/ui/stdio-agent) app and the [`@deepseek-ai/dsh-agent-core`](../../packages/core/agent-core) bundle it loads; the leaf wires the backends and model-facing optional tools:
| Entry | Demonstrates |
|---|---|
@@ -42,11 +41,15 @@ This example is a thin leaf `cordis.yml`: it picks the swappable backends and lo
| `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`) | the executor implementation — the swappable half of the bash seam. The model-facing `bash`/`bash_output`/`bash_kill` tool schemas (`tool-bash`) come from `agent-core`, so only the executor is a leaf choice |
| `stdio-agent` (`@deepseek-ai/dsh-stdio-agent`) | the app bundle: the agent-core spine + console logger + JSONL persistence + readline UI + a pre-created `main` agent. Its config carries the model, system prompt, `persistenceRoot` (`./.sessions`), and `resumeSessionId` — so persistence and the agent are configured here, not wired as separate leaf plugins |
| `subagent`, `subagent-spawn`, `subagent-fork` | the subagent provider registry plus the two in-process backends: a fresh child and a child seeded with the parent's completed-turn prefix |
| `tool-subagent`, `tool-subagent-fork` | two model-facing `dsh-tool-subagent` loads, each bound to a different provider and exposed under a distinct tool name (`subagent`, `subagent_fork`) |
| `tool-todo` | the model-facing `todo_write` tool; writes the whole task list to the session log and renders as a checklist in stdio |
## End-to-end tests (`pnpm run 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.
- `tests/resume.e2e.ts` — durable continuity across processes: run 1 tells the real model a secret code and persists the turn to a temp JSONL root, then the whole context is disposed; run 2 is a fresh context over the same root that RESUMES the session id and asks the model to recall the code. The recall can only come from the rehydrated log.
- `tests/todo-write.e2e.ts` — a real model drives the real `todo_write` tool and the test verifies the resulting `todo/write` session event.
Both self-skip without `DEEPSEEK_API_KEY`.
These self-skip without `DEEPSEEK_API_KEY`.