feat: add sense contract types to @uncaged/nerve-core

Export SenseComputeFn, SenseComputeOptions, SenseBlobStore,
SensePeerMap — formalizing the compute function signature that
senses must implement.

Closes #262
Refs #260

— 小橘 🍊（NEKO Team）

.knowledge/adapter.md

@@ -0,0 +1,47 @@
+# Agent Adapters (RFC-003)
+
+Adapter = capability. Role = scenario. Workflows declare adapters directly via import.
+
+## AgentFn Protocol
+
+```ts
+type AgentFn = (prompt: string, context: WorkflowContext) => Promise<string>
+```
+
+- Input: prompt + context (start frame, messages, workdir, AbortSignal)
+- Output: raw string — structured extraction is separate
+- Adapter handles tool-specific details internally
+
+## Available Adapters
+
+| Package | Adapter | Tool |
+|---------|---------|------|
+| `@uncaged/nerve-adapter-cursor` | `cursorAdapter` / `createCursorAdapter()` | cursor-agent CLI |
+| `@uncaged/nerve-adapter-hermes` | `hermesAdapter` / `createHermesAdapter()` | hermes chat CLI |
+
+Each exports a **default instance** (sensible defaults) and a **factory** for custom config.
+
+## Usage in Workflows
+
+Adapters are passed directly to `createRole`:
+
+```ts
+import { createRole } from "@uncaged/nerve-workflow-utils";
+import { cursorAdapter } from "@uncaged/nerve-adapter-cursor";
+
+const coder = createRole(cursorAdapter, prompt, schema, extractConfig);
+```
+
+No registry, no config indirection. TypeScript catches missing adapters at compile time.
+
+## Extract Layer
+
+Parses agent raw string → typed meta. Configured in `nerve.yaml`:
+
+```yaml
+extract:
+  provider: dashscope
+  model: qwen-plus
+```
+
+Two-level merge: global → role override. Retry once on parse failure (feeds error back to LLM), then throw `ExtractError`.

.knowledge/architecture.md

@@ -0,0 +1,33 @@
+# Nerve Architecture
+
+Observation engine for autonomous agents — sense the world, react to changes, run workflows.
+
+## Core Pipeline
+
+```
+External World → Sense → Signal → Reflex → Workflow → Log
+```
+
+Causality is **one-directional**. Logs are the end of the chain — they cannot trigger Reflexes (prevents feedback loops).
+
+## Three Orthogonal Extension Points
+
+| Extension | Question | Nature |
+|-----------|----------|--------|
+| **Sense** | What to compute | `compute()` function |
+| **Reflex** | When to compute | Declarative YAML (interval / on) |
+| **Workflow** | What to do | Roles + Moderator |
+
+Each is independent. Reflex doesn't know compute internals, Sense doesn't know when it's triggered, Workflow doesn't know why it was started.
+
+## Two Event Types
+
+- **Signal** — from Sense compute (non-null return). Pure fact, no intent. Drives the front half (perception).
+- **Command Event** — inside Workflow Threads. Has causal chain, must be responded to. Drives the back half (action).
+
+## Process Isolation
+
+- One worker per Sense group (long-lived)
+- One worker per Workflow type (on-demand)
+- Workers never talk to each other
+- All user code runs in isolated Workers; kernel never loads user code directly

.knowledge/cli.md

@@ -0,0 +1,78 @@
+# Nerve CLI
+
+`nerve` — CLI entry point for nerve workspace management.
+
+## Workspace Lifecycle
+
+```bash
+nerve init                    # scaffold a new workspace (nerve.yaml, senses/, workflows/)
+nerve validate                # validate nerve.yaml config
+nerve dev                     # run kernel foreground (development, Ctrl+C to stop)
+nerve start                   # start daemon (background)
+nerve stop                    # stop daemon
+nerve status                  # check daemon health (uptime, senses, workflows)
+nerve daemon                  # restart daemon (stop + start)
+```
+
+## Sense Management
+
+```bash
+nerve create sense <name>     # scaffold a new sense (compute.ts + schema.ts)
+nerve sense list              # list configured senses
+nerve sense trigger <name>    # manually trigger a sense compute
+nerve sense schema <name>     # show sense Drizzle schema
+nerve sense query <name>      # inspect sense SQLite database
+nerve sense query <name> --sql "SELECT * FROM samples LIMIT 5"
+```
+
+## Workflow Management
+
+```bash
+nerve create workflow <name>  # scaffold a new workflow
+nerve workflow trigger <name> --prompt "..." [--max-rounds N] [--dry-run]
+nerve workflow list           # list configured workflows
+nerve thread                  # list active (queued/started) workflow threads
+```
+
+## Knowledge
+
+```bash
+nerve knowledge sync          # chunk files per knowledge.yaml, compute embeddings → knowledge.db
+nerve knowledge query "text"  # search indexed knowledge (cosine similarity)
+nerve knowledge query -g "text"           # global search across all indexed repos
+nerve knowledge query --repo /path "text" # search specific repo
+```
+
+## Logs & Store
+
+```bash
+nerve logs                    # view daemon logs (last 50 lines)
+nerve logs -f                 # follow logs (tail -f style)
+nerve logs -n 200             # last N lines
+nerve store archive           # archive old log entries to JSONL
+```
+
+## Remote
+
+```bash
+nerve remote add <name> <url> # add a remote daemon endpoint
+nerve status --remote <name>  # check remote daemon health
+```
+
+## Workspace Layout
+
+```
+my-agent/
+  nerve.yaml                  # senses, workflows, extract config
+  knowledge.yaml              # knowledge index config (optional)
+  senses/
+    cpu-usage/
+      compute.ts              # sense implementation
+      schema.ts               # Drizzle schema
+      migrations/             # auto-generated
+  workflows/
+    cleanup/
+      src/index.ts            # workflow definition
+  knowledge.db                # generated by nerve knowledge sync
+  .knowledge/                 # curated knowledge cards
+```

.knowledge/coding-conventions.md

@@ -0,0 +1,57 @@
+# Nerve Coding Conventions
+
+## Functional-First
+
+- `type` over `interface`, `function` over `class`
+- No `this`, no inheritance, composition over inheritance
+- Immutability first: `Readonly<T>`, `as const`
+
+## No Optional Properties
+
+Never use `?:`. Use `T | null` for nullable fields. Use discriminated unions for mutually exclusive fields.
+
+```ts
+// ✅ Good
+type Config = { throttle: string | null }
+
+// ❌ Bad
+type Config = { throttle?: string }
+```
+
+## Error Handling
+
+- `Result<T, E>` for expected failures
+- `throw` only for programmer errors (bugs)
+- No try-catch for flow control
+
+## Naming
+
+| Type | Style |
+|------|-------|
+| Files | `kebab-case.ts` |
+| Types | `PascalCase` |
+| Functions/vars | `camelCase` |
+| Constants | `UPPER_SNAKE` |
+
+## Exports
+
+- Always named exports, never default
+- One module = one responsibility
+
+## Async
+
+- Always `async/await`, never `.then()` chains
+
+## No Dynamic Import
+
+Static `import` only. Exceptions: `sense-runtime.ts`, `workflow-worker.ts` (runtime module paths).
+
+## Toolchain
+
+pnpm + TypeScript (strict) + Biome (lint/format) + Vitest (test)
+
+```bash
+pnpm run check   # biome check
+pnpm test        # vitest
+pnpm run build   # full build
+```

.knowledge/knowledge-layer.md

@@ -0,0 +1,38 @@
+# Knowledge Layer (RFC-003 Phase 6)
+
+Local-first, repo-scoped knowledge base for project context.
+
+## Files
+
+- `knowledge.yaml` — repo root, defines include/exclude globs
+- `knowledge.db` — SQLite, stores chunks + embeddings
+- `.knowledge/` — curated knowledge cards (indexed by sync)
+
+## Commands
+
+```bash
+nerve knowledge sync              # chunk files, compute embeddings, write to knowledge.db
+nerve knowledge query "query"     # search by cosine similarity (or word overlap fallback)
+nerve knowledge query -g "query"  # global search across all indexed repos
+nerve knowledge query --repo /path "query"  # search specific repo
+```
+
+## Embedding
+
+- Remote service: configured via `EMBED_SERVICE_URL` env var (self-hosted Cloudflare Worker + KV cache)
+- Model: Dashscope text-embedding-v3 (1024 dims)
+- Cache: content-addressable (sha256 of model+text), never expires
+- Fallback: word-overlap scoring when embed service not configured
+
+## Chunking
+
+- Markdown: split by headings, large sections split further by paragraphs (max 24)
+- TypeScript/JS: split by function declarations, fallback to paragraphs
+- Other files: single chunk
+
+## Env Config
+
+```
+EMBED_SERVICE_URL=https://embed.shazhou.workers.dev
+EMBED_AUTH_TOKEN=<token>
+```

.knowledge/monorepo.md

@@ -0,0 +1,24 @@
+# Nerve Monorepo Structure
+
+```
+nerve/
+  packages/
+    core/              # @uncaged/nerve-core — shared types, config parser, Result, spawn-safe
+    cli/               # @uncaged/nerve-cli — CLI (init, validate, dev, daemon, knowledge)
+    daemon/            # @uncaged/nerve-daemon — kernel, workers, signal bus, scheduler
+    store/             # @uncaged/nerve-store — append-only log, SQLite, CAS blob store
+    workflow-utils/    # @uncaged/nerve-workflow-utils — role factories, extract, LLM helpers
+    adapter-cursor/    # @uncaged/nerve-adapter-cursor — cursor-agent CLI adapter
+    adapter-hermes/    # @uncaged/nerve-adapter-hermes — hermes chat CLI adapter
+    khala/             # Khala — Sense marketplace (future)
+    skills/            # nerve-managed skills
+  docs/                # RFCs, conventions
+  .knowledge/          # curated knowledge cards (this directory)
+```
+
+## Dependency Rules
+
+- `core` is the shared layer — everyone depends on it
+- `cli` and `daemon` must NOT depend on each other
+- Adapter packages depend only on `core`
+- `workflow-utils` depends on `core`

.knowledge/sense.md

@@ -0,0 +1,29 @@
+# Sense
+
+A `compute()` function that samples or derives external data. The only first-class citizen in nerve.
+
+## Behavior
+
+- Returns `T | null` — non-null emits a Signal, null is silent (no storage write, no signal, no downstream trigger)
+- Each Sense has its own **independent SQLite database**
+- Cross-sense reads are read-only via `peers` parameter
+- Schema defined with Drizzle ORM (`schema.ts` is single source of truth)
+
+## Sense → Workflow
+
+If `compute()` returns an object with `workflow: "name|maxRounds|prompt"`, the engine starts that workflow and does **not** emit a Signal. `workflow: null` or `""` means emit signal normally.
+
+See `routeSenseComputeOutput` / `parseSenseWorkflowDirective` in `@uncaged/nerve-core`.
+
+## Config (nerve.yaml)
+
+```yaml
+senses:
+  cpu-usage:
+    group: system        # senses in same group share a worker
+    throttle: 10s        # min interval between computes
+    timeout: 30s         # max compute duration
+    grace_period: 5s     # wait before first compute
+    interval: 30s        # periodic trigger (optional)
+    on: [disk-pressure]  # trigger on signals from other senses (optional)
+```

.knowledge/workflow.md

@@ -0,0 +1,59 @@
+# Workflow Engine
+
+Stateful multi-step execution driven by Roles and a Moderator.
+
+## Core Concepts
+
+- **Workflow** — definition with concurrency strategy
+- **Thread** — one execution instance, unique `runId`
+- **Role** — executes actions (has side effects). `(start, messages) → { content, meta }`
+- **Moderator** — pure routing function. `(context) → next role | END`
+
+## Thread Lifecycle
+
+```
+trigger → queued → started → step_complete ↺ → completed
+                                    ↓
+                              failed / crashed
+```
+
+## Concurrency Config (nerve.yaml)
+
+```yaml
+workflows:
+  cleanup:
+    concurrency: 1
+    overflow: drop       # discard if already running
+  code-review:
+    concurrency: 3
+    overflow: queue
+    max_queue: 20        # queue limit, oldest discarded
+```
+
+## createRole Helper
+
+`createRole` builds a `Role<M>` from an adapter, prompt, Zod schema, and extract config:
+
+```ts
+import { createRole } from "@uncaged/nerve-workflow-utils";
+import { cursorAdapter } from "@uncaged/nerve-adapter-cursor";
+import { z } from "zod";
+
+const coderSchema = z.object({ plan: z.string(), files: z.array(z.string()) });
+
+const coder = createRole(cursorAdapter, coderPrompt, coderSchema, {
+  provider: { baseUrl: "...", apiKey: "...", model: "qwen-plus" },
+});
+
+// Use in WorkflowDefinition
+const workflow: WorkflowDefinition<MyMeta> = {
+  name: "develop",
+  roles: { coder, reviewer },
+  moderator,
+};
+```
+
+- `adapter: AgentFn` — direct function reference
+- `prompt: string | ((start, messages) => Promise<string>)` — static or dynamic
+- `meta: z.ZodType<M>` — Zod schema, directly (no wrapper needed)
+- `extract: LlmExtractorConfig` — provider for structured extraction

README.md

@@ -30,7 +30,7 @@ Three extension points for **what / when / multi-step action** — reflexes neve
 |---------|-------------|
 | [`@uncaged/nerve-core`](./packages/core) | Shared types, config parser, Sense→workflow routing, daemon IPC protocol |
 | [`@uncaged/nerve-store`](./packages/store) | Append-only log SQLite, JSONL archive, CAS blob store, workflow run rows |
-| [`@uncaged/nerve-daemon`](./packages/daemon) | Kernel, workers, signal bus, reflex scheduler, workflow manager, file watcher, IPC |
+| [`@uncaged/nerve-daemon`](./packages/daemon) | Kernel, workers, signal bus, sense scheduler, workflow manager, file watcher, IPC |
 | [`@uncaged/nerve-cli`](./packages/cli) | CLI (`nerve`) — init, validate, daemon, dev, logs, sense, store, workflow |
 
 ## Quick Start

biome.json

@@ -19,7 +19,7 @@
   },
   "overrides": [
     {
-      "include": ["tsup.config.ts", "*/rslib.config.ts"],
+      "include": ["tsup.config.ts", "*/rslib.config.ts", "packages/khala/src/index.ts"],
       "linter": {
         "rules": {
           "style": {

docs/plans/2026-04-25-khala-mvp.md

@@ -0,0 +1,558 @@
+# Khala MVP Implementation Plan
+
+> **For Hermes:** Use subagent-driven-development skill to implement this plan task-by-task.
+
+**Goal:** Build Khala — a Cloudflare Workers + D1 + Durable Objects cloud workflow orchestrator that lets agents coordinate multi-agent workflows as a stateless worker pool.
+
+**Architecture:** Khala is a CF Worker that receives events from agents via REST API. Each workflow thread runs in a Durable Object with a JSONata moderator. Agents poll a task queue for unclaimed turns, execute locally, and POST results back. Thread messages are stored in D1.
+
+**Tech Stack:** Cloudflare Workers, D1 (SQLite), Durable Objects, Hono (routing), JSONata (moderator engine), TypeScript
+
+---
+
+## Phase 0: Project Scaffolding
+
+### Task 0.1: Create khala package
+
+**Objective:** Set up the `packages/khala` CF Worker project with wrangler, Hono, and D1 binding.
+
+**Files:**
+- Create: `packages/khala/package.json`
+- Create: `packages/khala/wrangler.toml`
+- Create: `packages/khala/tsconfig.json`
+- Create: `packages/khala/src/index.ts`
+
+**Step 1: Create package.json**
+
+```json
+{
+  "name": "@uncaged/khala",
+  "version": "0.0.1",
+  "private": true,
+  "scripts": {
+    "dev": "wrangler dev",
+    "deploy": "wrangler deploy",
+    "test": "vitest run"
+  },
+  "dependencies": {
+    "hono": "^4.7.0",
+    "jsonata": "^2.0.5"
+  },
+  "devDependencies": {
+    "@cloudflare/workers-types": "^4.20250410.0",
+    "vitest": "^4.1.5",
+    "wrangler": "^4.14.0"
+  }
+}
+```
+
+**Step 2: Create wrangler.toml**
+
+```toml
+name = "khala"
+main = "src/index.ts"
+compatibility_date = "2025-04-01"
+
+[[d1_databases]]
+binding = "DB"
+database_name = "khala"
+database_id = "placeholder"
+
+[durable_objects]
+bindings = [
+  { name = "THREAD", class_name = "ThreadDO" }
+]
+
+[[migrations]]
+tag = "v1"
+new_classes = ["ThreadDO"]
+```
+
+**Step 3: Create minimal Hono entrypoint**
+
+```typescript
+// src/index.ts
+import { Hono } from "hono";
+
+export type Env = {
+  DB: D1Database;
+  THREAD: DurableObjectNamespace;
+};
+
+const app = new Hono<{ Bindings: Env }>();
+
+app.get("/health", (c) => c.json({ ok: true }));
+
+export default app;
+```
+
+**Step 4: Create tsconfig.json**
+
+```json
+{
+  "compilerOptions": {
+    "target": "ES2022",
+    "module": "ES2022",
+    "moduleResolution": "bundler",
+    "strict": true,
+    "noUncheckedIndexedAccess": true,
+    "types": ["@cloudflare/workers-types"]
+  },
+  "include": ["src"]
+}
+```
+
+**Step 5: Install dependencies and verify**
+
+```bash
+cd packages/khala && pnpm install
+pnpm exec wrangler types  # generates worker-configuration.d.ts
+```
+
+**Step 6: Commit**
+
+```bash
+git add packages/khala/
+git commit -m "chore(khala): scaffold CF Worker package"
+```
+
+---
+
+## Phase 1: D1 Schema & Data Layer
+
+### Task 1.1: Create D1 migration — core tables
+
+**Objective:** Define D1 schema for agents, threads, messages, and task queue.
+
+**Files:**
+- Create: `packages/khala/migrations/0001_initial.sql`
+
+**SQL:**
+
+```sql
+-- Agent registry
+CREATE TABLE agents (
+  id TEXT PRIMARY KEY,           -- agent name (e.g. "tuanzi")
+  token_hash TEXT NOT NULL,      -- bcrypt/sha256 hash of agent token
+  created_at TEXT NOT NULL DEFAULT (datetime('now'))
+);
+
+-- Workflow threads
+CREATE TABLE threads (
+  id TEXT PRIMARY KEY,           -- ulid
+  workflow TEXT NOT NULL,        -- workflow name (e.g. "code-review")
+  status TEXT NOT NULL DEFAULT 'active',  -- active | completed | failed
+  initiator TEXT NOT NULL,       -- agent id or external caller
+  result TEXT,                   -- final result JSON (set on completion)
+  created_at TEXT NOT NULL DEFAULT (datetime('now')),
+  updated_at TEXT NOT NULL DEFAULT (datetime('now'))
+);
+
+-- Thread messages (append-only)
+CREATE TABLE messages (
+  id INTEGER PRIMARY KEY AUTOINCREMENT,
+  thread_id TEXT NOT NULL REFERENCES threads(id),
+  role TEXT NOT NULL,            -- role name or "__moderator__"
+  content TEXT NOT NULL,
+  meta TEXT,                     -- JSON
+  step INTEGER NOT NULL,         -- 0-indexed step number
+  agent_id TEXT,                 -- which agent executed this turn
+  created_at TEXT NOT NULL DEFAULT (datetime('now'))
+);
+
+CREATE INDEX idx_messages_thread ON messages(thread_id, step);
+
+-- Task queue
+CREATE TABLE tasks (
+  id TEXT PRIMARY KEY,           -- ulid
+  thread_id TEXT NOT NULL REFERENCES threads(id),
+  role TEXT NOT NULL,
+  instruction TEXT NOT NULL,     -- turn instruction from moderator
+  status TEXT NOT NULL DEFAULT 'open',  -- open | claimed | completed | expired
+  claim_id TEXT,                 -- set when claimed
+  claimed_by TEXT,               -- agent id
+  claimed_at TEXT,
+  timeout_seconds INTEGER NOT NULL DEFAULT 300,
+  created_at TEXT NOT NULL DEFAULT (datetime('now'))
+);
+
+CREATE INDEX idx_tasks_status ON tasks(status, created_at);
+```
+
+**Step 1: Write the migration file**
+
+**Step 2: Apply locally**
+
+```bash
+cd packages/khala
+pnpm exec wrangler d1 migrations apply khala --local
+```
+
+**Step 3: Commit**
+
+```bash
+git add packages/khala/migrations/
+git commit -m "feat(khala): D1 schema — agents, threads, messages, tasks"
+```
+
+### Task 1.2: Create data access functions
+
+**Objective:** Type-safe D1 query functions for all tables.
+
+**Files:**
+- Create: `packages/khala/src/db.ts`
+- Create: `packages/khala/src/types.ts`
+
+**types.ts:**
+
+```typescript
+export type Agent = {
+  id: string;
+  token_hash: string;
+  created_at: string;
+};
+
+export type Thread = {
+  id: string;
+  workflow: string;
+  status: "active" | "completed" | "failed";
+  initiator: string;
+  result: string | null;
+  created_at: string;
+  updated_at: string;
+};
+
+export type Message = {
+  id: number;
+  thread_id: string;
+  role: string;
+  content: string;
+  meta: string | null;
+  step: number;
+  agent_id: string | null;
+  created_at: string;
+};
+
+export type Task = {
+  id: string;
+  thread_id: string;
+  role: string;
+  instruction: string;
+  status: "open" | "claimed" | "completed" | "expired";
+  claim_id: string | null;
+  claimed_by: string | null;
+  claimed_at: string | null;
+  timeout_seconds: number;
+  created_at: string;
+};
+```
+
+**db.ts:** Query functions — `createThread`, `appendMessage`, `createTask`, `claimTask`, `completeTask`, `getOpenTasks`, `getThreadMessages`, etc. Each is a plain function taking `D1Database` as first arg.
+
+**Step 1: Write types.ts**
+
+**Step 2: Write db.ts with all query functions**
+
+Key functions:
+- `createThread(db, workflow, initiator) → Thread`
+- `appendMessage(db, threadId, role, content, meta, step, agentId) → Message`
+- `createTask(db, threadId, role, instruction, timeoutSeconds) → Task`
+- `claimTask(db, taskId, agentId) → { ok: true, claimId } | { ok: false }`
+- `completeTask(db, taskId, claimId) → boolean`
+- `expireTimedOutTasks(db) → number` (count expired)
+- `getOpenTasks(db, limit) → Task[]`
+- `getThreadMessages(db, threadId, opts?) → Message[]` (opts: role, since, step, last)
+
+Use `ulid()` for IDs (add `ulidx` dependency).
+
+**Step 3: Commit**
+
+```bash
+git add packages/khala/src/
+git commit -m "feat(khala): data access layer — types and D1 queries"
+```
+
+---
+
+## Phase 2: Auth & Agent Registry
+
+### Task 2.1: Agent auth middleware
+
+**Objective:** Bearer token auth for agents. Hash-based token verification.
+
+**Files:**
+- Create: `packages/khala/src/auth.ts`
+- Modify: `packages/khala/src/index.ts`
+
+**auth.ts:**
+
+```typescript
+import { createMiddleware } from "hono/factory";
+import type { Env } from "./index.ts";
+
+export const agentAuth = createMiddleware<{ Bindings: Env }>(async (c, next) => {
+  const header = c.req.header("Authorization");
+  if (!header?.startsWith("Bearer ")) {
+    return c.json({ error: "missing token" }, 401);
+  }
+  const token = header.slice(7);
+  const hash = await sha256(token);
+  const agent = await c.env.DB.prepare(
+    "SELECT id FROM agents WHERE token_hash = ?"
+  ).bind(hash).first<{ id: string }>();
+  if (!agent) {
+    return c.json({ error: "invalid token" }, 401);
+  }
+  c.set("agentId", agent.id);
+  await next();
+});
+
+async function sha256(input: string): Promise<string> {
+  const data = new TextEncoder().encode(input);
+  const buf = await crypto.subtle.digest("SHA-256", data);
+  return [...new Uint8Array(buf)].map(b => b.toString(16).padStart(2, "0")).join("");
+}
+```
+
+### Task 2.2: Admin routes for agent management
+
+**Objective:** Admin API to register/remove agents (protected by admin secret in env).
+
+**Files:**
+- Create: `packages/khala/src/routes/admin.ts`
+
+**Routes:**
+- `POST /admin/agents` — body `{ id, token }` → hash token, insert agent
+- `DELETE /admin/agents/:id` — remove agent
+- `GET /admin/agents` — list agents (no tokens)
+
+Protected by `ADMIN_SECRET` env var check.
+
+**Commit:**
+
+```bash
+git commit -m "feat(khala): agent auth middleware and admin API"
+```
+
+---
+
+## Phase 3: Workflow Engine (Durable Object)
+
+### Task 3.1: Workflow registry
+
+**Objective:** Load workflow definitions from a simple in-memory registry (hardcoded for MVP, later from D1 or KV).
+
+**Files:**
+- Create: `packages/khala/src/workflows.ts`
+
+**Structure:**
+
+```typescript
+export type CloudRole = {
+  prompt: string;
+};
+
+export type CloudWorkflowDef = {
+  name: string;
+  roles: Record<string, CloudRole>;
+  moderator: string;  // JSONata expression
+};
+
+// For MVP: hardcoded registry
+const registry = new Map<string, CloudWorkflowDef>();
+
+export function registerWorkflow(def: CloudWorkflowDef): void {
+  registry.set(def.name, def);
+}
+
+export function getWorkflow(name: string): CloudWorkflowDef | null {
+  return registry.get(name) ?? null;
+}
+```
+
+### Task 3.2: ThreadDO — Durable Object
+
+**Objective:** Each workflow thread runs as a Durable Object. The DO manages the moderator state machine, creates tasks, and processes responses.
+
+**Files:**
+- Create: `packages/khala/src/thread-do.ts`
+
+**Key behavior:**
+
+1. `POST /start` — Initialize thread: save workflow def, run moderator to get first turn, create task
+2. `POST /response` — Agent posts turn result: validate claim_id, append message, run moderator for next turn or END
+3. `GET /messages` — Query thread messages with filters
+
+**Moderator execution:**
+- Build context from messages (start frame + role steps)
+- Evaluate JSONata expression → returns `{ role: "reviewer" }` or `{ role: "__end__" }`
+- If not END, create new task in queue
+- If END, mark thread completed, set result
+
+**Important:** The DO holds workflow state in memory during the request but persists everything to D1. The DO itself uses `ctx.storage` only for the thread ID mapping.
+
+### Task 3.3: Wire ThreadDO into worker
+
+**Objective:** Export the DO class, add routes that proxy to the DO.
+
+**Files:**
+- Modify: `packages/khala/src/index.ts`
+
+**Routes:**
+- `POST /workflows/:name/threads` — Create thread → instantiate DO → start
+- `POST /threads/:id/response` — Forward to DO
+- `GET /threads/:id/messages` — Forward to DO (or query D1 directly)
+- `GET /threads/:id` — Thread status
+
+**Commit:**
+
+```bash
+git commit -m "feat(khala): ThreadDO workflow engine with JSONata moderator"
+```
+
+---
+
+## Phase 4: Task Queue API
+
+### Task 4.1: Task queue endpoints
+
+**Objective:** Agents poll for work and claim tasks.
+
+**Files:**
+- Create: `packages/khala/src/routes/tasks.ts`
+
+**Routes (all require agentAuth):**
+- `GET /tasks` — List open tasks (optionally filter by workflow)
+- `POST /tasks/:id/claim` — Claim a task → returns `{ claimId, role, instruction, threadId }`
+- `POST /tasks/:id/release` — Release a claimed task back to queue
+
+**Claim logic:**
+- Atomic: UPDATE ... WHERE status = 'open' → if rowsWritten = 0, already claimed
+- Returns claim_id (ulid) for optimistic lock on response
+
+### Task 4.2: Task timeout sweep
+
+**Objective:** Periodically expire timed-out tasks back to open.
+
+**Implementation:** CF Worker Cron Trigger (every 1 minute) that calls `expireTimedOutTasks(db)`.
+
+**Files:**
+- Modify: `packages/khala/src/index.ts` (add scheduled handler)
+- Modify: `packages/khala/wrangler.toml` (add cron trigger)
+
+```toml
+[triggers]
+crons = ["* * * * *"]
+```
+
+**Commit:**
+
+```bash
+git commit -m "feat(khala): task queue API with claim/release and timeout sweep"
+```
+
+---
+
+## Phase 5: Agent-Side Integration (KhalaSense)
+
+### Task 5.1: Khala client library
+
+**Objective:** A small client that agents use to interact with Khala.
+
+**Files:**
+- Create: `packages/core/src/khala-client.ts`
+
+**API:**
+
+```typescript
+export type KhalaClientConfig = {
+  baseUrl: string;
+  token: string;
+};
+
+export function createKhalaClient(config: KhalaClientConfig) {
+  return {
+    pollTasks: () => GET /tasks,
+    claimTask: (taskId) => POST /tasks/:id/claim,
+    submitResponse: (threadId, content, meta, claimId) => POST /threads/:id/response,
+    getMessages: (threadId, opts) => GET /threads/:id/messages,
+  };
+}
+```
+
+### Task 5.2: KhalaSense
+
+**Objective:** A Sense that polls Khala for open tasks and emits signals.
+
+**Files:**
+- Create: `packages/daemon/src/senses/khala-sense.ts`
+
+**Behavior:**
+- `compute()`: poll `/tasks`, if tasks available → return task info as signal value
+- Reflex picks up signal → triggers a workflow that executes the turn locally
+- After local execution → POST response back to Khala
+
+**This task depends on understanding the existing Sense pattern in daemon. Check `packages/daemon/src/` for examples.**
+
+**Commit:**
+
+```bash
+git commit -m "feat(khala): KhalaSense — agent-side polling and integration"
+```
+
+---
+
+## Phase 6: End-to-End Demo
+
+### Task 6.1: Register a demo workflow
+
+**Objective:** Register a simple 2-role "ping-pong" workflow for testing.
+
+**Files:**
+- Create: `packages/khala/src/workflows/ping-pong.ts`
+
+**Workflow:**
+- Roles: `pinger` (says ping), `ponger` (says pong)
+- Moderator: alternate pinger/ponger for 3 rounds then END
+- JSONata: `steps.length >= 6 ? { "role": "__end__" } : steps.length % 2 = 0 ? { "role": "pinger" } : { "role": "ponger" }`
+
+### Task 6.2: Integration test
+
+**Objective:** Test the full flow with miniflare.
+
+**Files:**
+- Create: `packages/khala/src/__tests__/e2e.test.ts`
+
+**Test:**
+1. Create thread via API
+2. Poll tasks → get first task
+3. Claim task
+4. POST response
+5. Poll again → get next task
+6. Repeat until workflow completes
+7. Verify thread status = completed and all messages present
+
+**Commit:**
+
+```bash
+git commit -m "feat(khala): ping-pong demo workflow and e2e test"
+```
+
+---
+
+## Summary
+
+| Phase | Tasks | Description |
+|-------|-------|-------------|
+| 0 | 0.1 | Project scaffolding |
+| 1 | 1.1-1.2 | D1 schema & data layer |
+| 2 | 2.1-2.2 | Auth & agent registry |
+| 3 | 3.1-3.3 | Workflow engine (DO + moderator) |
+| 4 | 4.1-4.2 | Task queue API |
+| 5 | 5.1-5.2 | Agent-side integration |
+| 6 | 6.1-6.2 | End-to-end demo |
+
+**Deployment:** `khala.shazhou.workers.dev`
+
+**First milestone:** Phase 0-4 (cloud side complete), testable with curl.
+**Second milestone:** Phase 5-6 (agent integration + demo).

docs/rfc-001-observation-engine.md

@@ -473,7 +473,7 @@ Sense 的运行时属性（`group`、`throttle`、`timeout`）在 `nerve.yaml`
 ```sql
 CREATE TABLE logs (
   id        INTEGER PRIMARY KEY AUTOINCREMENT,
-  source    TEXT NOT NULL,    -- "reflex", "workflow", "system"
+  source    TEXT NOT NULL,    -- "sense_scheduler", "sense", "workflow", "system"
   type      TEXT NOT NULL,    -- "run_start", "run_complete", "error", "state_change"
   ref_id    TEXT,             -- 关联的 reflex name / workflow run_id
   payload   TEXT,             -- JSON

docs/rfc-002-workflow-engine.md

@@ -350,12 +350,12 @@ export type WorkflowManager = {
 };
 ```
 
-### 7.2 Reflex Scheduler 扩展
+### 7.2 Sense Scheduler 扩展
 
-当前 `ReflexScheduler` 只处理 `kind: "sense"` 的 reflex。扩展为同时处理 `kind: "workflow"`：
+当前 `SenseScheduler` 只处理 `kind: "sense"` 的 reflex。扩展为同时处理 `kind: "workflow"`：
 
 ```typescript
-// reflex-scheduler.ts 扩展
+// sense-scheduler.ts 扩展
 if (reflex.kind === "workflow") {
   const workflowName = reflex.workflow;
   if (reflex.on !== null && reflex.on.length > 0) {
@@ -393,8 +393,8 @@ if (reflex.kind === "workflow") {
 ### Phase 2：Kernel 集成
 
 - [ ] `packages/daemon/src/kernel.ts` — 集成 WorkflowManager，处理 workflow worker 的生命周期
-- [ ] `packages/daemon/src/reflex-scheduler.ts` — 扩展支持 `kind: "workflow"` 的 reflex
-- [ ] 集成测试：Sense signal → Reflex → Workflow 全链路
+- [ ] `packages/daemon/src/sense-scheduler.ts` — 扩展支持 `kind: "workflow"` 的 reflex
+- [ ] 集成测试：Sense signal → SenseScheduler → Workflow 全链路
 
 ### Phase 3：崩溃恢复与热更新
 

docs/rfc-003-agent-config-layer.md

@@ -0,0 +1,318 @@
+# RFC-003: Agent Configuration Layer
+
+**Author:** 小橘 🍊（NEKO Team）
+**Status:** Draft
+**Created:** 2026-04-29
+
+## Summary
+
+Define a minimal agent abstraction where **adapter = capability** and **role = scenario**. Workflows directly declare which adapter each role uses — no intermediate registry or `nerve.yaml` agent config. `nerve.yaml` only holds `extract` config and `knowledge` settings.
+
+## Motivation
+
+The original design introduced a `nerve.yaml` agents registry to map logical names (e.g. `developer`) to adapter implementations. In practice this added an unnecessary layer of indirection:
+
+- **Agent names are arbitrary** — `developer` vs `coder` vs `engineer` is a naming exercise, not architecture
+- **One more config to maintain** — adding/changing an adapter requires editing both `nerve.yaml` and the workflow
+- **Same adapter, same config** — in reality, most workflows just need "use cursor" or "use hermes", not a named abstraction on top
+
+The simpler model: **workflow roles declare their adapter directly**. The adapter *is* the capability.
+
+## Key Concepts
+
+### Adapter vs Role
+
+| | Adapter | Role |
+|---|---|---|
+| **What** | Capability — what tools are available | Scenario — what to do with those tools |
+| **Granularity** | Few (cursor, hermes, claude, codex) | Many (per workflow step) |
+| **Defines** | How to spawn an agent, tool access | Prompt, schema, timeout |
+| **Layer** | Infrastructure (packages) | Business logic (WorkflowSpec) |
+
+A `cursor` adapter becomes an architect, coder, or reviewer depending on the role's prompt. The adapter defines *what it can do*; the role defines *what it does right now*.
+
+### Agent Protocol
+
+All agent types implement a single unified interface:
+
+```ts
+type AgentFn = (prompt: string, context: WorkflowContext) => Promise<string>
+```
+
+- **Input**: prompt (assembled by Role) + context (start frame + prior messages + workdir + abort signal)
+- **Output**: raw string — structured data is extracted separately
+- **Internals**: adapter handles tool-specific details (cursor CLI, hermes subagent, codex API, etc.)
+
+Workflow runtime never interacts with agent internals.
+
+### Extract Layer
+
+A separate concern that parses agent output (raw string) into typed meta:
+
+```ts
+type ExtractFn<T> = (raw: string, schema: Schema<T>) => Promise<T>
+```
+
+Configured globally in `nerve.yaml`, overridable per role (two-level merge: global → role).
+
+**Error handling**: retry once (feed raw output + parse error back to LLM for correction), then throw `ExtractError`. The workflow moderator decides the recovery strategy (retry role, skip, or terminate) — extract never makes workflow-level decisions.
+
+## Design
+
+### Configuration (`nerve.yaml`)
+
+`nerve.yaml` holds only extract and knowledge config — no agent registry:
+
+```yaml
+extract:
+  provider: dashscope
+  model: qwen-plus
+```
+
+### Workflow Definition (TypeScript)
+
+Roles declare their adapter directly — no indirection through named agents:
+
+```ts
+import { cursorAdapter, createCursorAdapter } from "@uncaged/nerve-adapter-cursor";
+import { hermesAdapter } from "@uncaged/nerve-adapter-hermes";
+
+const workflow: WorkflowSpec<MyMeta> = {
+  name: "develop-workflow",
+  roles: {
+    architect: { adapter: cursorAdapter,  prompt: architectPrompt, meta: architectSchema },
+    coder:     { adapter: createCursorAdapter({ model: "claude-sonnet-4", timeout: 600 }), prompt: coderPrompt, meta: coderSchema },
+    reviewer:  { adapter: hermesAdapter,  prompt: reviewPrompt,    meta: reviewSchema },
+    deployer:  { adapter: hermesAdapter,  prompt: deployPrompt,    meta: deploySchema },
+  },
+  moderator,
+};
+```
+
+### Runtime Assembly
+
+```
+WorkflowSpec      →  Role(adapter fn + prompt)  →  adapter(prompt, ctx) → string
+                                                                            ↓
+nerve.yaml#extract →  ExtractFn(string, schema) → T (typed meta)
+```
+
+Adapter is a direct function reference on each role — no map, no lookup, no registry.
+
+### Adapter Packages
+
+Each agent adapter lives in its own package to avoid pulling unnecessary dependencies:
+
+```
+packages/
+  adapter-cursor/     # @uncaged/nerve-adapter-cursor — cursor-agent CLI
+  adapter-hermes/     # @uncaged/nerve-adapter-hermes — hermes CLI subagent
+  adapter-claude/     # @uncaged/nerve-adapter-claude — claude-code CLI (future)
+  adapter-codex/      # @uncaged/nerve-adapter-codex — codex CLI (future)
+```
+
+Each adapter exports a **default instance** and a **factory** for customization:
+
+```ts
+// @uncaged/nerve-adapter-cursor
+import type { AgentConfig, AgentFn } from "@uncaged/nerve-core";
+
+// Factory — custom config
+export function createCursorAdapter(config: AgentConfig): AgentFn;
+
+// Default — sensible defaults (model: "auto", timeout: 300)
+export const cursorAdapter: AgentFn;
+```
+
+The factory receives adapter config (model, timeout) and returns an `AgentFn` that spawns the CLI tool, passes the prompt, and returns raw output.
+
+**Wiring** — workflows import adapters directly, no daemon-level registry:
+
+```ts
+import { cursorAdapter } from "@uncaged/nerve-adapter-cursor";
+import { hermesAdapter } from "@uncaged/nerve-adapter-hermes";
+
+// Use default instances directly in roles
+{ adapter: cursorAdapter, prompt: "...", meta: schema }
+```
+
+Adapters not installed simply can't be imported — TypeScript catches missing dependencies at compile time.
+
+**Workspace `package.json`** only lists the adapters it actually uses:
+
+```json
+{
+  "dependencies": {
+    "@uncaged/nerve-adapter-cursor": "workspace:*",
+    "@uncaged/nerve-adapter-hermes": "workspace:*"
+  }
+}
+```
+
+**Migration from `workflow-utils`** — the existing `role-cursor.ts` / `shared/cursor-agent.ts` spawn logic moves to `@uncaged/nerve-adapter-cursor`. `role-hermes.ts` / `shared/hermes-agent.ts` moves to `@uncaged/nerve-adapter-hermes`. `workflow-utils` retains only extract, prompt utilities, and shared spawn infrastructure.
+
+### Dynamic Prompts
+
+`RoleSpec.prompt` supports both static strings and async functions:
+
+```ts
+type PromptInput = string | ((start: StartStep, messages: WorkflowMessage[]) => Promise<string>);
+
+type RoleSpec<M> = {
+  adapter: AgentFn;
+  prompt: PromptInput;
+  meta: Schema<M>;
+};
+```
+
+Static prompts cover simple cases. Dynamic prompts (functions) are needed when the prompt depends on thread context — e.g. reading issue content, injecting prior step results, or resolving repo paths at runtime.
+
+### Timeout Resolution
+
+Timeout is an **adapter concern**, not a role concern. Roles define *what to do* (prompt + schema); adapters define *how to do it* (tool, model, timeout).
+
+When different roles need different timeouts, create separate adapter instances:
+
+```ts
+import { cursorAdapter, createCursorAdapter } from "@uncaged/nerve-adapter-cursor";
+
+const fastCursor = createCursorAdapter({ model: "auto", timeout: 60 });
+const slowCursor = createCursorAdapter({ model: "auto", timeout: 600 });
+
+roles: {
+  reviewer: { adapter: fastCursor, prompt: reviewPrompt, meta: reviewSchema },
+  coder:    { adapter: slowCursor, prompt: coderPrompt,  meta: coderSchema },
+}
+```
+
+### No Runtime Fallback
+
+- **`nerve init`** — detects agent availability (CLI exists? service reachable?), reports errors immediately
+- **Runtime** — if an agent is unavailable, the workflow fails with a clear error. No silent degradation.
+
+Rationale: silent fallback hides quality differences (cursor → hermes subagent produces very different output) and makes debugging harder.
+
+### Adapter Hot-Reload
+
+Follows the existing `nerve.yaml` hot-reload mechanism. On config change, adapters are rebuilt. Running workflow threads are not affected (they use the `AdapterFn` bound at thread start). New threads automatically use the updated config.
+
+### WorkflowContext
+
+```ts
+type WorkflowContext = {
+  start: StartStep;
+  messages: WorkflowMessage[];
+  workdir: string;        // repo root — coding agent working directory
+  signal: AbortSignal;    // graceful cancellation
+};
+```
+
+`workdir` is required for coding agents. `signal` enables graceful cancellation of long-running agent calls — adapters must respect it (e.g. kill subprocess on abort).
+
+### Configuration Validation
+
+`nerve validate` checks:
+- All roles have a valid adapter function (not null/undefined)
+- Adapter CLIs are available (binary exists in PATH)
+- Extract provider is configured and reachable
+
+## Compatibility with Current Types
+
+The existing `Role<Meta>` signature:
+
+```ts
+type Role<Meta> = (start: StartStep, messages: WorkflowMessage[]) => Promise<RoleResult<Meta>>
+```
+
+remains the runtime interface. The new config layer is syntactic sugar — the runtime assembles `Role<Meta>` functions from `(adapter + prompt + schema)` instead of users writing them by hand. `WorkflowDefinition` stays the same at the engine level; `WorkflowSpec` is the new user-facing authoring format that compiles down to it at daemon startup / hot-reload time (runtime lazy compile, not `nerve init`).
+
+Existing hand-written `Role` functions continue to work — `WorkflowSpec` is additive, not a breaking change.
+
+## Knowledge Layer
+
+Project knowledge is a **built-in nerve feature**. Scope is the **repo** — each repo has its own knowledge base, tracked in git.
+
+### Architecture
+
+```
+Local (per repo)                         Remote Service
+┌───────────────────────┐           ┌─────────────────────┐
+│ knowledge.yaml        │           │ Embedding API       │
+│ ├── include/exclude   │   ──→     │ text → vector       │
+│ knowledge.db (SQLite) │   ←──     │ content-hash cache  │
+│ ├── chunk text        │           │ (avoid recompute)   │
+│ ├── embedding bytes   │           └─────────────────────┘
+│ └── cosine search     │
+└───────────────────────┘
+```
+
+- **Local-first** — `knowledge.db` stores chunks + embeddings, search runs locally (in-memory cosine similarity)
+- **Remote service only computes embeddings** — content-addressable cache keyed by text hash, avoids redundant computation across agents
+- **Branch-aware by design** — different agents on different branches naturally have different `knowledge.db` contents
+
+### Configuration (`knowledge.yaml` at repo root)
+
+```yaml
+include:
+  - "src/**/*.ts"
+  - "docs/**/*.md"
+  - "*.md"
+
+exclude:
+  - "node_modules/**"
+  - "dist/**"
+  - "*.test.ts"
+```
+
+`knowledge.yaml` is committed to git. `knowledge.db` is gitignored — it's a local cache rebuilt from source files + remote embedding service.
+
+### CLI
+
+```bash
+nerve knowledge sync              # index/re-index changed files
+nerve knowledge query "how does the signal bus work"
+
+# Scope
+nerve knowledge query "..." # default: cwd repo
+nerve knowledge query --repo /path/to/other/repo "..."
+nerve knowledge query -g "..."   # global search (all indexed repos)
+# --repo and -g are mutually exclusive
+```
+
+### Search Implementation
+
+Project-scale knowledge (hundreds to low thousands of chunks) does not need vector indices. Full scan with cosine similarity in memory is sufficient and adds zero native dependencies.
+
+```ts
+// Pseudocode
+const chunks = db.all("SELECT slug, chunk, embedding FROM chunks");
+const query_vec = await embed(query);
+const results = chunks
+  .map(c => ({ ...c, score: cosine(query_vec, c.embedding) }))
+  .sort((a, b) => b.score - a.score)
+  .slice(0, limit);
+```
+
+### Knowledge Layers
+
+```
+Project knowledge (knowledge.yaml)  Per repo, git managed, any agent reads
+Agent long-term memory              Per agent, domain expertise, cross-run
+Workflow context (start + msgs)     Per run, moderator-controlled history
+```
+
+## Open Questions
+
+1. **Agent long-term memory** — storage format and mechanism for persisting domain expertise across runs
+
+### Resolved
+
+- **Agent naming / registry** → removed; workflow roles declare adapter directly, no intermediate registry
+- **Extract override granularity** → two-level merge: global → role (agent level removed)
+- **Context threading** → `WorkflowContext` includes `workdir` and `signal` (see design above)
+- **Embedding service** → self-hosted, 1024-dim vectors, content-hash cache
+
+## References
+
+- [RFC-002: Workflow Engine](./rfc-002-workflow-engine.md)
+- Current `Role` / `Moderator` types: `packages/core/src/workflow.ts`

docs/rfc-004-package-architecture.md

@@ -0,0 +1,187 @@
+# RFC-004: Package Architecture — Shareable Workflows, Roles & Senses
+
+**Author:** 小橘 🍊（NEKO Team）
+**Status:** Draft
+**Created:** 2026-04-29
+
+## Summary
+
+Make workflows, roles, and senses publishable as lightweight npm packages. Workspaces become pure configuration — selecting packages, wiring adapters, and providing credentials. No builtin workflows in the nerve core.
+
+## Motivation
+
+Currently, workflows like `develop-sense` and `develop-workflow` live inside the workspace (`~/.uncaged-nerve/workflows/`). This creates problems:
+
+1. **No sharing** — every workspace duplicates the same workflow code
+2. **No versioning** — upgrading a workflow means manual file edits
+3. **Builtin is a trap** — if we bake workflows into nerve core, they require adapters and LLM providers that may not be installed. A fresh `nerve` install on a bare machine would fail to load builtins.
+4. **Roles are already shared** — `_shared/workspace-committer.ts` proves the pattern works; we just need to formalize it as packages
+
+The adapter pattern (`@uncaged/nerve-adapter-hermes`, `@uncaged/nerve-adapter-cursor`) already established the precedent: infrastructure as packages, workspace as wiring.
+
+## Design
+
+### Package Taxonomy
+
+```
+@uncaged/nerve-core              # types, engine
+@uncaged/nerve-daemon            # runtime
+@uncaged/nerve-workflow-utils    # createRole, decorateRole, withDryRun, onFail, etc.
+
+# Adapters (existing)
+@uncaged/nerve-adapter-hermes
+@uncaged/nerve-adapter-cursor
+
+# Workflows (new)
+@uncaged/nerve-workflow-solve-issue
+@uncaged/nerve-workflow-develop-sense
+@uncaged/nerve-workflow-develop-workflow
+
+# Shared Roles (new)
+@uncaged/nerve-role-committer    # workspace committer (branch, commit, push)
+@uncaged/nerve-role-reviewer     # code review role
+@uncaged/nerve-role-publisher    # PR creation role
+
+# Senses (existing pattern, formalized)
+@uncaged/nerve-sense-cpu-usage
+@uncaged/nerve-sense-disk-usage
+```
+
+### Package Contract
+
+Each package type exports a factory function:
+
+#### Workflow Package
+
+```ts
+// @uncaged/nerve-workflow-develop-sense
+import type { AgentFn, WorkflowDefinition } from "@uncaged/nerve-core";
+import type { LlmExtractorConfig } from "@uncaged/nerve-workflow-utils";
+
+export type SenseMeta = { /* ... */ };
+
+export type CreateDevelopSenseDeps = {
+  defaultAdapter: AgentFn;
+  adapters?: Partial<Record<keyof SenseMeta, AgentFn>>;
+  extract: LlmExtractorConfig;
+  cwd: string;
+};
+
+export function createDevelopSenseWorkflow(deps: CreateDevelopSenseDeps): WorkflowDefinition<SenseMeta>;
+```
+
+Key design decisions:
+- `defaultAdapter` + optional `adapters` override per role — via `Partial<Record<keyof Meta, AgentFn>>`
+- Adapter keys are derived from `Meta` type — adding/removing a role automatically updates the adapter map
+- Roles that don't need an agent simply don't appear in `adapters` (the `Partial` allows this)
+
+#### Role Package
+
+```ts
+// @uncaged/nerve-role-committer
+import type { AgentFn, Role } from "@uncaged/nerve-core";
+import type { LlmExtractorConfig } from "@uncaged/nerve-workflow-utils";
+import { createRole, decorateRole, withDryRun, onFail } from "@uncaged/nerve-workflow-utils";
+
+export type CommitterMeta = { committed: boolean };
+
+export function createCommitterRole(adapter: AgentFn, extract: LlmExtractorConfig): Role<CommitterMeta> {
+  const inner = createRole(adapter, prompt, committerMetaSchema, extract);
+  return decorateRole(inner, [
+    withDryRun({ label: "committer", meta: { committed: true } }),
+    onFail({ label: "committer", meta: { committed: false } }),
+  ]);
+}
+```
+
+Roles compose with the decorator chain from `workflow-utils`:
+- `withDryRun` — skip execution in dry-run mode
+- `onFail` — catch errors into structured failure results
+- `decorateRole(role, [...])` — apply decorators left-to-right
+- Custom `RoleDecorator<M>` can be created for project-specific needs
+
+#### Sense Package
+
+```ts
+// @uncaged/nerve-sense-cpu-usage
+export const senseName = "cpu-usage";
+export const schema = { /* drizzle schema */ };
+export async function compute(ctx: SenseContext): Promise<SenseResult>;
+```
+
+### Workspace as Configuration
+
+The workspace becomes a thin wiring layer:
+
+```
+~/.uncaged-nerve/
+  nerve.yaml           # senses, extract config
+  package.json         # depends on workflow/role/adapter packages
+  workflows/
+    develop-sense/
+      index.ts         # ~10 lines: import package, wire adapters, export
+    solve-issue/
+      index.ts         # same pattern
+```
+
+A typical `index.ts`:
+
+```ts
+import { createDevelopSenseWorkflow } from "@uncaged/nerve-workflow-develop-sense";
+import { hermesAdapter } from "@uncaged/nerve-adapter-hermes";
+import { cursorAdapter } from "@uncaged/nerve-adapter-cursor";
+
+export default createDevelopSenseWorkflow({
+  defaultAdapter: hermesAdapter,
+  adapters: { planner: cursorAdapter, coder: cursorAdapter },
+  extract: { provider: { apiKey, baseUrl, model } },
+  cwd: nerveRoot,
+});
+```
+
+### What Stays in Workspace
+
+- **Custom workflows** — project-specific workflows that aren't general enough to share
+- **Custom senses** — project-specific metrics
+- **Configuration** — adapter selection, credentials, `nerve.yaml`
+- **Overrides** — a workspace can always write its own role/workflow instead of using a package
+
+### Dependency Rules
+
+```
+nerve-core           ← no deps on other nerve packages
+nerve-workflow-utils ← depends on nerve-core
+nerve-adapter-*      ← depends on nerve-core
+nerve-role-*         ← depends on nerve-core, nerve-workflow-utils
+nerve-workflow-*     ← depends on nerve-core, nerve-workflow-utils, may depend on nerve-role-*
+nerve-sense-*        ← depends on nerve-core
+nerve-daemon         ← depends on nerve-core, nerve-store
+```
+
+Workflow packages depend on role packages (not adapters). Adapters are injected at the workspace level.
+
+### Migration Path
+
+1. **Phase 1: Extract role packages** — Start with `@uncaged/nerve-role-committer` (already `_shared/workspace-committer.ts`). Publish, update workspace to import from package.
+2. **Phase 2: Extract workflow packages** — Move `develop-sense` and `develop-workflow` to packages. Workspace `index.ts` becomes pure wiring.
+3. **Phase 3: Sense packages** — Formalize sense packaging (lower priority, senses are already self-contained directories).
+4. **Phase 4: Community** — Document the package contract so others can publish workflows/roles/senses.
+
+### Not in Scope
+
+- **No builtin workflows** — nerve core ships zero workflows. All workflows are packages installed by the workspace.
+- **No workflow marketplace/registry** — just npm packages. `pnpm add @uncaged/nerve-workflow-solve-issue`.
+- **No nerve.yaml workflow declaration** — workflows are still TypeScript entry points. The daemon discovers them the same way it does today.
+
+## Open Questions
+
+1. **Monorepo vs separate repos?** — Should workflow/role packages live in the nerve monorepo or separate repos? Monorepo is easier for coordinated releases; separate repos allow independent versioning.
+2. **Sense package format** — Senses currently bundle with esbuild. Should sense packages ship pre-bundled or as TypeScript source?
+3. **Version coupling** — How tightly should workflow packages pin `nerve-core`? Peer deps with semver range?
+
+## Prior Art
+
+- Adapter packages (`@uncaged/nerve-adapter-*`) — established the factory + injection pattern
+- `_shared/workspace-committer.ts` — proved roles can be shared across workflows
+- `createRole` / `decorateRole` / `withDryRun` / `onFail` in `workflow-utils` — building blocks that role packages compose
+- `defaultAdapter` + `Partial<Record<keyof Meta, AgentFn>>` pattern — adapter injection without coupling

examples/cpu-usage/index.ts

@@ -8,10 +8,9 @@ import { samples } from "./schema.js";
  * Read the 1-minute CPU load average, persist it, and emit a Signal.
  *
  * Returns `null` only if `loadavg` is unavailable (non-POSIX platforms).
- * On every successful read a row is inserted and the value is returned,
- * which causes the engine to emit a Signal.
+ * On every successful read a row is inserted and a Signal is emitted with the load value.
  */
-export async function compute(db: DrizzleDB, _peers: PeerMap): Promise<number | null> {
+export async function compute(db: DrizzleDB, _peers: PeerMap) {
   const [oneMin] = loadavg();
 
   if (typeof oneMin !== "number" || Number.isNaN(oneMin)) {
@@ -19,5 +18,5 @@ export async function compute(db: DrizzleDB, _peers: PeerMap): Promise<number |
   }
 
   await db.insert(samples).values({ ts: Date.now(), value: oneMin });
-  return oneMin;
+  return { signal: oneMin, workflow: null };
 }

examples/nerve.yaml

@@ -11,30 +11,20 @@ senses:
     throttle: 5s
     timeout: 8s
     grace_period: null
+    interval: 10s
 
   disk-usage:
     group: system
     throttle: null
     timeout: 15s
     grace_period: null
+    interval: 30s
 
   system-health:
     group: derived
     throttle: 2s
     timeout: 10s
     grace_period: null
-
-reflexes:
-  # cpu-usage runs on a 10-second interval
-  - sense: cpu-usage
-    interval: 10s
-
-  # disk-usage runs on a 30-second interval
-  - sense: disk-usage
-    interval: 30s
-
-  # system-health is event-driven: fires whenever cpu-usage or disk-usage emits a signal
-  - sense: system-health
     on:
       - cpu-usage
       - disk-usage

examples/senses/nerve-health.ts

@@ -11,9 +11,6 @@
  *       group: internal
  *       throttle: 30s
  *       timeout: 5s
- *
- *   reflexes:
- *     - sense: nerve-health
  *       interval: 30s
  */
 
@@ -25,9 +22,9 @@ export type NerveHealth = {
   workerUptime: number;
 };
 
-export async function compute(): Promise<NerveHealth | null> {
+export async function compute() {
   const health = await requestHealthFromKernel();
-  return health;
+  return { signal: health, workflow: null };
 }
 
 function requestHealthFromKernel(): Promise<NerveHealth> {

knowledge.yaml

@@ -0,0 +1,4 @@
+include:
+  - ".knowledge/**/*.md"
+
+exclude: []

package.json

@@ -8,7 +8,8 @@
     "prepare": "husky",
     "build": "pnpm -r run build",
     "check": "biome check .",
-    "format": "biome format --write ."
+    "format": "biome format --write .",
+    "link:dev": "bash scripts/link-dev.sh"
   },
   "devDependencies": {
     "@biomejs/biome": "^1.9.0",

packages/adapter-cursor/package.json

@@ -0,0 +1,24 @@
+{
+  "name": "@uncaged/nerve-adapter-cursor",
+  "version": "0.5.0",
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": ["dist"],
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "prepublishOnly": "bash ../../scripts/prepublish-check.sh",
+    "build": "rslib build",
+    "test": "vitest run --passWithNoTests"
+  },
+  "dependencies": {
+    "@uncaged/nerve-core": "workspace:*"
+  },
+  "devDependencies": {
+    "@rslib/core": "^0.21.3",
+    "@types/node": "^22.0.0",
+    "vitest": "^4.1.5"
+  }
+}

packages/adapter-cursor/rslib.config.ts

@@ -0,0 +1,19 @@
+import { defineConfig } from "@rslib/core";
+
+export default defineConfig({
+  lib: [
+    {
+      format: "esm",
+      dts: true,
+    },
+  ],
+  source: {
+    entry: {
+      index: "src/index.ts",
+    },
+  },
+  output: {
+    target: "node",
+    cleanDistPath: true,
+  },
+});

packages/adapter-cursor/src/index.ts

@@ -0,0 +1,122 @@
+import type { AgentConfig, AgentFn, WorkflowContext } from "@uncaged/nerve-core";
+import { type Result, type SpawnEnv, type SpawnError, ok, spawnSafe } from "@uncaged/nerve-core";
+
+export type CursorAgentMode = "plan" | "ask" | "default";
+
+export type CursorAgentOptions = {
+  prompt: string;
+  mode: CursorAgentMode;
+  model: string;
+  cwd: string;
+  env: SpawnEnv | null;
+  timeoutMs: number | null;
+  dryRun: boolean;
+  abortSignal: AbortSignal | null;
+};
+
+type CursorAgentOptionsInput = CursorAgentOptions | Omit<CursorAgentOptions, "dryRun">;
+
+function resolveCursorAgentDryRun(options: CursorAgentOptionsInput): boolean {
+  return "dryRun" in options ? options.dryRun : false;
+}
+
+function normalizeAbortSignal(options: CursorAgentOptionsInput): AbortSignal | null {
+  return "abortSignal" in options ? options.abortSignal : null;
+}
+
+/**
+ * Invokes `cursor-agent` with the prompt passed as a single argv slot (`shell: false`).
+ */
+export async function cursorAgent(
+  options: CursorAgentOptionsInput,
+): Promise<Result<string, SpawnError>> {
+  const dryRun = resolveCursorAgentDryRun(options);
+  if (dryRun) {
+    return ok("[dryRun] skipped");
+  }
+
+  const args: string[] = [
+    "-p",
+    options.prompt,
+    "--model",
+    options.model,
+    "--output-format",
+    "text",
+    "--trust",
+    "--force",
+  ];
+  if (options.mode === "plan") {
+    args.push("--mode=plan");
+  } else if (options.mode === "ask") {
+    args.push("--mode=ask");
+  }
+
+  const run = await spawnSafe("cursor-agent", args, {
+    cwd: options.cwd,
+    env: options.env,
+    timeoutMs: options.timeoutMs,
+    dryRun: false,
+    abortSignal: normalizeAbortSignal(options),
+  });
+
+  if (!run.ok) {
+    return run;
+  }
+
+  return ok(run.value.stdout);
+}
+
+function throwCursorSpawnError(error: SpawnError): never {
+  if (error.kind === "non_zero_exit") {
+    throw new Error(
+      `cursor-agent: exitCode=${error.exitCode} stdout=${error.stdout} stderr=${error.stderr}`,
+    );
+  }
+  if (error.kind === "timeout") {
+    throw new Error("cursor-agent: timeout");
+  }
+  if (error.kind === "aborted") {
+    throw new Error("cursor-agent: aborted");
+  }
+  throw new Error(`cursor-agent: ${error.message}`);
+}
+
+/** Default adapter config: model auto-selection and 300s wall-clock cap (milliseconds). */
+const CURSOR_ADAPTER_DEFAULT_MS = 300_000;
+
+export type CursorAdapterConfig = AgentConfig & {
+  /** When set, passes `--mode=ask` or `--mode=plan` to `cursor-agent` (default runs without extra mode). */
+  mode?: CursorAgentMode;
+};
+
+/**
+ * Builds a Cursor CLI `AgentFn` from adapter config (model, timeout).
+ */
+export function createCursorAdapter(config: CursorAdapterConfig): AgentFn {
+  const timeoutMs = config.timeout;
+  const mode = config.mode ?? "default";
+
+  return async (prompt: string, context: WorkflowContext): Promise<string> => {
+    const run = await cursorAgent({
+      prompt,
+      mode,
+      model: config.model,
+      cwd: context.workdir,
+      env: null,
+      timeoutMs,
+      dryRun: context.start.meta.dryRun,
+      abortSignal: context.signal,
+    });
+    if (!run.ok) {
+      throwCursorSpawnError(run.error);
+    }
+    return run.value;
+  };
+}
+
+/** Default instance — `model: "auto"`, `timeout: 300` seconds (as milliseconds). */
+export const cursorAdapter: AgentFn = createCursorAdapter({
+  type: "cursor",
+  model: "auto",
+  timeout: CURSOR_ADAPTER_DEFAULT_MS,
+});

packages/adapter-cursor/tsconfig.json

@@ -0,0 +1,9 @@
+{
+  "extends": "../../tsconfig.json",
+  "compilerOptions": {
+    "outDir": "dist",
+    "rootDir": "src",
+    "composite": false
+  },
+  "include": ["src"]
+}

packages/adapter-hermes/package.json

@@ -0,0 +1,24 @@
+{
+  "name": "@uncaged/nerve-adapter-hermes",
+  "version": "0.5.0",
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": ["dist"],
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "prepublishOnly": "bash ../../scripts/prepublish-check.sh",
+    "build": "rslib build",
+    "test": "vitest run --passWithNoTests"
+  },
+  "dependencies": {
+    "@uncaged/nerve-core": "workspace:*"
+  },
+  "devDependencies": {
+    "@rslib/core": "^0.21.3",
+    "@types/node": "^22.0.0",
+    "vitest": "^4.1.5"
+  }
+}

packages/adapter-hermes/rslib.config.ts

@@ -0,0 +1,19 @@
+import { defineConfig } from "@rslib/core";
+
+export default defineConfig({
+  lib: [
+    {
+      format: "esm",
+      dts: true,
+    },
+  ],
+  source: {
+    entry: {
+      index: "src/index.ts",
+    },
+  },
+  output: {
+    target: "node",
+    cleanDistPath: true,
+  },
+});

packages/adapter-hermes/src/index.ts

@@ -0,0 +1,124 @@
+import type { AgentConfig, AgentFn, WorkflowContext } from "@uncaged/nerve-core";
+import { type Result, type SpawnEnv, type SpawnError, ok, spawnSafe } from "@uncaged/nerve-core";
+
+/**
+ * Spawns a non-interactive `hermes chat` invocation with YOLO enabled, argv-only
+ * (shell: false) following the Nerve issue #208 contract.
+ */
+export type HermesAgentOptions = {
+  prompt: string;
+  model: string | null;
+  provider: string | null;
+  skills: string[];
+  /** When true, suppresses interactive UI noise. */
+  quiet: boolean;
+  maxTurns: number;
+  env: SpawnEnv | null;
+  timeoutMs: number | null;
+  dryRun: boolean;
+  abortSignal: AbortSignal | null;
+};
+
+type HermesAgentOptionsInput = HermesAgentOptions | Omit<HermesAgentOptions, "dryRun">;
+
+function resolveHermesDryRun(options: HermesAgentOptionsInput): boolean {
+  return "dryRun" in options ? options.dryRun : false;
+}
+
+function normalizeAbortSignal(options: HermesAgentOptionsInput): AbortSignal | null {
+  return "abortSignal" in options ? options.abortSignal : null;
+}
+
+export async function hermesAgent(
+  options: HermesAgentOptionsInput,
+): Promise<Result<string, SpawnError>> {
+  const dryRun = resolveHermesDryRun(options);
+  if (dryRun) {
+    return ok("[dryRun] hermes stub");
+  }
+  const args: string[] = [
+    "chat",
+    "-q",
+    options.prompt,
+    "--yolo",
+    "--max-turns",
+    String(options.maxTurns),
+  ];
+  if (options.model) {
+    args.push("--model", options.model);
+  }
+  if (options.provider) {
+    args.push("--provider", options.provider);
+  }
+  for (const s of options.skills) {
+    args.push("-s", s);
+  }
+  if (options.quiet) {
+    args.push("--quiet");
+  }
+  const run = await spawnSafe("hermes", args, {
+    cwd: null,
+    env: options.env,
+    timeoutMs: options.timeoutMs,
+    dryRun: false,
+    abortSignal: normalizeAbortSignal(options),
+  });
+  if (!run.ok) {
+    return run;
+  }
+  return ok(run.value.stdout);
+}
+
+function throwHermesSpawnError(error: SpawnError): never {
+  if (error.kind === "non_zero_exit") {
+    throw new Error(
+      `hermes: exitCode=${error.exitCode} stdout=${error.stdout} stderr=${error.stderr}`,
+    );
+  }
+  if (error.kind === "timeout") {
+    throw new Error("hermes: timeout");
+  }
+  if (error.kind === "aborted") {
+    throw new Error("hermes: aborted");
+  }
+  throw new Error(`hermes: ${error.message}`);
+}
+
+const HERMES_ADAPTER_DEFAULT_MAX_TURNS = 90;
+
+/** Default wall-clock cap: 300 seconds (milliseconds). */
+const HERMES_ADAPTER_DEFAULT_MS = 300_000;
+
+/**
+ * Builds a Hermes CLI `AgentFn` from adapter config (model, timeout).
+ */
+export function createHermesAdapter(config: AgentConfig): AgentFn {
+  const modelFromConfig = config.model === "auto" ? null : config.model;
+  const timeoutMs = config.timeout;
+
+  return async (prompt: string, context: WorkflowContext): Promise<string> => {
+    const run = await hermesAgent({
+      prompt,
+      model: modelFromConfig,
+      provider: null,
+      skills: [],
+      quiet: true,
+      maxTurns: HERMES_ADAPTER_DEFAULT_MAX_TURNS,
+      env: null,
+      timeoutMs,
+      dryRun: context.start.meta.dryRun,
+      abortSignal: context.signal,
+    });
+    if (!run.ok) {
+      throwHermesSpawnError(run.error);
+    }
+    return run.value;
+  };
+}
+
+/** Default instance — `model: "auto"`, `timeout: 300` seconds (as milliseconds). */
+export const hermesAdapter: AgentFn = createHermesAdapter({
+  type: "hermes",
+  model: "auto",
+  timeout: HERMES_ADAPTER_DEFAULT_MS,
+});

packages/adapter-hermes/tsconfig.json

@@ -0,0 +1,9 @@
+{
+  "extends": "../../tsconfig.json",
+  "compilerOptions": {
+    "outDir": "dist",
+    "rootDir": "src",
+    "composite": false
+  },
+  "include": ["src"]
+}

packages/cli/package.json

@@ -3,7 +3,7 @@
   "engines": {
     "node": ">=22.5.0"
   },
-  "version": "0.4.0",
+  "version": "0.5.0",
   "type": "module",
   "bin": {
     "nerve": "dist/cli.js"
@@ -23,11 +23,13 @@
     "@uncaged/nerve-core": "workspace:*",
     "@uncaged/nerve-store": "workspace:*",
     "citty": "^0.1.6",
+    "picomatch": "^4.0.2",
     "yaml": "^2.8.3"
   },
   "devDependencies": {
     "@rslib/core": "^0.21.3",
     "@types/node": "^22.0.0",
+    "@uncaged/nerve-daemon": "workspace:*",
     "vitest": "^4.1.5"
   }
 }

packages/cli/rslib.config.ts

@@ -6,7 +6,7 @@ export default defineConfig({
       format: "esm",
       dts: true,
       banner: {
-        js: "#!/usr/bin/env node",
+        js: "#!/usr/bin/env -S node --disable-warning=ExperimentalWarning",
       },
     },
   ],

packages/cli/src/__tests__/chunk-markdown.test.ts

@@ -0,0 +1,35 @@
+import { describe, expect, it } from "vitest";
+
+import { chunkMarkdown } from "../knowledge/chunk-markdown.js";
+
+describe("chunkMarkdown", () => {
+  it("splits markdown by headings into separate chunks", () => {
+    const md = `# Title One
+
+Intro para under first heading.
+
+## Title Two
+
+Second section body.
+
+`;
+    const chunks = chunkMarkdown("docs/guide.md", md);
+    expect(chunks.length).toBeGreaterThanOrEqual(2);
+    const joined = chunks.map((c) => c.text).join("\n");
+    expect(joined).toContain("Title One");
+    expect(joined).toContain("Title Two");
+  });
+
+  it("includes preamble before first heading as its own chunk when present", () => {
+    const md = `Preamble line here.
+
+# First Real Heading
+
+Under heading.
+`;
+    const chunks = chunkMarkdown("readme.md", md);
+    const preamble = chunks.find((c) => c.slug.includes("preamble"));
+    expect(preamble).toBeDefined();
+    expect(preamble?.text).toContain("Preamble");
+  });
+});

packages/cli/src/__tests__/cli-global.test.ts

@@ -0,0 +1,31 @@
+import { describe, expect, it } from "vitest";
+
+import {
+  consumeGlobalDaemonCliFlags,
+  getCliDaemonApiToken,
+  getCliDaemonHost,
+} from "../cli-global.js";
+
+describe("consumeGlobalDaemonCliFlags", () => {
+  it("strips --host and --api-token and populates getters", () => {
+    const out = consumeGlobalDaemonCliFlags([
+      "--host",
+      "192.168.1.5:9800",
+      "--api-token=abc",
+      "sense",
+      "list",
+    ]);
+    expect(out).toEqual(["sense", "list"]);
+    expect(getCliDaemonHost()).toBe("192.168.1.5:9800");
+    expect(getCliDaemonApiToken()).toBe("abc");
+  });
+
+  it("supports --host=value form", () => {
+    consumeGlobalDaemonCliFlags(["--host=luming:9800", "status"]);
+    expect(getCliDaemonHost()).toBe("luming:9800");
+  });
+
+  it("throws when --host has no value", () => {
+    expect(() => consumeGlobalDaemonCliFlags(["--host", "--api-token", "x"])).toThrow(/--host/);
+  });
+});

packages/cli/src/__tests__/create-sense.test.ts

@@ -0,0 +1,73 @@
+/**
+ * Tests for nerve create sense template helpers.
+ */
+
+import { describe, expect, it } from "vitest";
+
+import {
+  buildSenseIndexTs,
+  buildSenseMigrationSql,
+  buildSensePackageJson,
+  buildSenseSchemaTs,
+  validateResourceName,
+} from "../commands/create.js";
+
+describe("validateSenseName", () => {
+  it("accepts valid ids", () => {
+    expect(validateResourceName("a", "Sense")).toBe(null);
+    expect(validateResourceName("my-sense", "Sense")).toBe(null);
+    expect(validateResourceName("cpu-usage", "Sense")).toBe(null);
+  });
+
+  it("rejects invalid ids", () => {
+    expect(validateResourceName("", "Sense")).not.toBe(null);
+    expect(validateResourceName("My-Sense", "Sense")).not.toBe(null);
+    expect(validateResourceName("-bad", "Sense")).not.toBe(null);
+  });
+});
+
+describe("buildSenseSchemaTs", () => {
+  it("maps kebab-case id to snake table and camel export", () => {
+    const src = buildSenseSchemaTs("my-sense");
+    expect(src).toContain('sqliteTable("my_sense"');
+    expect(src).toContain("export const mySense = ");
+  });
+
+  it("handles single-segment id", () => {
+    const src = buildSenseSchemaTs("metrics");
+    expect(src).toContain('sqliteTable("metrics"');
+    expect(src).toContain("export const metrics = ");
+  });
+});
+
+describe("buildSenseMigrationSql", () => {
+  it("uses snake_case table name", () => {
+    expect(buildSenseMigrationSql("disk-io")).toContain("CREATE TABLE IF NOT EXISTS disk_io");
+  });
+});
+
+describe("buildSensePackageJson", () => {
+  it("includes esbuild script and sense name", () => {
+    const pkg = JSON.parse(buildSensePackageJson("my-sense"));
+    expect(pkg.name).toBe("nerve-sense-my-sense");
+    expect(pkg.scripts.build).toContain("esbuild");
+    expect(pkg.scripts.build).toContain("src/index.ts");
+    expect(pkg.devDependencies.esbuild).toBeTruthy();
+  });
+});
+
+describe("buildSenseIndexTs", () => {
+  it("embeds sense id in stub with TypeScript types", () => {
+    const ts = buildSenseIndexTs("my-sense");
+    expect(ts).toContain("my-sense");
+    expect(ts).toContain("export async function compute");
+    expect(ts).toContain("LibSQLDatabase");
+    expect(ts).toContain("Promise<SenseResult>");
+    expect(ts).toContain('from "./schema.js"');
+  });
+
+  it("imports the correct schema export", () => {
+    const ts = buildSenseIndexTs("cpu-usage");
+    expect(ts).toContain("cpuUsage");
+  });
+});

packages/cli/src/__tests__/create-workflow.test.ts

@@ -0,0 +1,116 @@
+/**
+ * Tests for nerve create workflow scaffold logic.
+ *
+ * We test the file-generation path by isolating the template rendering,
+ * not by invoking the full citty command (which calls process.exit).
+ */
+
+import { mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { afterEach, beforeEach, describe, expect, it } from "vitest";
+import { buildWorkflowPackageJson, buildWorkflowScaffold } from "../commands/create.js";
+
+let tmpDir: string;
+
+beforeEach(() => {
+  tmpDir = mkdtempSync(join(tmpdir(), "nerve-cli-init-test-"));
+});
+
+afterEach(() => {
+  rmSync(tmpDir, { recursive: true, force: true });
+});
+
+describe("buildWorkflowScaffold", () => {
+  it("includes the workflow name in the main role content", () => {
+    const { roleMainIndexTs } = buildWorkflowScaffold("my-workflow");
+    expect(roleMainIndexTs).toContain("my-workflow started");
+  });
+
+  it("root index contains WorkflowDefinition import from nerve-core", () => {
+    const { indexTs } = buildWorkflowScaffold("test");
+    expect(indexTs).toContain("WorkflowDefinition");
+    expect(indexTs).toContain("@uncaged/nerve-core");
+  });
+
+  it("root index wires moderator and END", () => {
+    const { indexTs } = buildWorkflowScaffold("test");
+    expect(indexTs).toContain("moderator");
+    expect(indexTs).toContain("END");
+  });
+
+  it("root index imports main role and sets name field", () => {
+    const { indexTs } = buildWorkflowScaffold("test");
+    expect(indexTs).toContain('name: "test"');
+    expect(indexTs).toContain("main: mainRole");
+    expect(indexTs).toContain("./roles/main/index.js");
+  });
+
+  it("main role module exports mainRole function", () => {
+    const { roleMainIndexTs } = buildWorkflowScaffold("test");
+    expect(roleMainIndexTs).toContain("export async function mainRole");
+  });
+
+  it("uses different names per call", () => {
+    const a = buildWorkflowScaffold("workflow-a");
+    const b = buildWorkflowScaffold("workflow-b");
+    expect(a.roleMainIndexTs).toContain("workflow-a started");
+    expect(b.roleMainIndexTs).toContain("workflow-b started");
+    expect(a.roleMainIndexTs).not.toContain("workflow-b");
+  });
+
+  it("produces valid TypeScript syntax for index (no unclosed braces)", () => {
+    const { indexTs } = buildWorkflowScaffold("test");
+    const opens = (indexTs.match(/\{/g) ?? []).length;
+    const closes = (indexTs.match(/\}/g) ?? []).length;
+    expect(opens).toBe(closes);
+  });
+
+  it("ends root index with export default workflow", () => {
+    const { indexTs } = buildWorkflowScaffold("test");
+    expect(indexTs.trim().endsWith("export default workflow;")).toBe(true);
+  });
+
+  it("prompt markdown names the workflow", () => {
+    const { roleMainPromptMd } = buildWorkflowScaffold("my-flow");
+    expect(roleMainPromptMd).toContain("# my-flow — main role");
+  });
+
+  it("package.json defines esbuild bundling to dist/", () => {
+    const pkg = JSON.parse(buildWorkflowPackageJson("my-flow")) as {
+      scripts: { build: string };
+      devDependencies: { esbuild: string };
+    };
+    expect(pkg.scripts.build).toContain("esbuild");
+    expect(pkg.scripts.build).toContain("--outdir=dist");
+    expect(pkg.devDependencies.esbuild).toBeTruthy();
+  });
+
+  it("buildWorkflowScaffold includes package.json body", () => {
+    const { packageJson } = buildWorkflowScaffold("wf");
+    expect(JSON.parse(packageJson).scripts.build).toContain("esbuild");
+  });
+});
+
+describe("workflow scaffold file writing (simulated)", () => {
+  it("writes all scaffold files to disk correctly", () => {
+    const workflowDir = join(tmpDir, "workflows", "my-task");
+    mkdirSync(join(workflowDir, "roles", "main"), { recursive: true });
+    const scaffold = buildWorkflowScaffold("my-task");
+    writeFileSync(join(workflowDir, "index.ts"), scaffold.indexTs, "utf8");
+    writeFileSync(join(workflowDir, "roles", "main", "index.ts"), scaffold.roleMainIndexTs, "utf8");
+    writeFileSync(
+      join(workflowDir, "roles", "main", "prompt.md"),
+      scaffold.roleMainPromptMd,
+      "utf8",
+    );
+
+    expect(readFileSync(join(workflowDir, "index.ts"), "utf8")).toContain('name: "my-task"');
+    expect(readFileSync(join(workflowDir, "roles", "main", "index.ts"), "utf8")).toContain(
+      "my-task started",
+    );
+    expect(readFileSync(join(workflowDir, "roles", "main", "prompt.md"), "utf8")).toContain(
+      "# my-task — main role",
+    );
+  });
+});

packages/cli/src/__tests__/e2e-create.test.ts

@@ -0,0 +1,190 @@
+/**
+ * E2E-style tests for `nerve create workflow` and `nerve create sense`.
+ */
+
+import { existsSync, mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { defineCommand, runCommand } from "citty";
+import { afterEach, describe, expect, it } from "vitest";
+
+import { createCommand } from "../commands/create.js";
+import { initCommand } from "../commands/init.js";
+
+const testRootCommand = defineCommand({
+  meta: { name: "nerve", description: "e2e-create" },
+  subCommands: {
+    init: initCommand,
+    create: createCommand,
+  },
+});
+
+type CliRunResult = {
+  stdout: string;
+  stderr: string;
+  exitCode: number;
+};
+
+class ProcessExitError extends Error {
+  readonly code: number;
+  constructor(code: number) {
+    super(`process.exit(${String(code)})`);
+    this.name = "ProcessExitError";
+    this.code = code;
+  }
+}
+
+function patchWriteStream(stream: NodeJS.WriteStream, sink: string[]): () => void {
+  const orig = stream.write.bind(stream) as (
+    chunk: string | Uint8Array,
+    encodingOrCb?: BufferEncoding | ((err: Error | null | undefined) => void),
+    cb?: (err: Error | null | undefined) => void,
+  ) => boolean;
+
+  stream.write = ((
+    chunk: string | Uint8Array,
+    encodingOrCb?: BufferEncoding | ((err: Error | null | undefined) => void),
+    cb?: (err: Error | null | undefined) => void,
+  ) => {
+    if (typeof chunk === "string") {
+      sink.push(chunk);
+    } else {
+      sink.push(Buffer.from(chunk).toString("utf8"));
+    }
+    if (typeof encodingOrCb === "function") {
+      encodingOrCb(null);
+      return true;
+    }
+    if (cb !== undefined) {
+      cb(null);
+    }
+    return true;
+  }) as typeof stream.write;
+
+  return () => {
+    stream.write = orig as typeof stream.write;
+  };
+}
+
+async function runTestCli(fakeHome: string, args: string[]): Promise<CliRunResult> {
+  const stdoutChunks: string[] = [];
+  const stderrChunks: string[] = [];
+  const restoreOut = patchWriteStream(process.stdout, stdoutChunks);
+  const restoreErr = patchWriteStream(process.stderr, stderrChunks);
+
+  const prevHome = process.env.HOME;
+  process.env.HOME = fakeHome;
+
+  let exitCode = 0;
+  const origExit = process.exit;
+  process.exit = ((code?: number) => {
+    exitCode = typeof code === "number" ? code : 0;
+    throw new ProcessExitError(exitCode);
+  }) as typeof process.exit;
+
+  try {
+    await runCommand(testRootCommand, { rawArgs: args });
+  } catch (e) {
+    if (e instanceof ProcessExitError) {
+      exitCode = e.code;
+    } else {
+      exitCode = 1;
+      stderrChunks.push(e instanceof Error ? e.message : String(e));
+    }
+  } finally {
+    process.exit = origExit;
+    if (prevHome === undefined) {
+      // biome-ignore lint/performance/noDelete: semantically correct for env cleanup
+      delete process.env.HOME;
+    } else {
+      process.env.HOME = prevHome;
+    }
+    restoreOut();
+    restoreErr();
+  }
+
+  return {
+    stdout: stdoutChunks.join(""),
+    stderr: stderrChunks.join(""),
+    exitCode,
+  };
+}
+
+describe("e2e create", () => {
+  let fakeHome: string | null = null;
+
+  afterEach(() => {
+    if (fakeHome !== null) {
+      rmSync(fakeHome, { recursive: true, force: true });
+      fakeHome = null;
+    }
+  });
+
+  it(
+    "create workflow scaffolds sources and package.json with esbuild build",
+    { timeout: 10_000 },
+    async () => {
+      fakeHome = mkdtempSync(join(tmpdir(), "nerve-create-e2e-"));
+      const nerveRoot = join(fakeHome, ".uncaged-nerve");
+
+      await runTestCli(fakeHome, ["init", "--force", "--skip-install"]);
+
+      const wf = await runTestCli(fakeHome, ["create", "workflow", "e2e-flow"]);
+      expect(wf.exitCode).toBe(0);
+      expect(wf.stdout).toContain("✅");
+
+      const pkgPath = join(nerveRoot, "workflows", "e2e-flow", "package.json");
+      const indexPath = join(nerveRoot, "workflows", "e2e-flow", "index.ts");
+      const mainRolePath = join(nerveRoot, "workflows", "e2e-flow", "roles", "main", "index.ts");
+      expect(existsSync(pkgPath)).toBe(true);
+      expect(JSON.parse(readFileSync(pkgPath, "utf8")).scripts.build).toContain("esbuild");
+      expect(existsSync(indexPath)).toBe(true);
+      expect(existsSync(mainRolePath)).toBe(true);
+      expect(readFileSync(indexPath, "utf8")).toContain('name: "e2e-flow"');
+      expect(readFileSync(mainRolePath, "utf8")).toContain("e2e-flow started");
+    },
+  );
+
+  it(
+    "create sense scaffolds src/index.ts, src/schema.ts, package.json and migration",
+    { timeout: 60_000 },
+    async () => {
+      fakeHome = mkdtempSync(join(tmpdir(), "nerve-create-e2e-"));
+      const nerveRoot = join(fakeHome, ".uncaged-nerve");
+
+      await runTestCli(fakeHome, ["init", "--force", "--skip-install"]);
+
+      const sense = await runTestCli(fakeHome, ["create", "sense", "e2e-sense"]);
+      expect(sense.exitCode).toBe(0);
+      expect(sense.stdout).toContain("✅");
+
+      const base = join(nerveRoot, "senses", "e2e-sense");
+      expect(existsSync(join(base, "package.json"))).toBe(true);
+      expect(existsSync(join(base, "src", "index.ts"))).toBe(true);
+      expect(existsSync(join(base, "src", "schema.ts"))).toBe(true);
+      expect(existsSync(join(base, "migrations", "0001_init.sql"))).toBe(true);
+
+      const pkg = JSON.parse(readFileSync(join(base, "package.json"), "utf8"));
+      expect(pkg.scripts.build).toContain("esbuild");
+
+      // pnpm install + build should produce index.js
+      expect(existsSync(join(base, "index.js"))).toBe(true);
+    },
+  );
+
+  it(
+    "create workflow exits 1 when directory exists without --force",
+    { timeout: 10_000 },
+    async () => {
+      fakeHome = mkdtempSync(join(tmpdir(), "nerve-create-e2e-"));
+      const nerveRoot = join(fakeHome, ".uncaged-nerve");
+      mkdirSync(join(nerveRoot, "workflows", "dup-wf"), { recursive: true });
+      writeFileSync(join(nerveRoot, "workflows", "dup-wf", "index.ts"), "// x", "utf8");
+
+      const first = await runTestCli(fakeHome, ["create", "workflow", "dup-wf"]);
+      expect(first.exitCode).toBe(1);
+      expect(first.stderr).toContain("already exists");
+    },
+  );
+});

packages/cli/src/__tests__/e2e-daemon-lifecycle.test.ts

@@ -0,0 +1,71 @@
+/**
+ * E2E: daemon start / status / stop lifecycle against the in-process test harness.
+ *
+ * Does not invoke the `stop` CLI while the harness PID file points at the current process
+ * (that would SIGTERM the test runner). After `status` shows running, we stop the kernel
+ * and remove `nerve.pid`, then assert `status` reports not running; `afterEach` tears down
+ * the temp HOME.
+ */
+
+import { existsSync, unlinkSync } from "node:fs";
+import { join } from "node:path";
+
+import { afterEach, describe, expect, it } from "vitest";
+
+import { type TestDaemonHandle, runCli, startTestDaemon, stopTestDaemon } from "./e2e-harness.js";
+
+describe("e2e daemon lifecycle", () => {
+  let daemon: TestDaemonHandle | null = null;
+  let kernelAlreadyStopped = false;
+
+  afterEach(async () => {
+    const h = daemon;
+    const skipKernel = kernelAlreadyStopped;
+    daemon = null;
+    kernelAlreadyStopped = false;
+    if (h === null) return;
+    await Promise.race([
+      stopTestDaemon(h, skipKernel),
+      new Promise<never>((_, reject) =>
+        setTimeout(() => reject(new Error("stopTestDaemon timed out after 10s")), 10_000),
+      ),
+    ]);
+  });
+
+  it(
+    "nerve.pid + kernel up, status running, then stopped + pid cleared, status not running",
+    { timeout: 30_000 },
+    async () => {
+      daemon = await startTestDaemon();
+
+      const pidPath = join(daemon.nerveRoot, "nerve.pid");
+      expect(existsSync(pidPath)).toBe(true);
+
+      const health = daemon.kernel.getHealth();
+      expect(health.activeGroups).toBeGreaterThan(0);
+      expect(daemon.kernel.getWorkerPid("e2e")).not.toBeNull();
+      expect(existsSync(daemon.socketPath)).toBe(true);
+
+      const statusUp = await runCli(daemon, ["daemon", "status"]);
+      expect(statusUp.exitCode).toBe(0);
+      expect(statusUp.stdout).toContain("running");
+      expect(statusUp.stdout).toContain("✅ Nerve daemon is running.");
+
+      const statusTopLevel = await runCli(daemon, ["status"]);
+      expect(statusTopLevel.exitCode).toBe(0);
+      expect(statusTopLevel.stdout).toContain("running");
+
+      await daemon.kernel.stop();
+      kernelAlreadyStopped = true;
+      unlinkSync(pidPath);
+
+      expect(existsSync(pidPath)).toBe(false);
+      expect(existsSync(daemon.socketPath)).toBe(false);
+
+      const statusDown = await runCli(daemon, ["daemon", "status"]);
+      expect(statusDown.exitCode).toBe(0);
+      expect(statusDown.stdout).toContain("not running");
+      expect(statusDown.stdout).toContain("😴 Nerve daemon is not running.");
+    },
+  );
+});

packages/cli/src/__tests__/e2e-harness.ts

@@ -0,0 +1,454 @@
+/**
+ * Shared E2E harness: temp HOME layout (`.uncaged-nerve`), real kernel + sense worker,
+ * IPC socket for CLI, and `runCommand` helpers with captured stdio.
+ *
+ * ## Signal persistence (CLI `nerve sense list`)
+ *
+ * The kernel appends a `source: "sense", type: "signal"` row to `data/logs.db` when a
+ * worker emits a signal (see `packages/daemon/src/kernel.ts`). The daemon also
+ * auto-persists each signal into a `_signals` table in the per-sense SQLite DB
+ * (see `runtime.persistSignal` in `packages/daemon/src/sense-runtime.ts`).
+ * `listSenses()` reads `lastSignalTimestamp` from the kernel's in-memory state,
+ * while `sense query` reads from the `_signals` table (or a user-defined preview table).
+ *
+ * ## Timeout guard (vitest)
+ *
+ * Always tear down the daemon in `afterEach` so a failed assertion does not leave a
+ * kernel and worker children running. Optionally race `stopTestDaemon` against a timer
+ * so CI does not hang if shutdown stalls:
+ *
+ * ```ts
+ * import { afterEach } from "vitest";
+ * import { stopTestDaemon, type TestDaemonHandle } from "./e2e-harness.js";
+ *
+ * let daemon: TestDaemonHandle | null = null;
+ *
+ * afterEach(async () => {
+ *   const h = daemon;
+ *   daemon = null;
+ *   if (h === null) return;
+ *   await Promise.race([
+ *     stopTestDaemon(h),
+ *     new Promise<never>((_, reject) =>
+ *       setTimeout(() => reject(new Error("stopTestDaemon timed out after 10s")), 10_000),
+ *     ),
+ *   ]);
+ * });
+ * ```
+ */
+
+import { existsSync, mkdirSync, mkdtempSync, rmSync, symlinkSync, writeFileSync } from "node:fs";
+import { createRequire } from "node:module";
+import { tmpdir } from "node:os";
+import { dirname, join } from "node:path";
+
+import type { NerveConfig } from "@uncaged/nerve-core";
+import { createKernel } from "@uncaged/nerve-daemon";
+import type { Kernel } from "@uncaged/nerve-daemon";
+import { defineCommand, runCommand } from "citty";
+
+import { daemonCommand } from "../commands/daemon.js";
+import { logsCommand } from "../commands/logs.js";
+import { senseCommand } from "../commands/sense.js";
+import { statusCommand } from "../commands/status.js";
+import { stopCommand } from "../commands/stop.js";
+import { storeCommand } from "../commands/store.js";
+import { threadCommand } from "../commands/thread.js";
+import { workflowCommand } from "../commands/workflow.js";
+
+const require = createRequire(import.meta.url);
+const nerveDaemonRoot = dirname(require.resolve("@uncaged/nerve-daemon/package.json"));
+const senseWorkerScript = join(nerveDaemonRoot, "dist", "sense-worker.js");
+const workflowWorkerScript = join(nerveDaemonRoot, "dist", "workflow-worker.js");
+
+const nerveYamlTemplate = `senses:
+  counter:
+    group: e2e
+
+workflows:
+  echo:
+    concurrency: 1
+    overflow: queue
+    max_queue: 10
+
+max_rounds: 10
+
+api:
+  port: null
+  token: null
+  host: 127.0.0.1
+`;
+
+/**
+ * Minimal echo workflow (one role round then END).
+ * Short delay in the role so two sequential CLI triggers can observe a queued run while the first is active.
+ */
+const echoWorkflowIndexJs = `const END = "__end__";
+
+export default {
+  name: "echo",
+  roles: {
+    echo: async (start, _messages) => {
+      await new Promise((r) => setTimeout(r, 350));
+      const p = typeof start.content === "string" ? start.content : "";
+      return {
+        content: p.length > 0 ? "echo:" + p : "echo:empty",
+        meta: {},
+      };
+    },
+  },
+  moderator({ steps }) {
+    if (steps.length === 0) return "echo";
+    return END;
+  },
+};
+`;
+
+const nerveYamlWithNoopWorkflow = `senses:
+  counter:
+    group: e2e
+
+workflows:
+  noop:
+    concurrency: 1
+    overflow: drop
+
+max_rounds: 10
+
+api:
+  port: null
+  token: null
+  host: 127.0.0.1
+`;
+
+/** Empty migration — counter sense uses only `_signals` (auto-created by daemon). */
+const counterMigration = `-- no-op migration for e2e counter sense
+SELECT 1;
+`;
+
+/**
+ * Minimal counter sense — each compute returns an incrementing count.
+ * Does NOT touch the DB directly; signal persistence is handled by the daemon
+ * (`runtime.persistSignal`) which writes to `_signals` automatically.
+ */
+const counterIndexJs = `let _count = 0;
+export async function compute(_db, _peers, _options) {
+  _count += 1;
+  return { signal: { count: _count }, workflow: null };
+}
+`;
+
+/** First trigger launches local noop workflow; later triggers emit a plain signal. */
+const counterIndexJsWithNoopWorkflow = `let _launched = false;
+export async function compute(_db, _peers, _options) {
+  if (!_launched) {
+    _launched = true;
+    return {
+      signal: { launched: true },
+      workflow: {
+        name: "noop",
+        maxRounds: 3,
+        prompt: "e2e-archive",
+        dryRun: false,
+      },
+    };
+  }
+  return { signal: { idle: true }, workflow: null };
+}
+`;
+
+/** Minimal workflow: moderator ends immediately (no role rounds). */
+const noopWorkflowIndexJs = `const END = "__end__";
+export default {
+  name: "noop",
+  roles: {
+    bot: async () => ({ content: "ok", meta: {} }),
+  },
+  moderator: () => END,
+};
+`;
+
+const e2eRootCommand = defineCommand({
+  meta: { name: "nerve", description: "e2e" },
+  subCommands: {
+    sense: senseCommand,
+    logs: logsCommand,
+    daemon: daemonCommand,
+    status: statusCommand,
+    stop: stopCommand,
+    workflow: workflowCommand,
+    store: storeCommand,
+    thread: threadCommand,
+  },
+});
+
+function defaultTestConfig(withNoopWorkflow: boolean): NerveConfig {
+  return {
+    senses: {
+      counter: {
+        group: "e2e",
+        throttle: null,
+        timeout: null,
+        gracePeriod: null,
+        retention: 10_000,
+        interval: null,
+        on: [],
+      },
+    },
+    workflows: {
+      echo: { concurrency: 1, overflow: "queue" as const, maxQueue: 10 },
+      ...(withNoopWorkflow ? { noop: { concurrency: 1, overflow: "drop" as const } } : {}),
+    },
+    maxRounds: 10,
+    extract: null,
+    api: { port: null, token: null, host: "127.0.0.1" },
+  };
+}
+
+function writeWorkspaceLayout(nerveRoot: string, withNoopWorkflow: boolean): void {
+  mkdirSync(join(nerveRoot, "data", "senses"), { recursive: true });
+  mkdirSync(join(nerveRoot, "data", "blobs"), { recursive: true });
+  mkdirSync(join(nerveRoot, "senses", "counter", "migrations"), { recursive: true });
+  mkdirSync(join(nerveRoot, "workflows", "echo", "dist"), { recursive: true });
+  writeFileSync(
+    join(nerveRoot, "nerve.yaml"),
+    withNoopWorkflow ? nerveYamlWithNoopWorkflow : nerveYamlTemplate,
+    "utf8",
+  );
+  writeFileSync(
+    join(nerveRoot, "senses", "counter", "migrations", "001.sql"),
+    counterMigration,
+    "utf8",
+  );
+  writeFileSync(
+    join(nerveRoot, "senses", "counter", "index.js"),
+    withNoopWorkflow ? counterIndexJsWithNoopWorkflow : counterIndexJs,
+    "utf8",
+  );
+  writeFileSync(
+    join(nerveRoot, "workflows", "echo", "dist", "index.js"),
+    echoWorkflowIndexJs,
+    "utf8",
+  );
+  if (withNoopWorkflow) {
+    mkdirSync(join(nerveRoot, "workflows", "noop", "dist"), { recursive: true });
+    mkdirSync(join(nerveRoot, "workflows", "noop", "migrations"), { recursive: true });
+    writeFileSync(
+      join(nerveRoot, "workflows", "noop", "dist", "index.js"),
+      noopWorkflowIndexJs,
+      "utf8",
+    );
+  }
+  linkWorkspaceDaemonIntoNerveRoot(nerveRoot);
+}
+
+export type TestDaemonHandle = {
+  fakeHome: string;
+  nerveRoot: string;
+  socketPath: string;
+  kernel: Kernel;
+};
+
+export type StartTestDaemonOpts = {
+  /**
+   * When true, counter sense's first compute launches a local `noop` workflow (real
+   * workflow-worker child). Requires built `workflow-worker.js` next to `sense-worker.js`.
+   */
+  withNoopWorkflow: boolean;
+} | null;
+
+function useNoopWorkflow(opts: StartTestDaemonOpts): boolean {
+  return opts !== null && opts.withNoopWorkflow === true;
+}
+
+/**
+ * Symlink workspace `@uncaged/nerve-daemon` into `<nerveRoot>/node_modules` so
+ * `loadDaemonModule(nerveRoot)` resolves for `nerve store` / `nerve thread` in e2e.
+ */
+export function linkWorkspaceDaemonIntoNerveRoot(nerveRoot: string): void {
+  const daemonPkgRoot = dirname(require.resolve("@uncaged/nerve-daemon/package.json"));
+  const linkDir = join(nerveRoot, "node_modules", "@uncaged");
+  const linkPath = join(linkDir, "nerve-daemon");
+  mkdirSync(linkDir, { recursive: true });
+  if (existsSync(linkPath)) return;
+  symlinkSync(daemonPkgRoot, linkPath);
+}
+
+/**
+ * Poll until predicate returns true, or reject after `timeoutMs`.
+ * (Same idea as `packages/daemon/src/__tests__/kernel-integration.test.ts`.)
+ */
+export async function pollUntil(
+  predicate: () => boolean,
+  timeoutMs: number,
+  intervalMs = 50,
+): Promise<void> {
+  return new Promise((resolve, reject) => {
+    const timer = setTimeout(
+      () => reject(new Error(`pollUntil timed out after ${String(timeoutMs)}ms`)),
+      timeoutMs,
+    );
+    const check = setInterval(() => {
+      if (predicate()) {
+        clearTimeout(timer);
+        clearInterval(check);
+        resolve();
+      }
+    }, intervalMs);
+  });
+}
+
+/**
+ * Creates `fakeHome`, lays out `fakeHome/.uncaged-nerve` (nerve.yaml + counter sense),
+ * starts a real kernel (sense-worker child + IPC on `nerve.sock`), writes `nerve.pid`
+ * to the current test process so `isRunning()` succeeds under that HOME, and awaits
+ * `kernel.ready`.
+ */
+export async function startTestDaemon(
+  _opts: StartTestDaemonOpts = null,
+): Promise<TestDaemonHandle> {
+  const withNoop = useNoopWorkflow(_opts);
+  if (!existsSync(senseWorkerScript)) {
+    throw new Error(
+      `Missing "${senseWorkerScript}". Run \`pnpm --filter @uncaged/nerve-daemon build\` (cli package "pretest" runs this automatically).`,
+    );
+  }
+  if (!existsSync(workflowWorkerScript)) {
+    throw new Error(
+      `Missing "${workflowWorkerScript}". Run \`pnpm --filter @uncaged/nerve-daemon build\`.`,
+    );
+  }
+
+  const fakeHome = mkdtempSync(join(tmpdir(), "nerve-cli-e2e-"));
+  const nerveRoot = join(fakeHome, ".uncaged-nerve");
+  writeWorkspaceLayout(nerveRoot, withNoop);
+
+  const config = defaultTestConfig(withNoop);
+  const socketPath = join(nerveRoot, "nerve.sock");
+  const kernel = createKernel(config, nerveRoot, {
+    workerScript: senseWorkerScript,
+    ipcSocketPath: socketPath,
+    enableFileWatcher: false,
+  });
+
+  await kernel.ready;
+  writeFileSync(join(nerveRoot, "nerve.pid"), String(process.pid), "utf8");
+
+  return { fakeHome, nerveRoot, socketPath, kernel };
+}
+
+/**
+ * Stops the kernel (workers + IPC) and removes the temp HOME tree.
+ *
+ * @param kernelAlreadyStopped — pass `true` when the test already called `kernel.stop()`
+ *   (e.g. daemon lifecycle e2e); only the temp directory is removed.
+ */
+export async function stopTestDaemon(
+  handle: TestDaemonHandle,
+  kernelAlreadyStopped = false,
+): Promise<void> {
+  if (!kernelAlreadyStopped) {
+    await handle.kernel.stop();
+  }
+  try {
+    rmSync(handle.fakeHome, { recursive: true, force: true });
+  } catch {
+    // best-effort cleanup
+  }
+}
+
+export type CliRunResult = {
+  stdout: string;
+  stderr: string;
+  exitCode: number;
+};
+
+function patchWriteStream(stream: NodeJS.WriteStream, sink: string[]): () => void {
+  const orig = stream.write.bind(stream) as (
+    chunk: string | Uint8Array,
+    encodingOrCb?: BufferEncoding | ((err: Error | null | undefined) => void),
+    cb?: (err: Error | null | undefined) => void,
+  ) => boolean;
+
+  stream.write = ((
+    chunk: string | Uint8Array,
+    encodingOrCb?: BufferEncoding | ((err: Error | null | undefined) => void),
+    cb?: (err: Error | null | undefined) => void,
+  ) => {
+    if (typeof chunk === "string") {
+      sink.push(chunk);
+    } else {
+      sink.push(Buffer.from(chunk).toString("utf8"));
+    }
+    if (typeof encodingOrCb === "function") {
+      encodingOrCb(null);
+      return true;
+    }
+    if (cb !== undefined) {
+      cb(null);
+    }
+    return true;
+  }) as typeof stream.write;
+
+  return () => {
+    stream.write = orig as typeof stream.write;
+  };
+}
+
+/**
+ * Runs `nerve <args>` for the subset wired in `e2eRootCommand` (`sense`, `logs`, `daemon`,
+ * `status`, `stop`, `store`, `workflow`, `thread`), with `process.env.HOME` pointing at `handle.fakeHome`
+ * so `getNerveRoot()` resolves to the test workspace. Captures stdout/stderr; sets `exitCode`
+ * when `process.exit` is invoked or on thrown errors.
+ */
+export async function runCli(handle: TestDaemonHandle, args: string[]): Promise<CliRunResult> {
+  const stdoutChunks: string[] = [];
+  const stderrChunks: string[] = [];
+  const restoreOut = patchWriteStream(process.stdout, stdoutChunks);
+  const restoreErr = patchWriteStream(process.stderr, stderrChunks);
+
+  const prevHome = process.env.HOME;
+  process.env.HOME = handle.fakeHome;
+
+  let exitCode = 0;
+  const origExit = process.exit;
+  process.exit = ((code?: number) => {
+    exitCode = typeof code === "number" ? code : 0;
+    throw new ProcessExitError(exitCode);
+  }) as typeof process.exit;
+
+  try {
+    await runCommand(e2eRootCommand, { rawArgs: args });
+  } catch (e) {
+    if (e instanceof ProcessExitError) {
+      exitCode = e.code;
+    } else {
+      exitCode = 1;
+      stderrChunks.push(e instanceof Error ? e.message : String(e));
+    }
+  } finally {
+    process.exit = origExit;
+    if (prevHome === undefined) {
+      process.env.HOME = undefined;
+    } else {
+      process.env.HOME = prevHome;
+    }
+    restoreOut();
+    restoreErr();
+  }
+
+  return {
+    stdout: stdoutChunks.join(""),
+    stderr: stderrChunks.join(""),
+    exitCode,
+  };
+}
+
+class ProcessExitError extends Error {
+  readonly code: number;
+  constructor(code: number) {
+    super(`process.exit(${String(code)})`);
+    this.name = "ProcessExitError";
+    this.code = code;
+  }
+}

packages/cli/src/__tests__/e2e-logs.test.ts

@@ -0,0 +1,133 @@
+/**
+ * E2E test for `nerve logs` command (#161).
+ *
+ * The logs command reads from a plain text log file at
+ * `<nerveRoot>/logs/nerve.log`. Since the e2e harness starts the kernel
+ * in-process (not as a detached daemon), no log file is created automatically.
+ * We manually write test log content to the expected path.
+ */
+
+import { mkdirSync, writeFileSync } from "node:fs";
+import { join } from "node:path";
+
+import { afterEach, describe, expect, it } from "vitest";
+
+import { type TestDaemonHandle, runCli, startTestDaemon, stopTestDaemon } from "./e2e-harness.js";
+
+/** Generate N log lines for testing. */
+function generateLogLines(count: number): string[] {
+  const lines: string[] = [];
+  for (let i = 1; i <= count; i++) {
+    const ts = new Date(Date.UTC(2025, 0, 1, 0, 0, i)).toISOString();
+    lines.push(`${ts} [INFO] log entry ${i}`);
+  }
+  return lines;
+}
+
+/** Write fake log content to the daemon log path. */
+function writeTestLogFile(nerveRoot: string, lines: string[]): void {
+  const logsDir = join(nerveRoot, "logs");
+  mkdirSync(logsDir, { recursive: true });
+  writeFileSync(join(logsDir, "nerve.log"), `${lines.join("\n")}\n`, "utf8");
+}
+
+describe("e2e logs", () => {
+  let daemon: TestDaemonHandle | null = null;
+
+  afterEach(async () => {
+    const h = daemon;
+    daemon = null;
+    if (h === null) return;
+    await Promise.race([
+      stopTestDaemon(h),
+      new Promise<never>((_, reject) =>
+        setTimeout(() => reject(new Error("stopTestDaemon timed out after 10s")), 10_000),
+      ),
+    ]);
+  });
+
+  it("shows log file not found when no log exists", { timeout: 30_000 }, async () => {
+    daemon = await startTestDaemon();
+
+    // No log file written — command should fail
+    const result = await runCli(daemon, ["logs"]);
+    expect(result.exitCode).toBe(1);
+    expect(result.stderr).toContain("Log file not found");
+  });
+
+  it("displays last N lines (tail mode)", { timeout: 30_000 }, async () => {
+    daemon = await startTestDaemon();
+
+    const lines = generateLogLines(10);
+    writeTestLogFile(daemon.nerveRoot, lines);
+
+    // Default: last 50 lines, but we only have 10
+    const result = await runCli(daemon, ["logs"]);
+    expect(result.exitCode).toBe(0);
+    expect(result.stdout).toContain("log entry 1");
+    expect(result.stdout).toContain("log entry 10");
+    expect(result.stdout).toContain("lines 1-10 of 10");
+  });
+
+  it("respects -n flag to limit lines", { timeout: 30_000 }, async () => {
+    daemon = await startTestDaemon();
+
+    const lines = generateLogLines(20);
+    writeTestLogFile(daemon.nerveRoot, lines);
+
+    // Request only last 5 lines
+    const result = await runCli(daemon, ["logs", "-n", "5"]);
+    expect(result.exitCode).toBe(0);
+
+    // Should show lines 16-20 (last 5)
+    expect(result.stdout).toContain("log entry 16");
+    expect(result.stdout).toContain("log entry 20");
+    expect(result.stdout).toContain("lines 16-20 of 20");
+
+    // Should NOT contain earlier lines
+    expect(result.stdout).not.toContain("log entry 1\n");
+    expect(result.stdout).not.toContain("log entry 15\n");
+  });
+
+  it("supports --offset for pagination", { timeout: 30_000 }, async () => {
+    daemon = await startTestDaemon();
+
+    const lines = generateLogLines(20);
+    writeTestLogFile(daemon.nerveRoot, lines);
+
+    // Offset 5 means start at line 5, show default 50 (will get 5-20)
+    const result = await runCli(daemon, ["logs", "--offset", "5", "-n", "5"]);
+    expect(result.exitCode).toBe(0);
+
+    // Should show lines 5-9
+    expect(result.stdout).toContain("log entry 5");
+    expect(result.stdout).toContain("log entry 9");
+    expect(result.stdout).toContain("lines 5-9 of 20");
+  });
+
+  it("shows pagination hint when earlier lines exist", { timeout: 30_000 }, async () => {
+    daemon = await startTestDaemon();
+
+    const lines = generateLogLines(100);
+    writeTestLogFile(daemon.nerveRoot, lines);
+
+    // Request last 10 lines — there should be a "previous page" hint
+    const result = await runCli(daemon, ["logs", "-n", "10"]);
+    expect(result.exitCode).toBe(0);
+    expect(result.stdout).toContain("Earlier lines available");
+    expect(result.stdout).toContain("nerve logs --offset");
+  });
+
+  it("shows empty message for empty log file", { timeout: 30_000 }, async () => {
+    daemon = await startTestDaemon();
+
+    // Write an empty log file
+    const logsDir = join(daemon.nerveRoot, "logs");
+    mkdirSync(logsDir, { recursive: true });
+    writeFileSync(join(logsDir, "nerve.log"), "", "utf8");
+
+    const result = await runCli(daemon, ["logs"]);
+    expect(result.exitCode).toBe(0);
+    expect(result.stdout).toContain("Log file is empty");
+  });
+});

packages/cli/src/__tests__/e2e-sense-query.test.ts

@@ -0,0 +1,121 @@
+/**
+ * E2E: `nerve sense query` against a real daemon + persisted `_signals` (issue #156).
+ */
+
+import { existsSync } from "node:fs";
+import { join } from "node:path";
+import { DatabaseSync } from "node:sqlite";
+
+import { afterEach, describe, expect, it } from "vitest";
+
+import {
+  type TestDaemonHandle,
+  pollUntil,
+  runCli,
+  startTestDaemon,
+  stopTestDaemon,
+} from "./e2e-harness.js";
+
+describe("e2e sense query", () => {
+  let daemon: TestDaemonHandle | null = null;
+
+  afterEach(async () => {
+    const h = daemon;
+    daemon = null;
+    if (h === null) return;
+    await Promise.race([
+      stopTestDaemon(h),
+      new Promise<never>((_, reject) =>
+        setTimeout(() => reject(new Error("stopTestDaemon timed out after 10s")), 10_000),
+      ),
+    ]);
+  });
+
+  async function waitForSignalsPersisted(handle: TestDaemonHandle): Promise<void> {
+    const dbPath = join(handle.nerveRoot, "data", "senses", "counter.db");
+    await pollUntil(() => {
+      if (!existsSync(dbPath)) return false;
+      try {
+        const db = new DatabaseSync(dbPath, { readOnly: true });
+        const row = db.prepare("SELECT COUNT(*) as cnt FROM _signals").get() as
+          | { cnt: number }
+          | undefined;
+        db.close();
+        return row !== undefined && row.cnt > 0;
+      } catch {
+        return false;
+      }
+    }, 10_000);
+  }
+
+  /** Start daemon, trigger counter, wait until `_signals` has a row. */
+  async function startDaemonWithPersistedSignal(): Promise<TestDaemonHandle> {
+    const handle = await startTestDaemon();
+    const triggerResult = await runCli(handle, ["sense", "trigger", "counter"]);
+    expect(triggerResult.exitCode).toBe(0);
+    expect(triggerResult.stdout).toContain("Triggered");
+    await waitForSignalsPersisted(handle);
+    return handle;
+  }
+
+  it(
+    "after trigger, persisted _signals and sense query counter returns at least one row",
+    { timeout: 30_000 },
+    async () => {
+      daemon = await startDaemonWithPersistedSignal();
+
+      const queryResult = await runCli(daemon, ["sense", "query", "counter"]);
+      expect(queryResult.exitCode).toBe(0);
+      expect(queryResult.stdout).not.toContain("(0 rows)");
+    },
+  );
+
+  it(
+    "default sense query output lists payload column and counter count in payload",
+    { timeout: 30_000 },
+    async () => {
+      daemon = await startDaemonWithPersistedSignal();
+
+      const queryResult = await runCli(daemon, ["sense", "query", "counter"]);
+      expect(queryResult.exitCode).toBe(0);
+      expect(queryResult.stdout).toContain("payload");
+      expect(queryResult.stdout).toMatch(/count/);
+    },
+  );
+
+  it(
+    "nerve sense query counter --json prints a JSON array with payload on each row",
+    { timeout: 30_000 },
+    async () => {
+      daemon = await startDaemonWithPersistedSignal();
+
+      const jsonResult = await runCli(daemon, ["sense", "query", "counter", "--json"]);
+      expect(jsonResult.exitCode).toBe(0);
+      const rows = JSON.parse(jsonResult.stdout.trim()) as unknown;
+      expect(Array.isArray(rows)).toBe(true);
+      expect(rows.length).toBeGreaterThanOrEqual(1);
+      for (const row of rows as Record<string, unknown>[]) {
+        expect(Object.keys(row)).toContain("payload");
+      }
+    },
+  );
+
+  it(
+    "nerve sense query counter --sql runs custom read-only SQL and prints total column",
+    { timeout: 30_000 },
+    async () => {
+      daemon = await startDaemonWithPersistedSignal();
+
+      const sqlResult = await runCli(daemon, [
+        "sense",
+        "query",
+        "counter",
+        "--sql",
+        "SELECT count(*) as total FROM _signals",
+      ]);
+      expect(sqlResult.exitCode).toBe(0);
+      expect(sqlResult.stdout).toContain("total");
+      expect(sqlResult.stdout).not.toContain("(0 rows)");
+    },
+  );
+});

packages/cli/src/__tests__/e2e-smoke.test.ts

@@ -0,0 +1,73 @@
+/**
+ * Smoke test: start a real daemon with a counter sense, trigger it,
+ * then verify CLI commands can list and query the persisted signal.
+ */
+
+import { afterEach, describe, expect, it } from "vitest";
+
+import {
+  type TestDaemonHandle,
+  pollUntil,
+  runCli,
+  startTestDaemon,
+  stopTestDaemon,
+} from "./e2e-harness.js";
+
+describe("e2e smoke", () => {
+  let daemon: TestDaemonHandle | null = null;
+
+  afterEach(async () => {
+    const h = daemon;
+    daemon = null;
+    if (h === null) return;
+    await Promise.race([
+      stopTestDaemon(h),
+      new Promise<never>((_, reject) =>
+        setTimeout(() => reject(new Error("stopTestDaemon timed out after 10s")), 10_000),
+      ),
+    ]);
+  });
+
+  it("sense list + sense query after trigger", { timeout: 30_000 }, async () => {
+    daemon = await startTestDaemon();
+
+    // Trigger counter sense via IPC
+    const triggerResult = await runCli(daemon, ["sense", "trigger", "counter"]);
+    expect(triggerResult.exitCode).toBe(0);
+    expect(triggerResult.stdout).toContain("Triggered");
+
+    // Wait for signal to be persisted (_signals table in the sense DB)
+    const { existsSync } = await import("node:fs");
+    const { join } = await import("node:path");
+    const { DatabaseSync } = await import("node:sqlite");
+
+    const dbPath = join(daemon.nerveRoot, "data", "senses", "counter.db");
+    await pollUntil(() => {
+      if (!existsSync(dbPath)) return false;
+      try {
+        const db = new DatabaseSync(dbPath, { readOnly: true });
+        const row = db.prepare("SELECT COUNT(*) as cnt FROM _signals").get() as
+          | { cnt: number }
+          | undefined;
+        db.close();
+        return row !== undefined && row.cnt > 0;
+      } catch {
+        return false;
+      }
+    }, 10_000);
+
+    // nerve sense list — should show counter with a last signal timestamp
+    const listResult = await runCli(daemon, ["sense", "list"]);
+    expect(listResult.exitCode).toBe(0);
+    expect(listResult.stdout).toContain("counter");
+    expect(listResult.stdout).toContain("last signal:");
+    // Should NOT say "(never)" since we triggered and persisted
+    expect(listResult.stdout).not.toContain("(never)");
+
+    // nerve sense query counter — should return rows from _signals
+    const queryResult = await runCli(daemon, ["sense", "query", "counter"]);
+    expect(queryResult.exitCode).toBe(0);
+    // Should have actual data rows (not "(0 rows)")
+    expect(queryResult.stdout).not.toContain("(0 rows)");
+  });
+});

packages/cli/src/__tests__/e2e-store-archive.test.ts

@@ -0,0 +1,132 @@
+/**
+ * E2E: `nerve store archive` against a real daemon + logs.db (issue #163).
+ *
+ * Archive eligibility is by `logs.timestamp` (ms; there is no `created_at` column);
+ * RFC-001 §5.4 cold-archive uses UTC days.
+ */
+
+import { existsSync, readFileSync, readdirSync } from "node:fs";
+import { join } from "node:path";
+import { DatabaseSync } from "node:sqlite";
+
+import { afterEach, describe, expect, it } from "vitest";
+
+import {
+  type TestDaemonHandle,
+  linkWorkspaceDaemonIntoNerveRoot,
+  pollUntil,
+  runCli,
+  startTestDaemon,
+  stopTestDaemon,
+} from "./e2e-harness.js";
+
+/** Wall time safely outside the 30-day hot window (RFC-001 archive). */
+const ARCHIVED_TEST_TS = Date.UTC(2020, 5, 15, 12, 0, 0);
+const EXPECTED_ARCHIVE_DAY = "2020-06-15";
+
+describe("e2e store archive", () => {
+  let daemon: TestDaemonHandle | null = null;
+
+  afterEach(async () => {
+    const h = daemon;
+    daemon = null;
+    if (h === null) return;
+    await Promise.race([
+      stopTestDaemon(h),
+      new Promise<never>((_, reject) =>
+        setTimeout(() => reject(new Error("stopTestDaemon timed out after 10s")), 10_000),
+      ),
+    ]);
+  });
+
+  it(
+    "archives old workflow logs to JSONL, removes rows from logs, thread list still reads workflow_runs",
+    { timeout: 60_000 },
+    async () => {
+      daemon = await startTestDaemon({ withNoopWorkflow: true });
+      linkWorkspaceDaemonIntoNerveRoot(daemon.nerveRoot);
+
+      const triggerResult = await runCli(daemon, ["sense", "trigger", "counter"]);
+      expect(triggerResult.exitCode).toBe(0);
+
+      const logsDb = join(daemon.nerveRoot, "data", "logs.db");
+      await pollUntil(() => {
+        if (!existsSync(logsDb)) return false;
+        try {
+          const db = new DatabaseSync(logsDb, { readOnly: true });
+          const row = db
+            .prepare(
+              "SELECT COUNT(*) AS c FROM logs WHERE source = 'workflow' AND type = 'completed'",
+            )
+            .get() as { c: number } | undefined;
+          db.close();
+          return (row?.c ?? 0) > 0;
+        } catch {
+          return false;
+        }
+      }, 20_000);
+
+      const dbMut = new DatabaseSync(logsDb);
+      dbMut.exec(`UPDATE logs SET timestamp = ${String(ARCHIVED_TEST_TS)} WHERE 1=1`);
+      dbMut.close();
+
+      const archiveResult = await runCli(daemon, ["store", "archive"]);
+      expect(archiveResult.exitCode).toBe(0);
+      expect(archiveResult.stdout).toContain("✅ Archived");
+      expect(archiveResult.stdout).toContain("rows=");
+      expect(archiveResult.stdout).toContain(EXPECTED_ARCHIVE_DAY);
+
+      const dbAfter = new DatabaseSync(logsDb, { readOnly: true });
+      const logCountRow = dbAfter.prepare("SELECT COUNT(*) AS c FROM logs").get() as { c: number };
+      dbAfter.close();
+      expect(logCountRow.c).toBe(0);
+
+      const archiveDir = join(daemon.nerveRoot, "data", "archive", "logs");
+      expect(existsSync(archiveDir)).toBe(true);
+      const names = readdirSync(archiveDir);
+      expect(names.some((n) => n === `${EXPECTED_ARCHIVE_DAY}.jsonl`)).toBe(true);
+      const jsonlPath = join(archiveDir, `${EXPECTED_ARCHIVE_DAY}.jsonl`);
+      const jsonl = readFileSync(jsonlPath, "utf8");
+      expect(jsonl.length).toBeGreaterThan(0);
+      expect(jsonl).toContain('"source":"workflow"');
+
+      const listResult = await runCli(daemon, ["thread", "list", "--all"]);
+      expect(listResult.exitCode).toBe(0);
+      // workflow_runs is not pruned by archive — list may still show completed runs; hot logs are empty.
+      expect(listResult.stdout).toContain("noop");
+    },
+  );
+
+  it("store archive --vacuum completes VACUUM after archiving", { timeout: 60_000 }, async () => {
+    daemon = await startTestDaemon({ withNoopWorkflow: true });
+    linkWorkspaceDaemonIntoNerveRoot(daemon.nerveRoot);
+
+    const triggerResult = await runCli(daemon, ["sense", "trigger", "counter"]);
+    expect(triggerResult.exitCode).toBe(0);
+
+    const logsDb = join(daemon.nerveRoot, "data", "logs.db");
+    await pollUntil(() => {
+      if (!existsSync(logsDb)) return false;
+      try {
+        const db = new DatabaseSync(logsDb, { readOnly: true });
+        const row = db
+          .prepare(
+            "SELECT COUNT(*) AS c FROM logs WHERE source = 'workflow' AND type = 'completed'",
+          )
+          .get() as { c: number } | undefined;
+        db.close();
+        return (row?.c ?? 0) > 0;
+      } catch {
+        return false;
+      }
+    }, 20_000);
+
+    const dbMut = new DatabaseSync(logsDb);
+    dbMut.exec(`UPDATE logs SET timestamp = ${String(ARCHIVED_TEST_TS)} WHERE 1=1`);
+    dbMut.close();
+
+    const archiveVac = await runCli(daemon, ["store", "archive", "--vacuum"]);
+    expect(archiveVac.exitCode).toBe(0);
+    expect(archiveVac.stdout).toContain("VACUUM completed.");
+  });
+});

packages/cli/src/__tests__/e2e-validate-init.test.ts

@@ -0,0 +1,253 @@
+/**
+ * E2E tests for `nerve validate` and `nerve init` commands (#162).
+ * No running daemon needed — just temp dirs with HOME manipulation.
+ */
+
+import { existsSync, mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { defineCommand, runCommand } from "citty";
+import { afterEach, describe, expect, it } from "vitest";
+
+import { initCommand } from "../commands/init.js";
+import { validateCommand } from "../commands/validate.js";
+
+const testRootCommand = defineCommand({
+  meta: { name: "nerve", description: "e2e-validate-init" },
+  subCommands: {
+    validate: validateCommand,
+    init: initCommand,
+  },
+});
+
+type CliRunResult = {
+  stdout: string;
+  stderr: string;
+  exitCode: number;
+};
+
+class ProcessExitError extends Error {
+  readonly code: number;
+  constructor(code: number) {
+    super(`process.exit(${String(code)})`);
+    this.name = "ProcessExitError";
+    this.code = code;
+  }
+}
+
+function patchWriteStream(stream: NodeJS.WriteStream, sink: string[]): () => void {
+  const orig = stream.write.bind(stream) as (
+    chunk: string | Uint8Array,
+    encodingOrCb?: BufferEncoding | ((err: Error | null | undefined) => void),
+    cb?: (err: Error | null | undefined) => void,
+  ) => boolean;
+
+  stream.write = ((
+    chunk: string | Uint8Array,
+    encodingOrCb?: BufferEncoding | ((err: Error | null | undefined) => void),
+    cb?: (err: Error | null | undefined) => void,
+  ) => {
+    if (typeof chunk === "string") {
+      sink.push(chunk);
+    } else {
+      sink.push(Buffer.from(chunk).toString("utf8"));
+    }
+    if (typeof encodingOrCb === "function") {
+      encodingOrCb(null);
+      return true;
+    }
+    if (cb !== undefined) {
+      cb(null);
+    }
+    return true;
+  }) as typeof stream.write;
+
+  return () => {
+    stream.write = orig as typeof stream.write;
+  };
+}
+
+async function runTestCli(fakeHome: string, args: string[]): Promise<CliRunResult> {
+  const stdoutChunks: string[] = [];
+  const stderrChunks: string[] = [];
+  const restoreOut = patchWriteStream(process.stdout, stdoutChunks);
+  const restoreErr = patchWriteStream(process.stderr, stderrChunks);
+
+  const prevHome = process.env.HOME;
+  process.env.HOME = fakeHome;
+
+  let exitCode = 0;
+  const origExit = process.exit;
+  process.exit = ((code?: number) => {
+    exitCode = typeof code === "number" ? code : 0;
+    throw new ProcessExitError(exitCode);
+  }) as typeof process.exit;
+
+  try {
+    await runCommand(testRootCommand, { rawArgs: args });
+  } catch (e) {
+    if (e instanceof ProcessExitError) {
+      exitCode = e.code;
+    } else {
+      exitCode = 1;
+      stderrChunks.push(e instanceof Error ? e.message : String(e));
+    }
+  } finally {
+    process.exit = origExit;
+    if (prevHome === undefined) {
+      // biome-ignore lint/performance/noDelete: semantically correct for env cleanup
+      delete process.env.HOME;
+    } else {
+      process.env.HOME = prevHome;
+    }
+    restoreOut();
+    restoreErr();
+  }
+
+  return {
+    stdout: stdoutChunks.join(""),
+    stderr: stderrChunks.join(""),
+    exitCode,
+  };
+}
+
+const VALID_NERVE_YAML = `senses:
+  counter:
+    group: e2e
+
+workflows: {}
+
+max_rounds: 10
+
+api:
+  port: null
+  token: null
+  host: 127.0.0.1
+`;
+
+describe("e2e validate", () => {
+  let fakeHome: string | null = null;
+
+  afterEach(() => {
+    if (fakeHome !== null) {
+      rmSync(fakeHome, { recursive: true, force: true });
+      fakeHome = null;
+    }
+  });
+
+  it("exits 0 for valid nerve.yaml", { timeout: 10_000 }, async () => {
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-validate-e2e-"));
+    const nerveRoot = join(fakeHome, ".uncaged-nerve");
+    mkdirSync(nerveRoot, { recursive: true });
+    writeFileSync(join(nerveRoot, "nerve.yaml"), VALID_NERVE_YAML, "utf8");
+
+    const result = await runTestCli(fakeHome, ["validate"]);
+    expect(result.exitCode).toBe(0);
+    expect(result.stdout).toContain("✅");
+    expect(result.stdout).toContain("valid");
+  });
+
+  it("exits 1 for invalid nerve.yaml", { timeout: 10_000 }, async () => {
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-validate-e2e-"));
+    const nerveRoot = join(fakeHome, ".uncaged-nerve");
+    mkdirSync(nerveRoot, { recursive: true });
+    writeFileSync(join(nerveRoot, "nerve.yaml"), "not: valid: yaml: {{{\n", "utf8");
+
+    const result = await runTestCli(fakeHome, ["validate"]);
+    expect(result.exitCode).toBe(1);
+    expect(result.stderr).toBeTruthy();
+  });
+
+  it("exits 1 for malformed config (missing required fields)", { timeout: 10_000 }, async () => {
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-validate-e2e-"));
+    const nerveRoot = join(fakeHome, ".uncaged-nerve");
+    mkdirSync(nerveRoot, { recursive: true });
+    writeFileSync(join(nerveRoot, "nerve.yaml"), "foo: bar\n", "utf8");
+
+    const result = await runTestCli(fakeHome, ["validate"]);
+    expect(result.exitCode).toBe(1);
+    expect(result.stderr).toContain("❌");
+  });
+
+  it("exits 1 when nerve.yaml is missing", { timeout: 10_000 }, async () => {
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-validate-e2e-"));
+    // Don't create .uncaged-nerve at all
+
+    const result = await runTestCli(fakeHome, ["validate"]);
+    expect(result.exitCode).toBe(1);
+    expect(result.stderr).toBeTruthy();
+  });
+});
+
+describe("e2e init", () => {
+  let fakeHome: string | null = null;
+
+  afterEach(() => {
+    if (fakeHome !== null) {
+      rmSync(fakeHome, { recursive: true, force: true });
+      fakeHome = null;
+    }
+  });
+
+  it("init --force creates workspace layout", { timeout: 10_000 }, async () => {
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-init-e2e-"));
+    const nerveRoot = join(fakeHome, ".uncaged-nerve");
+
+    const result = await runTestCli(fakeHome, ["init", "--force", "--skip-install"]);
+    // init should exit 0 (install/git failures are warnings, not fatal)
+    expect(result.exitCode).toBe(0);
+    expect(result.stdout).toContain("✅");
+
+    // Verify key files exist
+    expect(existsSync(join(nerveRoot, "nerve.yaml"))).toBe(true);
+    expect(existsSync(join(nerveRoot, "package.json"))).toBe(true);
+    expect(existsSync(join(nerveRoot, "pnpm-workspace.yaml"))).toBe(true);
+    expect(existsSync(join(nerveRoot, "biome.json"))).toBe(true);
+    expect(existsSync(join(nerveRoot, ".gitignore"))).toBe(true);
+    expect(existsSync(join(nerveRoot, "senses", "cpu-usage", "package.json"))).toBe(true);
+    expect(existsSync(join(nerveRoot, "senses", "cpu-usage", "src", "index.ts"))).toBe(true);
+    expect(existsSync(join(nerveRoot, "senses", "cpu-usage", "src", "schema.ts"))).toBe(true);
+    expect(existsSync(join(nerveRoot, "senses", "cpu-usage", "migrations", "0001_init.sql"))).toBe(
+      true,
+    );
+    expect(existsSync(join(nerveRoot, ".cursor", "rules", "nerve-skills.mdc"))).toBe(true);
+
+    const pkgJson = readFileSync(join(nerveRoot, "package.json"), "utf8");
+    expect(pkgJson).toContain('"@uncaged/nerve-skills": "latest"');
+    expect(pkgJson).toContain('"build": "pnpm -r build"');
+
+    const workspaceYaml = readFileSync(join(nerveRoot, "pnpm-workspace.yaml"), "utf8");
+    expect(workspaceYaml).toContain("workflows/*");
+    expect(workspaceYaml).toContain("senses/*");
+
+    const sensePkgJson = readFileSync(
+      join(nerveRoot, "senses", "cpu-usage", "package.json"),
+      "utf8",
+    );
+    expect(sensePkgJson).toContain("nerve-sense-cpu-usage");
+    expect(sensePkgJson).toContain("esbuild");
+  });
+
+  it("generated nerve.yaml passes validate", { timeout: 10_000 }, async () => {
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-init-e2e-"));
+
+    await runTestCli(fakeHome, ["init", "--force", "--skip-install"]);
+
+    const validateResult = await runTestCli(fakeHome, ["validate"]);
+    expect(validateResult.exitCode).toBe(0);
+    expect(validateResult.stdout).toContain("✅");
+    expect(validateResult.stdout).toContain("valid");
+  });
+
+  it("init without --force on existing dir exits 1", { timeout: 10_000 }, async () => {
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-init-e2e-"));
+    const nerveRoot = join(fakeHome, ".uncaged-nerve");
+    mkdirSync(nerveRoot, { recursive: true });
+    writeFileSync(join(nerveRoot, "marker"), "exists", "utf8");
+
+    const result = await runTestCli(fakeHome, ["init"]);
+    expect(result.exitCode).toBe(1);
+    expect(result.stderr).toContain("already exists");
+  });
+});

packages/cli/src/__tests__/e2e-workflow.test.ts

@@ -0,0 +1,122 @@
+/**
+ * E2E (issue #160): real kernel + workflow worker + IPC, then CLI `workflow` / `thread`
+ * against logs.db. Run listings live on `nerve thread list` (there is no `nerve workflow runs` subcommand).
+ */
+
+import { join } from "node:path";
+
+import { createLogStore } from "@uncaged/nerve-store";
+import { afterEach, describe, expect, it } from "vitest";
+
+import { type TestDaemonHandle, runCli, startTestDaemon, stopTestDaemon } from "./e2e-harness.js";
+
+async function waitForCompletedEchoRuns(
+  logsDbPath: string,
+  minCount: number,
+  timeoutMs: number,
+): Promise<void> {
+  const deadline = Date.now() + timeoutMs;
+  while (Date.now() < deadline) {
+    const store = createLogStore(logsDbPath);
+    try {
+      const done = store.getAllWorkflowRuns("echo").filter((r) => r.status === "completed");
+      if (done.length >= minCount) return;
+    } finally {
+      store.close();
+    }
+    await new Promise((r) => setTimeout(r, 40));
+  }
+  throw new Error(
+    `Timed out after ${String(timeoutMs)}ms waiting for ${String(minCount)} completed echo run(s)`,
+  );
+}
+
+describe("e2e workflow CLI (real daemon)", () => {
+  let daemon: TestDaemonHandle | null = null;
+
+  afterEach(async () => {
+    const h = daemon;
+    daemon = null;
+    if (h === null) return;
+    await Promise.race([
+      stopTestDaemon(h),
+      new Promise<never>((_, reject) =>
+        setTimeout(() => reject(new Error("stopTestDaemon timed out after 10s")), 10_000),
+      ),
+    ]);
+  });
+
+  it(
+    "trigger, thread list / --all, inspect, show (echo workflow)",
+    { timeout: 30_000 },
+    async () => {
+      daemon = await startTestDaemon();
+      const logsDb = join(daemon.nerveRoot, "data", "logs.db");
+
+      const t1 = await runCli(daemon, [
+        "workflow",
+        "trigger",
+        "echo",
+        "--prompt",
+        "alpha-e2e",
+        "--max-rounds",
+        "10",
+      ]);
+      expect(t1.exitCode).toBe(0);
+      expect(t1.stdout).toContain("Triggered");
+
+      const t2 = await runCli(daemon, [
+        "workflow",
+        "trigger",
+        "echo",
+        "--prompt",
+        "beta-e2e",
+        "--max-rounds",
+        "10",
+      ]);
+      expect(t2.exitCode).toBe(0);
+
+      const activeRightAfter = await runCli(daemon, ["thread", "list"]);
+      expect(activeRightAfter.exitCode).toBe(0);
+      expect(activeRightAfter.stdout).toContain("echo");
+      expect(activeRightAfter.stdout).toMatch(/queued|started/);
+
+      await waitForCompletedEchoRuns(logsDb, 2, 25_000);
+
+      const store = createLogStore(logsDb);
+      let runId: string;
+      try {
+        const completed = store
+          .getAllWorkflowRuns("echo")
+          .filter((r) => r.status === "completed")
+          .sort((a, b) => a.timestamp - b.timestamp);
+        expect(completed.length).toBeGreaterThanOrEqual(2);
+        runId = completed[0]?.runId ?? "";
+        expect(runId.length).toBeGreaterThan(0);
+      } finally {
+        store.close();
+      }
+
+      const listAll = await runCli(daemon, ["thread", "list", "--all"]);
+      expect(listAll.exitCode).toBe(0);
+      expect(listAll.stdout).toContain(runId);
+      expect(listAll.stdout).toContain("✅");
+      expect(listAll.stdout).toContain("workflow=echo");
+
+      const listDefault = await runCli(daemon, ["thread", "list"]);
+      expect(listDefault.exitCode).toBe(0);
+      expect(listDefault.stdout).toMatch(/No active workflow runs|📭 No active/);
+
+      const inspect = await runCli(daemon, ["thread", "inspect", runId, "--limit", "50"]);
+      expect(inspect.exitCode).toBe(0);
+      expect(inspect.stdout).toContain(`Workflow run: ${runId}`);
+      expect(inspect.stdout).toContain("type=started");
+      expect(inspect.stdout).toContain("type=completed");
+
+      const show = await runCli(daemon, ["thread", "show", runId, "--budget", "50000"]);
+      expect(show.exitCode).toBe(0);
+      expect(show.stdout).toContain("echo:alpha-e2e");
+      expect(show.stdout).toContain("[#1 echo]");
+    },
+  );
+});

packages/cli/src/__tests__/e2e/daemon.md

@@ -0,0 +1,32 @@
+# nerve daemon — E2E Scenarios
+
+## daemon start
+
+- ✅ starts daemon, writes PID file, kernel comes up (via lifecycle test)
+- 🔲 start when already running — error or no-op
+- 🔲 start with `--foreground` flag
+
+## daemon stop
+
+- ✅ stops daemon, clears PID file (via lifecycle test)
+- 🔲 stop when not running — graceful message
+
+## daemon status
+
+- ✅ reports "running" when daemon is up, "not running" when stopped (via lifecycle test)
+- 🔲 `--json` output
+
+## daemon restart
+
+- 🔲 restarts daemon — stop + start round-trip
+- 🔲 restart when not running — starts fresh
+
+## daemon logs (nerve logs)
+
+- ✅ shows "log file not found" when no log exists
+- ✅ displays last N lines (tail mode)
+- ✅ respects `-n` flag to limit lines
+- ✅ supports `--offset` for pagination
+- ✅ shows pagination hint when earlier lines exist
+- ✅ shows empty message for empty log file
+- 🔲 `--follow` / `-f` streams new lines

packages/cli/src/__tests__/e2e/dev.md

@@ -0,0 +1,5 @@
+# nerve dev — E2E Scenarios
+
+- 🔲 runs foreground kernel session with hot-reload
+- 🔲 exits cleanly on Ctrl+C / SIGINT
+- 🔲 detects sense file changes and reloads

packages/cli/src/__tests__/e2e/init.md

@@ -0,0 +1,14 @@
+# nerve init — E2E Scenarios
+
+## init (workspace)
+
+- ✅ `--force` creates workspace layout (nerve.yaml, senses/, workflows/)
+- ✅ generated nerve.yaml passes validate
+- ✅ init without `--force` on existing dir exits 1
+- 🔲 init in empty dir without `--force` — succeeds
+- 🔲 `--from <git-url>` clones and sets up workspace
+
+## create workflow / create sense
+
+- 🔲 `nerve create workflow <name>` scaffolds under workflows/
+- 🔲 `nerve create sense <name>` scaffolds under senses/

packages/cli/src/__tests__/e2e/remote.md

@@ -0,0 +1,36 @@
+# nerve remote — E2E Scenarios
+
+## remote add
+
+- 🔲 adds a named remote, persists to config
+- 🔲 duplicate name — error message
+
+## remote list
+
+- 🔲 lists all remotes with name and host
+- 🔲 empty state — no remotes
+
+## remote show
+
+- 🔲 shows remote details (host, token masked)
+- 🔲 non-existent remote — error message
+
+## remote set-url
+
+- 🔲 updates remote host
+- 🔲 non-existent remote — error message
+
+## remote set-token
+
+- 🔲 updates remote token
+- 🔲 non-existent remote — error message
+
+## remote remove
+
+- 🔲 removes a remote
+- 🔲 non-existent remote — error message
+
+## remote default
+
+- 🔲 set default remote
+- 🔲 show current default

packages/cli/src/__tests__/e2e/sense.md

@@ -0,0 +1,29 @@
+# nerve sense — E2E Scenarios
+
+## sense list
+
+- ✅ prints sense list with name, group, throttle, triggers, and last signal time
+- 🔲 empty state — no senses registered, prints empty message
+- 🔲 `--json` — outputs valid JSON array
+
+## sense trigger
+
+- ✅ trigger known sense exits 0, stdout contains "Triggered"
+- ✅ trigger non-existent sense writes error to stderr and exits 1
+- ✅ sends correct IPC message `{ type: trigger-sense, sense: <name> }` to daemon
+
+## sense query
+
+- ✅ after trigger, persisted `_signals` table has at least one row
+- ✅ default output lists payload column and counter count
+- ✅ `--json` prints valid JSON array with payload on each row
+- ✅ `--sql` runs custom read-only SQL and prints result
+- 🔲 query non-existent sense — error message
+- 🔲 `--limit` / `--offset` pagination
+
+## sense schema
+
+- ✅ prints CREATE TABLE statements for the sense database
+- ✅ includes `_signals` table in output
+- ✅ `--json` prints valid JSON array of SQL strings
+- 🔲 schema for non-existent sense — error message

packages/cli/src/__tests__/e2e/smoke.md

@@ -0,0 +1,6 @@
+# nerve smoke — E2E Scenarios
+
+Full round-trip integration tests that exercise multiple subcommands together.
+
+- ✅ sense list + sense query after trigger — registers sense, triggers, verifies persisted signal and query output
+- 🔲 init → dev → trigger workflow → thread inspect round-trip

packages/cli/src/__tests__/e2e/store.md

@@ -0,0 +1,8 @@
+# nerve store — E2E Scenarios
+
+## store archive
+
+- ✅ archives old workflow logs to JSONL, removes rows from logs DB, thread list still reads workflow_runs
+- ✅ `--vacuum` completes VACUUM after archiving
+- 🔲 archive with no old data — exits cleanly with "nothing to archive"
+- 🔲 archive with custom `--before` date filter

packages/cli/src/__tests__/e2e/thread.md

@@ -0,0 +1,24 @@
+# nerve thread — E2E Scenarios
+
+## thread list
+
+- ✅ `--all` completes without throwing
+- 🔲 lists active threads with run ID, workflow name, status
+- 🔲 empty state — no threads
+
+## thread inspect
+
+- ✅ inspect `<runId>` completes without throwing
+- 🔲 inspect non-existent runId — error message
+- 🔲 output contains workflow name, roles, round count
+
+## thread show
+
+- ✅ show `<runId>` completes without throwing (role rounds path)
+- 🔲 show non-existent runId — error message
+- 🔲 output contains conversation messages
+
+## thread kill
+
+- 🔲 kill active thread — exits 0, thread stops
+- 🔲 kill non-existent thread — error message

packages/cli/src/__tests__/e2e/validate.md

@@ -0,0 +1,7 @@
+# nerve validate — E2E Scenarios
+
+- ✅ exits 0 for valid nerve.yaml
+- ✅ exits 1 for invalid nerve.yaml
+- ✅ exits 1 for malformed config (missing required fields)
+- ✅ exits 1 when nerve.yaml is missing
+- 🔲 `--json` outputs structured validation errors

packages/cli/src/__tests__/e2e/workflow.md

@@ -0,0 +1,17 @@
+# nerve workflow — E2E Scenarios
+
+## workflow list
+
+- 🔲 lists registered workflows with name and status
+- 🔲 empty state — no workflows registered
+
+## workflow status
+
+- 🔲 shows status of a specific workflow
+- 🔲 non-existent workflow — error message
+
+## workflow trigger
+
+- ✅ trigger + thread list/inspect/show round-trip (echo workflow)
+- 🔲 trigger non-existent workflow — error message
+- 🔲 trigger with `--input` JSON payload

packages/cli/src/__tests__/glob-files.test.ts

@@ -0,0 +1,24 @@
+import { mkdirSync, mkdtempSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { describe, expect, it } from "vitest";
+
+import { listKnowledgeFiles } from "../knowledge/glob-files.js";
+
+describe("listKnowledgeFiles", () => {
+  it("includes matching paths and applies exclude globs", () => {
+    const root = mkdtempSync(join(tmpdir(), "nerve-glob-"));
+    mkdirSync(join(root, "src"), { recursive: true });
+    writeFileSync(join(root, "src", "keep.ts"), "export function x() {}\n");
+    writeFileSync(join(root, "src", "drop.test.ts"), "// test\n");
+
+    const files = listKnowledgeFiles(root, {
+      include: ["src/**/*.ts"],
+      exclude: ["**/*.test.ts"],
+    });
+
+    expect(files).toContain("src/keep.ts");
+    expect(files).not.toContain("src/drop.test.ts");
+  });
+});

packages/cli/src/__tests__/init-workflow.test.ts

@@ -1,81 +0,0 @@
-/**
- * Tests for nerve init workflow scaffold logic.
- *
- * We test the file-generation path by isolating the template rendering,
- * not by invoking the full citty command (which calls process.exit).
- */
-
-import { mkdtempSync, readFileSync, rmSync } from "node:fs";
-import { tmpdir } from "node:os";
-import { join } from "node:path";
-import { afterEach, beforeEach, describe, expect, it } from "vitest";
-import { buildWorkflowTemplate } from "../commands/init.js";
-
-let tmpDir: string;
-
-beforeEach(() => {
-  tmpDir = mkdtempSync(join(tmpdir(), "nerve-cli-init-test-"));
-});
-
-afterEach(() => {
-  rmSync(tmpDir, { recursive: true, force: true });
-});
-
-describe("buildWorkflowTemplate", () => {
-  it("includes the workflow name in the template", () => {
-    const tpl = buildWorkflowTemplate("my-workflow");
-    expect(tpl).toContain("my-workflow started");
-  });
-
-  it("contains WorkflowDefinition type import", () => {
-    const tpl = buildWorkflowTemplate("test");
-    expect(tpl).toContain("WorkflowDefinition");
-    expect(tpl).toContain("@uncaged/nerve-daemon");
-  });
-
-  it("contains a moderate function that returns null to signal completion", () => {
-    const tpl = buildWorkflowTemplate("test");
-    expect(tpl).toContain("return null");
-    expect(tpl).toContain("moderate");
-  });
-
-  it("contains a roles map with main role", () => {
-    const tpl = buildWorkflowTemplate("test");
-    expect(tpl).toContain("roles:");
-    expect(tpl).toContain("main:");
-  });
-
-  it("uses different names per call", () => {
-    const a = buildWorkflowTemplate("workflow-a");
-    const b = buildWorkflowTemplate("workflow-b");
-    expect(a).toContain("workflow-a started");
-    expect(b).toContain("workflow-b started");
-    expect(a).not.toContain("workflow-b");
-  });
-
-  it("produces valid TypeScript syntax (no unclosed braces)", () => {
-    const tpl = buildWorkflowTemplate("test");
-    const opens = (tpl.match(/\{/g) ?? []).length;
-    const closes = (tpl.match(/\}/g) ?? []).length;
-    expect(opens).toBe(closes);
-  });
-
-  it("ends with export default workflow", () => {
-    const tpl = buildWorkflowTemplate("test");
-    expect(tpl.trim().endsWith("export default workflow;")).toBe(true);
-  });
-});
-
-describe("workflow scaffold file writing (simulated)", () => {
-  it("writes the template to disk correctly", () => {
-    const { mkdirSync, writeFileSync } = require("node:fs");
-    const workflowDir = join(tmpDir, "workflows", "my-task");
-    mkdirSync(workflowDir, { recursive: true });
-    const content = buildWorkflowTemplate("my-task");
-    writeFileSync(join(workflowDir, "index.ts"), content, "utf8");
-
-    const read = readFileSync(join(workflowDir, "index.ts"), "utf8");
-    expect(read).toContain("my-task started");
-    expect(read).toContain("WorkflowDefinition");
-  });
-});

packages/cli/src/__tests__/knowledge-query-scope.test.ts

@@ -0,0 +1,28 @@
+import { describe, expect, it } from "vitest";
+
+import { knowledgeQueryScopeConflictMessage } from "../knowledge/query-scope.js";
+
+describe("knowledgeQueryScopeConflictMessage", () => {
+  it("returns null when only -r is used", () => {
+    expect(knowledgeQueryScopeConflictMessage("/tmp/repo", false)).toBeNull();
+  });
+
+  it("returns null when only -g is used", () => {
+    expect(knowledgeQueryScopeConflictMessage(undefined, true)).toBeNull();
+  });
+
+  it("returns null when neither -r nor -g", () => {
+    expect(knowledgeQueryScopeConflictMessage(undefined, false)).toBeNull();
+  });
+
+  it("returns error when both -r and -g", () => {
+    const msg = knowledgeQueryScopeConflictMessage("/some/path", true);
+    expect(msg).not.toBeNull();
+    expect(msg).toContain("-r");
+    expect(msg).toContain("-g");
+  });
+
+  it("treats empty -r as absent", () => {
+    expect(knowledgeQueryScopeConflictMessage("", true)).toBeNull();
+  });
+});

packages/cli/src/__tests__/knowledge-query.test.ts

@@ -0,0 +1,201 @@
+import { mkdirSync, mkdtempSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+import { fakeEmbeddingBytes } from "../knowledge/fake-embedding.js";
+import { contentHash, openKnowledgeDb, replaceAllChunks } from "../knowledge/knowledge-db.js";
+import { KNOWLEDGE_DB } from "../knowledge/paths.js";
+
+const DIM = 1024;
+
+function fakeEmbedding1024(seed: string): Buffer {
+  const buf = Buffer.alloc(DIM * 4);
+  for (let i = 0; i < DIM; i++) {
+    const c = seed.charCodeAt(i % Math.max(seed.length, 1)) || 1;
+    buf.writeFloatLE((c / 255) * Math.sin(i + 0.1), i * 4);
+  }
+  return buf;
+}
+
+const embedMocks = vi.hoisted(() => ({
+  resolveEmbedConfig: vi.fn(),
+  embedQuery: vi.fn(),
+}));
+
+vi.mock("../knowledge/embed-service.js", async (importOriginal) => {
+  const actual = await importOriginal<typeof import("../knowledge/embed-service.js")>();
+  return {
+    ...actual,
+    resolveEmbedConfig: () => embedMocks.resolveEmbedConfig(),
+    embedQuery: (cfg: Parameters<typeof actual.embedQuery>[0], text: string) =>
+      embedMocks.embedQuery(cfg, text),
+  };
+});
+
+import { queryKnowledgeRepo } from "../knowledge/query.js";
+
+describe("queryKnowledgeRepo (word overlap fallback)", () => {
+  const savedUrl = process.env.EMBED_SERVICE_URL;
+  const savedToken = process.env.EMBED_AUTH_TOKEN;
+
+  beforeEach(() => {
+    process.env.EMBED_SERVICE_URL = undefined;
+    process.env.EMBED_AUTH_TOKEN = undefined;
+    embedMocks.resolveEmbedConfig.mockReturnValue(null);
+    embedMocks.embedQuery.mockReset();
+  });
+
+  afterEach(() => {
+    if (savedUrl !== undefined) {
+      process.env.EMBED_SERVICE_URL = savedUrl;
+    } else {
+      process.env.EMBED_SERVICE_URL = undefined;
+    }
+    if (savedToken !== undefined) {
+      process.env.EMBED_AUTH_TOKEN = savedToken;
+    } else {
+      process.env.EMBED_AUTH_TOKEN = undefined;
+    }
+  });
+
+  it("returns higher scores for chunks that share words with the query", async () => {
+    const root = mkdtempSync(join(tmpdir(), "nerve-q-"));
+    const dbPath = join(root, KNOWLEDGE_DB);
+    mkdirSync(root, { recursive: true });
+
+    const db = openKnowledgeDb(dbPath);
+    try {
+      replaceAllChunks(db, [
+        {
+          path: "a.md",
+          slug: "a.md#0",
+          chunkIndex: 0,
+          text: "the signal bus emits notifications",
+          contentHash: contentHash("the signal bus emits notifications"),
+          embedding: fakeEmbeddingBytes("a"),
+        },
+        {
+          path: "b.md",
+          slug: "b.md#0",
+          chunkIndex: 0,
+          text: "unrelated cooking recipes",
+          contentHash: contentHash("unrelated cooking recipes"),
+          embedding: fakeEmbeddingBytes("b"),
+        },
+      ]);
+    } finally {
+      db.close();
+    }
+
+    const ranked = await queryKnowledgeRepo(root, dbPath, "signal bus", 10);
+    expect(ranked.length).toBe(2);
+    expect(ranked[0]?.path).toBe("a.md");
+    expect(ranked[1]?.path).toBe("b.md");
+    expect(ranked[0]?.score).toBeGreaterThan(ranked[1]?.score ?? 0);
+  });
+
+  it("respects limit", async () => {
+    const root = mkdtempSync(join(tmpdir(), "nerve-q2-"));
+    const dbPath = join(root, KNOWLEDGE_DB);
+    mkdirSync(root, { recursive: true });
+
+    const db = openKnowledgeDb(dbPath);
+    try {
+      replaceAllChunks(db, [
+        {
+          path: "x.md",
+          slug: "x.md#0",
+          chunkIndex: 0,
+          text: "one",
+          contentHash: contentHash("one"),
+          embedding: fakeEmbeddingBytes("x"),
+        },
+        {
+          path: "y.md",
+          slug: "y.md#0",
+          chunkIndex: 0,
+          text: "two",
+          contentHash: contentHash("two"),
+          embedding: fakeEmbeddingBytes("y"),
+        },
+      ]);
+    } finally {
+      db.close();
+    }
+
+    const ranked = await queryKnowledgeRepo(root, dbPath, "one", 1);
+    expect(ranked).toHaveLength(1);
+  });
+});
+
+describe("queryKnowledgeRepo (embed service)", () => {
+  const savedUrl = process.env.EMBED_SERVICE_URL;
+  const savedToken = process.env.EMBED_AUTH_TOKEN;
+
+  beforeEach(() => {
+    process.env.EMBED_SERVICE_URL = "http://embed.test";
+    process.env.EMBED_AUTH_TOKEN = "test-token";
+    embedMocks.resolveEmbedConfig.mockReturnValue({
+      url: "http://embed.test",
+      token: "test-token",
+    });
+    embedMocks.embedQuery.mockImplementation(async (_c: unknown, text: string) =>
+      fakeEmbedding1024(text),
+    );
+  });
+
+  afterEach(() => {
+    embedMocks.embedQuery.mockReset();
+    embedMocks.resolveEmbedConfig.mockReset();
+    if (savedUrl !== undefined) {
+      process.env.EMBED_SERVICE_URL = savedUrl;
+    } else {
+      process.env.EMBED_SERVICE_URL = undefined;
+    }
+    if (savedToken !== undefined) {
+      process.env.EMBED_AUTH_TOKEN = savedToken;
+    } else {
+      process.env.EMBED_AUTH_TOKEN = undefined;
+    }
+  });
+
+  it("uses cosine similarity when embed config is present", async () => {
+    const root = mkdtempSync(join(tmpdir(), "nerve-q-embed-"));
+    const dbPath = join(root, KNOWLEDGE_DB);
+    mkdirSync(root, { recursive: true });
+
+    const textA = "alpha beta gamma";
+    const textB = "zzz unrelated";
+
+    const db = openKnowledgeDb(dbPath);
+    try {
+      replaceAllChunks(db, [
+        {
+          path: "a.md",
+          slug: "a.md#0",
+          chunkIndex: 0,
+          text: textA,
+          contentHash: contentHash(textA),
+          embedding: fakeEmbedding1024(textA),
+        },
+        {
+          path: "b.md",
+          slug: "b.md#0",
+          chunkIndex: 0,
+          text: textB,
+          contentHash: contentHash(textB),
+          embedding: fakeEmbedding1024(textB),
+        },
+      ]);
+    } finally {
+      db.close();
+    }
+
+    const ranked = await queryKnowledgeRepo(root, dbPath, textA, 10);
+    expect(ranked.length).toBe(2);
+    expect(ranked[0]?.path).toBe("a.md");
+    expect(ranked[0]?.score).toBeGreaterThan(ranked[1]?.score ?? 0);
+  });
+});

packages/cli/src/__tests__/knowledge-registry.test.ts

@@ -0,0 +1,26 @@
+import { mkdtempSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { describe, expect, it } from "vitest";
+
+import {
+  listRegisteredKnowledgeRoots,
+  readKnowledgeRegistry,
+  registerKnowledgeRepoRoot,
+} from "../knowledge/registry.js";
+
+describe("knowledge repo registry", () => {
+  it("accumulates registered repo roots under a nerve home", () => {
+    const nerveHome = mkdtempSync(join(tmpdir(), "nerve-reg-"));
+    const repoA = mkdtempSync(join(tmpdir(), "repo-a-"));
+    const repoB = mkdtempSync(join(tmpdir(), "repo-b-"));
+
+    registerKnowledgeRepoRoot(repoA, nerveHome);
+    registerKnowledgeRepoRoot(repoB, nerveHome);
+    registerKnowledgeRepoRoot(repoA, nerveHome);
+
+    expect(readKnowledgeRegistry(nerveHome).roots).toEqual([repoA, repoB].sort());
+    expect(listRegisteredKnowledgeRoots(nerveHome)).toEqual([repoA, repoB].sort());
+  });
+});

packages/cli/src/__tests__/knowledge-sync.test.ts

@@ -0,0 +1,87 @@
+import { mkdirSync, mkdtempSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { DatabaseSync } from "node:sqlite";
+
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+const DIM = 1024;
+
+function fakeEmbedding1024(seed: string): Buffer {
+  const buf = Buffer.alloc(DIM * 4);
+  for (let i = 0; i < DIM; i++) {
+    const c = seed.charCodeAt(i % Math.max(seed.length, 1)) || 1;
+    buf.writeFloatLE((c / 255) * Math.sin(i + 0.1), i * 4);
+  }
+  return buf;
+}
+
+vi.mock("../knowledge/embed-service.js", async (importOriginal) => {
+  const actual = await importOriginal<typeof import("../knowledge/embed-service.js")>();
+  return {
+    ...actual,
+    resolveEmbedConfig: vi.fn(() => ({ url: "http://embed.test", token: "test-token" })),
+    embedTexts: vi.fn(async (_config: unknown, texts: string[]) =>
+      texts.map((t) => fakeEmbedding1024(t)),
+    ),
+  };
+});
+
+import { runKnowledgeSync } from "../knowledge/sync.js";
+
+describe("runKnowledgeSync", () => {
+  const savedUrl = process.env.EMBED_SERVICE_URL;
+  const savedToken = process.env.EMBED_AUTH_TOKEN;
+
+  beforeEach(() => {
+    process.env.EMBED_SERVICE_URL = "http://embed.test";
+    process.env.EMBED_AUTH_TOKEN = "test-token";
+  });
+
+  afterEach(() => {
+    if (savedUrl !== undefined) {
+      process.env.EMBED_SERVICE_URL = savedUrl;
+    } else {
+      process.env.EMBED_SERVICE_URL = undefined;
+    }
+    if (savedToken !== undefined) {
+      process.env.EMBED_AUTH_TOKEN = savedToken;
+    } else {
+      process.env.EMBED_AUTH_TOKEN = undefined;
+    }
+  });
+
+  it("creates knowledge.db with chunk rows", async () => {
+    const nerveHome = mkdtempSync(join(tmpdir(), "nerve-home-"));
+    const root = mkdtempSync(join(tmpdir(), "nerve-know-sync-"));
+    mkdirSync(join(root, "docs"), { recursive: true });
+    writeFileSync(
+      join(root, "docs", "a.md"),
+      `# Hello
+
+Some body text about bananas.
+
+`,
+    );
+    writeFileSync(
+      join(root, "knowledge.yaml"),
+      `include:
+  - "docs/**/*.md"
+exclude: []
+`,
+    );
+
+    const result = await runKnowledgeSync(root, nerveHome);
+    expect(result.chunksWritten).toBeGreaterThan(0);
+    expect(result.embeddingSource).toBe("remote");
+
+    const db = new DatabaseSync(result.dbPath, { readOnly: true });
+    try {
+      const row = db.prepare("SELECT COUNT(*) AS c FROM chunks").get() as { c: number };
+      expect(row.c).toBe(result.chunksWritten);
+    } finally {
+      db.close();
+    }
+  });
+});

packages/cli/src/__tests__/remote.test.ts

@@ -0,0 +1,82 @@
+import * as node_fs from "node:fs";
+import * as node_os from "node:os";
+import * as node_path from "node:path";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+vi.mock("node:os", async () => {
+  const actual = await vi.importActual<typeof import("node:os")>("node:os");
+  return { ...actual, homedir: vi.fn(() => actual.homedir()) };
+});
+
+import {
+  type RemotesConfig,
+  getDefaultRemoteName,
+  loadRemotes,
+  resolveRemote,
+  saveRemotes,
+} from "../remotes.js";
+
+describe("remotes", () => {
+  let tmpDir: string;
+  const homedirMock = node_os.homedir as ReturnType<typeof vi.fn>;
+
+  beforeEach(() => {
+    tmpDir = node_fs.mkdtempSync(node_path.join(node_os.tmpdir(), "nerve-remote-test-"));
+    homedirMock.mockReturnValue(tmpDir);
+  });
+
+  afterEach(() => {
+    node_fs.rmSync(tmpDir, { recursive: true, force: true });
+  });
+
+  it("loadRemotes returns empty config when file does not exist", () => {
+    const config = loadRemotes();
+    expect(config).toEqual({ remotes: {}, default: null });
+  });
+
+  it("saveRemotes and loadRemotes round-trip", () => {
+    const config: RemotesConfig = {
+      remotes: {
+        luming: { host: "192.168.2.58:9800", token: "secret" },
+        tuanzi: { host: "100.89.82.86:9800", token: null },
+      },
+      default: "luming",
+    };
+    saveRemotes(config);
+    const loaded = loadRemotes();
+    expect(loaded).toEqual(config);
+  });
+
+  it("saveRemotes creates file with restricted permissions", () => {
+    saveRemotes({ remotes: {}, default: null });
+    const p = node_path.join(tmpDir, ".nerve", "remotes.json");
+    const stat = node_fs.statSync(p);
+    expect(stat.mode & 0o777).toBe(0o600);
+  });
+
+  it("resolveRemote returns entry when found", () => {
+    saveRemotes({
+      remotes: { mybox: { host: "10.0.0.1:9800", token: "tok" } },
+      default: null,
+    });
+    const result = resolveRemote("mybox");
+    expect(result).toEqual({ host: "10.0.0.1:9800", token: "tok" });
+  });
+
+  it("resolveRemote returns null when not found", () => {
+    saveRemotes({ remotes: {}, default: null });
+    expect(resolveRemote("nope")).toBeNull();
+  });
+
+  it("getDefaultRemoteName returns default", () => {
+    saveRemotes({
+      remotes: { a: { host: "h:1", token: null } },
+      default: "a",
+    });
+    expect(getDefaultRemoteName()).toBe("a");
+  });
+
+  it("getDefaultRemoteName returns null when unset", () => {
+    expect(getDefaultRemoteName()).toBeNull();
+  });
+});

packages/cli/src/__tests__/sense-list-e2e.test.ts

@@ -0,0 +1,139 @@
+/**
+ * Integration test for `nerve sense list` through citty `runCommand` with a temp
+ * HOME and nerve.yaml. The daemon IPC layer is exercised against a real Unix
+ * socket mock server (no daemon process). `workspace.isRunning` and
+ * `getSocketPath` are mocked so the CLI takes the live-daemon code path while
+ * the socket points at the fake IPC server.
+ */
+
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { type Server, createServer } from "node:net";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import type { SenseInfo } from "@uncaged/nerve-core";
+import { runCommand } from "citty";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+import { senseCommand } from "../commands/sense.js";
+import * as workspace from "../workspace.js";
+
+describe("nerve sense list CLI (runCommand + temp HOME + mock IPC socket)", () => {
+  let prevHome: string | undefined;
+  let fakeHome: string;
+  let sockDir: string;
+  let sockPath: string;
+  let ipcServer: Server | null;
+  let stdoutSpy: ReturnType<typeof vi.spyOn<typeof process.stdout, "write">> | null;
+  let listSensesRequests: unknown[];
+
+  const LAST_SIGNAL_TS = 1_714_521_600_000; // fixed wall time for stable ISO in assertions
+
+  const daemonSenseRow: SenseInfo = {
+    name: "cpu-usage",
+    group: "system",
+    throttle: 5000,
+    timeout: 3000,
+    triggers: ["every 5s"],
+    lastSignalTimestamp: LAST_SIGNAL_TS,
+  };
+
+  function nerveYamlFixture(): string {
+    return `
+senses:
+  cpu-usage:
+    group: system
+    throttle: 5s
+    timeout: 3s
+    interval: 5s
+`.trim();
+  }
+
+  function collectStdout(): string {
+    if (stdoutSpy === null) return "";
+    let out = "";
+    for (const call of stdoutSpy.mock.calls) {
+      const chunk = call[0];
+      if (typeof chunk === "string") out += chunk;
+      else if (Buffer.isBuffer(chunk)) out += chunk.toString("utf8");
+    }
+    return out;
+  }
+
+  beforeEach(async () => {
+    listSensesRequests = [];
+    ipcServer = null;
+    stdoutSpy = vi.spyOn(process.stdout, "write").mockImplementation(() => true);
+
+    prevHome = process.env.HOME;
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-sense-list-cli-e2e-"));
+    process.env.HOME = fakeHome;
+
+    const nerveRoot = join(fakeHome, ".uncaged-nerve");
+    mkdirSync(nerveRoot, { recursive: true });
+    writeFileSync(join(nerveRoot, "nerve.yaml"), `${nerveYamlFixture()}\n`, "utf8");
+
+    sockDir = mkdtempSync(join(tmpdir(), "nerve-sense-list-ipc-e2e-"));
+    sockPath = join(sockDir, "nerve.sock");
+
+    vi.spyOn(workspace, "getSocketPath").mockReturnValue(sockPath);
+    vi.spyOn(workspace, "isRunning").mockReturnValue(true);
+
+    ipcServer = createServer((socket) => {
+      socket.on("data", (chunk: Buffer) => {
+        const line = chunk.toString("utf8").trim();
+        try {
+          const req = JSON.parse(line) as { type: string };
+          if (req.type === "list-senses") {
+            listSensesRequests.push(req);
+            socket.write(`${JSON.stringify({ ok: true, senses: [daemonSenseRow] })}\n`);
+          }
+        } catch {
+          // ignore malformed lines
+        }
+      });
+    });
+    await new Promise<void>((resolve) => {
+      ipcServer?.listen(sockPath, resolve);
+    });
+  });
+
+  afterEach(async () => {
+    stdoutSpy?.mockRestore();
+    stdoutSpy = null;
+
+    if (ipcServer !== null) {
+      await new Promise<void>((resolve) => {
+        ipcServer?.close(() => resolve());
+      });
+      ipcServer = null;
+    }
+
+    if (prevHome === undefined) {
+      // biome-ignore lint/performance/noDelete: semantically correct for env cleanup
+      delete process.env.HOME;
+    } else {
+      process.env.HOME = prevHome;
+    }
+    rmSync(fakeHome, { recursive: true, force: true });
+    rmSync(sockDir, { recursive: true, force: true });
+  });
+
+  it("prints sense list from daemon path with name, group, throttle, trigger schedule, and last signal time", async () => {
+    // With a real daemon, we would wait for a compute cycle; the mock server
+    // returns SenseInfo as if one already produced lastSignalTimestamp.
+    await runCommand(senseCommand, { rawArgs: ["list"] });
+
+    expect(listSensesRequests).toHaveLength(1);
+    expect(listSensesRequests[0]).toMatchObject({ type: "list-senses" });
+
+    const out = collectStdout();
+    expect(out).toContain("cpu-usage");
+    expect(out).toContain("group:    system");
+    expect(out).toContain("throttle: 5s");
+    expect(out).toContain("timeout:  3s");
+    expect(out).toContain("trigger schedule: every 5s");
+    expect(out).not.toContain("(never)");
+    expect(out).toContain(new Date(LAST_SIGNAL_TS).toISOString());
+  });
+});

packages/cli/src/__tests__/sense-list.test.ts

@@ -29,6 +29,7 @@ const SAMPLE_SENSES: SenseInfo[] = [
     group: "system",
     throttle: 5000,
     timeout: 3000,
+    triggers: ["every 30s", "on: cpu-threshold"],
     lastSignalTimestamp: 1_700_000_000_000,
   },
   {
@@ -36,6 +37,7 @@ const SAMPLE_SENSES: SenseInfo[] = [
     group: "system",
     throttle: 30000,
     timeout: null,
+    triggers: [],
     lastSignalTimestamp: null,
   },
   {
@@ -43,6 +45,7 @@ const SAMPLE_SENSES: SenseInfo[] = [
     group: "tasks",
     throttle: 10000,
     timeout: 30000,
+    triggers: ["every 1m"],
     lastSignalTimestamp: null,
   },
 ];
@@ -112,6 +115,13 @@ describe("formatSenseList", () => {
     expect(output).toContain("—");
   });
 
+  it("shows trigger schedule from sense metadata", () => {
+    const output = formatSenseList(SAMPLE_SENSES);
+    expect(output).toContain("trigger schedule:");
+    expect(output).toContain("every 30s");
+    expect(output).toContain("(none)");
+  });
+
   it("shows '(never)' when lastSignalTimestamp is null", () => {
     const output = formatSenseList(SAMPLE_SENSES);
     expect(output).toContain("(never)");
@@ -164,7 +174,6 @@ senses:
   disk-usage:
     group: system
     throttle: 30s
-reflexes: []
 `.trim(),
     );
     const result = sensesFromConfig(path);
@@ -189,7 +198,6 @@ reflexes: []
 senses:
   my-sense:
     group: default
-reflexes: []
 `.trim(),
     );
     const result = sensesFromConfig(path);
@@ -206,13 +214,33 @@ senses:
     group: default
     throttle: 10s
     timeout: 5s
-reflexes: []
 `.trim(),
     );
     const result = sensesFromConfig(path);
     expect(result[0].throttle).toBe(10000);
     expect(result[0].timeout).toBe(5000);
   });
+
+  it("uses inline interval and on for trigger schedule labels", () => {
+    const path = join(tmpDir, "nerve.yaml");
+    writeFileSync(
+      path,
+      `
+senses:
+  downstream:
+    group: default
+    interval: 15s
+    on: [upstream]
+  upstream:
+    group: default
+`.trim(),
+    );
+    const result = sensesFromConfig(path);
+    const downstream = result.find((s) => s.name === "downstream");
+    const upstream = result.find((s) => s.name === "upstream");
+    expect(downstream?.triggers).toEqual(["every 15s · on: upstream"]);
+    expect(upstream?.triggers).toEqual([]);
+  });
 });
 
 // ---------------------------------------------------------------------------
@@ -263,6 +291,7 @@ describe("listSensesViaDaemon", () => {
         group: "system",
         throttle: 5000,
         timeout: 3000,
+        triggers: [],
         lastSignalTimestamp: 12345,
       },
     ];

packages/cli/src/__tests__/sense-schema-e2e.test.ts

@@ -0,0 +1,97 @@
+/**
+ * E2E-style tests for `nerve sense schema` with a temp HOME and a real sense SQLite file.
+ * `getNerveRoot()` uses `os.homedir()`, which respects `process.env.HOME` on POSIX.
+ */
+
+import { mkdirSync, mkdtempSync, rmSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { DatabaseSync } from "node:sqlite";
+
+import { runCommand } from "citty";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+import { senseCommand } from "../commands/sense.js";
+
+const SENSE_NAME = "e2e-schema-sense";
+
+function createFakeSenseDb(nerveRoot: string): void {
+  const sensesDir = join(nerveRoot, "data", "senses");
+  mkdirSync(sensesDir, { recursive: true });
+  const dbPath = join(sensesDir, `${SENSE_NAME}.db`);
+  const db = new DatabaseSync(dbPath);
+  db.exec(
+    "CREATE TABLE _signals(id INTEGER PRIMARY KEY, sense TEXT, timestamp INTEGER, payload TEXT)",
+  );
+  db.exec("CREATE TABLE _migrations (name TEXT PRIMARY KEY)");
+  db.close();
+}
+
+describe("nerve sense schema CLI (runCommand + temp HOME)", () => {
+  let prevHome: string | undefined;
+  let fakeHome: string;
+  let stdoutSpy: ReturnType<typeof vi.spyOn> | null;
+  let capturedStdout: string;
+
+  beforeEach(() => {
+    capturedStdout = "";
+    stdoutSpy = vi
+      .spyOn(process.stdout, "write")
+      .mockImplementation(
+        (chunk: string | Uint8Array, enc?: BufferEncoding, cb?: (err?: Error | null) => void) => {
+          if (typeof chunk === "string") {
+            capturedStdout += chunk;
+          } else {
+            capturedStdout += Buffer.from(chunk).toString(typeof enc === "string" ? enc : "utf8");
+          }
+          if (typeof cb === "function") {
+            cb();
+          }
+          return true;
+        },
+      );
+
+    prevHome = process.env.HOME;
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-sense-schema-e2e-"));
+    process.env.HOME = fakeHome;
+
+    const nerveRoot = join(fakeHome, ".uncaged-nerve");
+    createFakeSenseDb(nerveRoot);
+  });
+
+  afterEach(() => {
+    stdoutSpy?.mockRestore();
+    stdoutSpy = null;
+    if (prevHome === undefined) {
+      // biome-ignore lint/performance/noDelete: semantically correct for env cleanup
+      delete process.env.HOME;
+    } else {
+      process.env.HOME = prevHome;
+    }
+    rmSync(fakeHome, { recursive: true, force: true });
+  });
+
+  it("prints CREATE TABLE statements for the sense database", async () => {
+    await runCommand(senseCommand, { rawArgs: ["schema", SENSE_NAME] });
+    expect(capturedStdout).toMatch(/CREATE TABLE/i);
+  });
+
+  it("includes the _signals table in output", async () => {
+    await runCommand(senseCommand, { rawArgs: ["schema", SENSE_NAME] });
+    expect(capturedStdout).toContain("_signals");
+  });
+
+  it("with --json prints a valid JSON array of SQL strings", async () => {
+    await runCommand(senseCommand, { rawArgs: ["schema", SENSE_NAME, "--json"] });
+    const parsed: unknown = JSON.parse(capturedStdout.trim());
+    expect(Array.isArray(parsed)).toBe(true);
+    const arr = parsed as unknown[];
+    expect(arr.length).toBeGreaterThanOrEqual(1);
+    for (const item of arr) {
+      expect(typeof item).toBe("string");
+      expect(item).toMatch(/CREATE TABLE/i);
+    }
+    const joined = arr.join("\n");
+    expect(joined).toContain("_signals");
+  });
+});

packages/cli/src/__tests__/sense-sqlite.test.ts

@@ -105,6 +105,28 @@ describe("parseSenseQueryArgs", () => {
     expect(parseSenseQueryArgs(["cpu", "SELECT", "1"])).toEqual({ name: "cpu", sql: "SELECT 1" });
   });
 
+  it("uses --sql value instead of positional SQL", () => {
+    expect(parseSenseQueryArgs(["cpu", "--sql", "SELECT 2"])).toEqual({
+      name: "cpu",
+      sql: "SELECT 2",
+    });
+    expect(parseSenseQueryArgs(["cpu", "--sql=SELECT 3"])).toEqual({
+      name: "cpu",
+      sql: "SELECT 3",
+    });
+  });
+
+  it("prefers --sql over trailing positional SQL", () => {
+    expect(parseSenseQueryArgs(["cpu", "--sql", "SELECT a", "SELECT b"])).toEqual({
+      name: "cpu",
+      sql: "SELECT a",
+    });
+  });
+
+  it("throws when --sql has no value", () => {
+    expect(() => parseSenseQueryArgs(["cpu", "--sql"])).toThrow(/Missing value for --sql/);
+  });
+
   it("throws when name is missing", () => {
     expect(() => parseSenseQueryArgs(["--json"])).toThrow(/Missing sense name/);
   });

packages/cli/src/__tests__/sense-trigger-e2e.test.ts

@@ -0,0 +1,122 @@
+/**
+ * E2E-style tests for `nerve sense trigger` (issue #157): citty + workspace stubs
+ * and a mock daemon on a real Unix socket — no running nerve process required.
+ */
+
+import { mkdtempSync, rmSync } from "node:fs";
+import { type Server, createServer } from "node:net";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { runCommand } from "citty";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+import { senseCommand } from "../commands/sense.js";
+import * as workspace from "../workspace.js";
+
+describe("nerve sense trigger (e2e mock daemon)", () => {
+  let sockDir: string;
+  let sockPath: string;
+  let server: Server;
+  let ipcReceived: unknown[];
+  let knownOkSenses: Set<string>;
+  let stdoutBuf: string;
+  let stderrBuf: string;
+
+  beforeEach(async () => {
+    ipcReceived = [];
+    knownOkSenses = new Set(["cpu-usage"]);
+    stdoutBuf = "";
+    stderrBuf = "";
+
+    sockDir = mkdtempSync(join(tmpdir(), "nerve-sense-trigger-e2e-"));
+    sockPath = join(sockDir, "nerve.sock");
+
+    server = createServer((socket) => {
+      socket.on("data", (chunk: Buffer) => {
+        const line = chunk.toString("utf8").trim();
+        let req: unknown;
+        try {
+          req = JSON.parse(line);
+        } catch {
+          return;
+        }
+        ipcReceived.push(req);
+        const r = req as { type?: string; sense?: string };
+        if (
+          r.type === "trigger-sense" &&
+          typeof r.sense === "string" &&
+          knownOkSenses.has(r.sense)
+        ) {
+          socket.write(`${JSON.stringify({ ok: true })}\n`);
+        } else if (r.type === "trigger-sense" && typeof r.sense === "string") {
+          socket.write(`${JSON.stringify({ ok: false, error: `Unknown sense: "${r.sense}"` })}\n`);
+        }
+      });
+    });
+    await new Promise<void>((resolve) => {
+      server.listen(sockPath, resolve);
+    });
+
+    vi.spyOn(workspace, "isRunning").mockReturnValue(true);
+    vi.spyOn(workspace, "getSocketPath").mockReturnValue(sockPath);
+
+    vi.spyOn(process.stdout, "write").mockImplementation((chunk, encodingOrCb?, cb?) => {
+      stdoutBuf += typeof chunk === "string" ? chunk : Buffer.from(chunk).toString("utf8");
+      if (typeof encodingOrCb === "function") {
+        encodingOrCb(null);
+      } else if (cb !== undefined) {
+        cb(null);
+      }
+      return true;
+    });
+    vi.spyOn(process.stderr, "write").mockImplementation((chunk, encodingOrCb?, cb?) => {
+      stderrBuf += typeof chunk === "string" ? chunk : Buffer.from(chunk).toString("utf8");
+      if (typeof encodingOrCb === "function") {
+        encodingOrCb(null);
+      } else if (cb !== undefined) {
+        cb(null);
+      }
+      return true;
+    });
+
+    vi.spyOn(process, "exit").mockImplementation((code?: number | string | null) => {
+      const c = typeof code === "number" ? code : 1;
+      // Throw instead of actually exiting so the test runner stays alive;
+      // the test asserts on this message to verify the exit code.
+      throw new Error(`process.exit(${String(c)})`);
+    });
+  });
+
+  afterEach(async () => {
+    vi.restoreAllMocks();
+    await new Promise<void>((resolve) => {
+      server.close(() => resolve());
+    });
+    rmSync(sockDir, { recursive: true, force: true });
+  });
+
+  it("trigger known sense exits normally and stdout contains Triggered", async () => {
+    await runCommand(senseCommand, { rawArgs: ["trigger", "cpu-usage"] });
+    expect(stdoutBuf).toContain("Triggered");
+    expect(stdoutBuf).toContain("✅");
+    expect(stderrBuf).toBe("");
+  });
+
+  it("trigger non-existent sense writes daemon error to stderr and exits 1", async () => {
+    await expect(
+      runCommand(senseCommand, { rawArgs: ["trigger", "no-such-sense"] }),
+    ).rejects.toThrow("process.exit(1)");
+    expect(stdoutBuf).toBe("");
+    expect(stderrBuf).toContain("Daemon rejected trigger");
+    expect(stderrBuf).toContain("Unknown sense");
+    expect(stderrBuf).toContain("no-such-sense");
+  });
+
+  it("sends IPC { type: trigger-sense, sense: <name> } to the daemon", async () => {
+    knownOkSenses.add("custom-sense");
+    await runCommand(senseCommand, { rawArgs: ["trigger", "custom-sense"] });
+    expect(ipcReceived).toHaveLength(1);
+    expect(ipcReceived[0]).toEqual({ type: "trigger-sense", sense: "custom-sense" });
+  });
+});

packages/cli/src/__tests__/validate-workflow-agents.test.ts

@@ -0,0 +1,113 @@
+/**
+ * RFC-003 Phase 5: nerve validate — workflow adapter usage and extract.
+ */
+
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import type { NerveConfig } from "@uncaged/nerve-core";
+import { afterEach, describe, expect, it } from "vitest";
+
+import {
+  validateAgentConfigurationLayer,
+  workflowSourcesDeclareAdapterRoles,
+} from "../workflow-agent-validation.js";
+
+function baseConfig(overrides: Partial<NerveConfig> = {}): NerveConfig {
+  return {
+    maxRounds: 10,
+    senses: {},
+    workflows: {},
+    api: { port: null, token: null, host: "127.0.0.1" },
+    extract: null,
+    ...overrides,
+  };
+}
+
+describe("validateAgentConfigurationLayer", () => {
+  let nerveRoot: string;
+
+  afterEach(() => {
+    rmSync(nerveRoot, { recursive: true, force: true });
+  });
+
+  it("fails when workflow sources use adapters but extract is missing", () => {
+    nerveRoot = mkdtempSync(join(tmpdir(), "nerve-val-adapters-"));
+    mkdirSync(join(nerveRoot, "workflows", "demo", "src"), { recursive: true });
+    writeFileSync(
+      join(nerveRoot, "workflows", "demo", "src", "index.ts"),
+      `
+const adapter = async () => "";
+const spec = {
+  name: "demo",
+  roles: {
+    r: { adapter: adapter, prompt: "p", meta: {} as never },
+  },
+  moderator: () => "__end__" as never,
+};
+export default spec;
+`,
+      "utf8",
+    );
+
+    const result = validateAgentConfigurationLayer(baseConfig(), nerveRoot);
+    expect(result.ok).toBe(false);
+    if (!result.ok) {
+      expect(result.message).toMatch(/extract/i);
+    }
+  });
+
+  it("passes when adapters are used and extract is configured", () => {
+    nerveRoot = mkdtempSync(join(tmpdir(), "nerve-val-adapters-"));
+    mkdirSync(join(nerveRoot, "workflows", "demo", "src"), { recursive: true });
+    writeFileSync(
+      join(nerveRoot, "workflows", "demo", "src", "index.ts"),
+      `
+roles: { x: { adapter: foo, prompt: "", meta: {} as never } }
+`,
+      "utf8",
+    );
+
+    const result = validateAgentConfigurationLayer(
+      baseConfig({
+        extract: { provider: "dashscope", model: "qwen-plus" },
+      }),
+      nerveRoot,
+    );
+    expect(result.ok).toBe(true);
+  });
+
+  it("passes when no adapter usage is detected", () => {
+    nerveRoot = mkdtempSync(join(tmpdir(), "nerve-val-adapters-"));
+    mkdirSync(join(nerveRoot, "workflows", "demo", "src"), { recursive: true });
+    writeFileSync(
+      join(nerveRoot, "workflows", "demo", "src", "wf.ts"),
+      `const role = { prompt: "x" };`,
+      "utf8",
+    );
+
+    const result = validateAgentConfigurationLayer(baseConfig(), nerveRoot);
+    expect(result.ok).toBe(true);
+  });
+});
+
+describe("workflowSourcesDeclareAdapterRoles", () => {
+  let nerveRoot: string;
+
+  afterEach(() => {
+    rmSync(nerveRoot, { recursive: true, force: true });
+  });
+
+  it("detects adapter: identifiers under workflows/*/src", () => {
+    nerveRoot = mkdtempSync(join(tmpdir(), "nerve-collect-adapters-"));
+    mkdirSync(join(nerveRoot, "workflows", "w1", "src", "nested"), { recursive: true });
+    writeFileSync(
+      join(nerveRoot, "workflows", "w1", "src", "nested", "a.ts"),
+      "adapter: foo\nadapter: bar",
+      "utf8",
+    );
+
+    expect(workflowSourcesDeclareAdapterRoles(nerveRoot)).toBe(true);
+  });
+});

packages/cli/src/__tests__/workflow-cli-e2e.test.ts

@@ -0,0 +1,88 @@
+/**
+ * Smoke / integration tests for `nerve workflow` and `nerve thread` citty handlers with a real HOME
+ * layout and logs.db. `loadDaemonModule` is mocked so tests use workspace
+ * `@uncaged/nerve-store` directly (no ~/.uncaged-nerve daemon install required).
+ */
+
+import { mkdirSync, mkdtempSync, rmSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { runCommand } from "citty";
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+
+vi.mock("../workspace-daemon.js", async () => {
+  const { createLogStore } = await import("@uncaged/nerve-store");
+  return {
+    loadDaemonModule: vi.fn(async () => ({ createLogStore })),
+  };
+});
+
+import { createLogStore } from "@uncaged/nerve-store";
+
+import { threadCommand } from "../commands/thread.js";
+
+describe("nerve thread CLI (runCommand + temp HOME)", () => {
+  let prevHome: string | undefined;
+  let fakeHome: string;
+  let stdoutSpy: ReturnType<typeof vi.spyOn> | null;
+
+  beforeEach(() => {
+    stdoutSpy = vi.spyOn(process.stdout, "write").mockImplementation(() => true);
+    prevHome = process.env.HOME;
+    fakeHome = mkdtempSync(join(tmpdir(), "nerve-wf-cli-e2e-"));
+    process.env.HOME = fakeHome;
+
+    const nerveRoot = join(fakeHome, ".uncaged-nerve");
+    mkdirSync(join(nerveRoot, "data"), { recursive: true });
+    const dbPath = join(nerveRoot, "data", "logs.db");
+    const store = createLogStore(dbPath);
+
+    store.upsertWorkflowRun(
+      { source: "workflow", type: "started", refId: "e2e-run", payload: "{}", timestamp: 5000 },
+      { runId: "e2e-run", workflow: "demo", status: "completed", timestamp: 5000, exitCode: 0 },
+    );
+    store.append({
+      source: "workflow",
+      type: "completed",
+      refId: "e2e-run",
+      payload: null,
+      timestamp: 5001,
+    });
+    store.append({
+      source: "workflow",
+      type: "thread_command_event",
+      refId: "e2e-run",
+      payload: JSON.stringify({ type: "step", role: "bot", content: "hello" }),
+      timestamp: 5100,
+    });
+    store.close();
+  });
+
+  afterEach(() => {
+    stdoutSpy?.mockRestore();
+    stdoutSpy = null;
+    if (prevHome === undefined) {
+      process.env.HOME = undefined;
+    } else {
+      process.env.HOME = prevHome;
+    }
+    rmSync(fakeHome, { recursive: true, force: true });
+  });
+
+  it("thread list --all completes without throwing", async () => {
+    await expect(runCommand(threadCommand, { rawArgs: ["list", "--all"] })).resolves.toBeDefined();
+  });
+
+  it("thread inspect <runId> completes without throwing", async () => {
+    await expect(
+      runCommand(threadCommand, { rawArgs: ["inspect", "e2e-run", "--limit", "10"] }),
+    ).resolves.toBeDefined();
+  });
+
+  it("thread show <runId> completes without throwing (role rounds path)", async () => {
+    await expect(
+      runCommand(threadCommand, { rawArgs: ["show", "e2e-run", "--budget", "50000"] }),
+    ).resolves.toBeDefined();
+  });
+});

packages/cli/src/__tests__/workflow.test.ts

@@ -18,9 +18,11 @@ import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import type { LogStore, ThreadRoundRow, WorkflowRun } from "@uncaged/nerve-store";
 import {
   DEFAULT_THREAD_BUDGET_CHARS,
+  UNKNOWN_TIMESTAMP_LABEL,
   buildInspectOutput,
   buildListOutput,
   buildThreadCommandOutput,
+  formatRunLine,
   formatThreadRoundBlock,
   formatTs,
   getAllWorkflowRuns,
@@ -45,7 +47,7 @@ function upsertRun(
 ): void {
   store.upsertWorkflowRun(
     { source: "workflow", type: status, refId: runId, payload: null, timestamp: timestampMs },
-    { runId, workflow, status, timestamp: timestampMs },
+    { runId, workflow, status, timestamp: timestampMs, exitCode: null },
   );
 }
 
@@ -64,10 +66,75 @@ afterEach(() => {
 // ---------------------------------------------------------------------------
 
 describe("formatTs", () => {
-  it("returns ISO 8601 string", () => {
+  it("returns ISO 8601 string for a valid UTC instant", () => {
     const timestampMs = new Date("2026-01-01T00:00:00.000Z").getTime();
     expect(formatTs(timestampMs)).toBe("2026-01-01T00:00:00.000Z");
   });
+
+  it("returns placeholder for null and undefined", () => {
+    expect(formatTs(null)).toBe(UNKNOWN_TIMESTAMP_LABEL);
+    expect(formatTs(undefined)).toBe(UNKNOWN_TIMESTAMP_LABEL);
+  });
+
+  it("returns placeholder for NaN and non-finite numbers", () => {
+    expect(formatTs(Number.NaN)).toBe(UNKNOWN_TIMESTAMP_LABEL);
+    expect(formatTs(Number.POSITIVE_INFINITY)).toBe(UNKNOWN_TIMESTAMP_LABEL);
+    expect(formatTs(Number.NEGATIVE_INFINITY)).toBe(UNKNOWN_TIMESTAMP_LABEL);
+  });
+
+  it("returns placeholder for non-number runtime values", () => {
+    expect(formatTs("2024" as unknown as number)).toBe(UNKNOWN_TIMESTAMP_LABEL);
+    expect(formatTs({} as unknown as number)).toBe(UNKNOWN_TIMESTAMP_LABEL);
+  });
+
+  it("formats 0 as Unix epoch", () => {
+    expect(formatTs(0)).toBe("1970-01-01T00:00:00.000Z");
+  });
+
+  it("formats negative finite values as ISO strings", () => {
+    expect(formatTs(-1)).toBe("1969-12-31T23:59:59.999Z");
+  });
+});
+
+// ---------------------------------------------------------------------------
+// formatRunLine
+// ---------------------------------------------------------------------------
+
+describe("formatRunLine", () => {
+  it("omits exit_code segment when exitCode is null", () => {
+    const run: WorkflowRun = {
+      runId: "r1",
+      workflow: "wf",
+      status: "started",
+      timestamp: 1000,
+      exitCode: null,
+    };
+    const line = formatRunLine(run);
+    expect(line).not.toContain("exit_code");
+    expect(line).toContain("timestamp=1970-01-01T00:00:01.000Z");
+  });
+
+  it("includes exit_code when set", () => {
+    const run: WorkflowRun = {
+      runId: "r1",
+      workflow: "wf",
+      status: "failed",
+      timestamp: 2000,
+      exitCode: 7,
+    };
+    expect(formatRunLine(run)).toContain("exit_code=7");
+  });
+
+  it("uses unknown timestamp label for bad run timestamps", () => {
+    const run = {
+      runId: "r-bad",
+      workflow: "wf",
+      status: "completed" as const,
+      timestamp: Number.NaN,
+      exitCode: null,
+    } as WorkflowRun;
+    expect(formatRunLine(run)).toContain(`timestamp=${UNKNOWN_TIMESTAMP_LABEL}`);
+  });
 });
 
 // ---------------------------------------------------------------------------
@@ -83,6 +150,7 @@ describe("statusIcon", () => {
     ["crashed", "💥"],
     ["dropped", "🗑"],
     ["interrupted", "⚠️"],
+    ["killed", "🛑"],
   ] as const)("maps status=%s to icon=%s", (status, icon) => {
     expect(statusIcon(status)).toBe(icon);
   });
@@ -149,7 +217,7 @@ describe("buildListOutput", () => {
     status: WorkflowRun["status"],
     timestampMs: number,
   ): WorkflowRun {
-    return { runId, workflow, status, timestamp: timestampMs };
+    return { runId, workflow, status, timestamp: timestampMs, exitCode: null };
   }
 
   it("returns empty message when no runs and --all=false", () => {
@@ -191,6 +259,7 @@ describe("buildListOutput", () => {
     // header + 2 run lines
     expect(lines).toHaveLength(3);
     expect(paginationHint).not.toBeNull();
+    expect(paginationHint).toContain("nerve thread list");
     expect(paginationHint).toContain("--offset 2");
     expect(paginationHint).toContain("3 more");
   });
@@ -224,6 +293,22 @@ describe("buildListOutput", () => {
     expect(paginationHint).toContain("1 more");
     expect(paginationHint).toContain("--offset 4");
   });
+
+  it("does not throw when a run has null exit_code and invalid timestamp", () => {
+    const runs: WorkflowRun[] = [
+      {
+        runId: "bad-ts",
+        workflow: "wf",
+        status: "completed",
+        timestamp: null as unknown as number,
+        exitCode: null,
+      },
+    ];
+    const { lines } = buildListOutput(runs, 0, 20, true, null);
+    const text = lines.join("");
+    expect(text).toContain(UNKNOWN_TIMESTAMP_LABEL);
+    expect(text).not.toContain("exit_code");
+  });
 });
 
 // ---------------------------------------------------------------------------
@@ -236,6 +321,7 @@ describe("buildInspectOutput", () => {
     workflow: "cleanup",
     status: "completed",
     timestamp: 1_700_000_000_000,
+    exitCode: null,
   };
 
   it("shows header with run details", () => {
@@ -291,13 +377,28 @@ describe("buildInspectOutput", () => {
     const { paginationHint } = buildInspectOutput(baseRun, logs, 0, 20);
     expect(paginationHint).toBeNull();
   });
+
+  it("renders unknown labels for bad run and event timestamps without throwing", () => {
+    const run: WorkflowRun = {
+      ...baseRun,
+      timestamp: Number.NaN as unknown as number,
+    };
+    const logs = [{ timestamp: Number.NaN as unknown as number, type: "started", payload: null }];
+    const { header, eventLines } = buildInspectOutput(run, logs, 0, 20);
+    const all = [...header, ...eventLines].join("");
+    expect(all).toContain(UNKNOWN_TIMESTAMP_LABEL);
+    expect(all.match(new RegExp(UNKNOWN_TIMESTAMP_LABEL, "g"))).not.toBeNull();
+    expect(
+      (all.match(new RegExp(UNKNOWN_TIMESTAMP_LABEL, "g")) ?? []).length,
+    ).toBeGreaterThanOrEqual(2);
+  });
 });
 
 // ---------------------------------------------------------------------------
 // Integration: getAllWorkflowRuns + buildListOutput end-to-end with real store
 // ---------------------------------------------------------------------------
 
-describe("workflow list — integration with real store", () => {
+describe("workflow runs list — integration with real store", () => {
   it("lists active runs from the store", () => {
     upsertRun("r1", "cleanup", "started", 1000);
     upsertRun("r2", "cleanup", "queued", 2000);
@@ -336,6 +437,7 @@ describe("partitionWorkflowMessage", () => {
       role: "scanner",
       content: "ok",
       meta: { items: [1, 2] },
+      timestamp: 1,
     });
     expect(p.roleStr).toBe("scanner");
     expect(p.contentBody).toBe("ok");
@@ -369,6 +471,24 @@ describe("formatThreadRoundBlock", () => {
     expect(text).toContain("score: 0.5");
     expect(text).toContain("hi");
   });
+
+  it("uses unknown label when row timestamp is null (defensive)", () => {
+    const badRow = {
+      ...row,
+      timestamp: null as unknown as number,
+    };
+    expect(formatThreadRoundBlock(badRow)).toContain(UNKNOWN_TIMESTAMP_LABEL);
+  });
+
+  it("uses unknown label when row timestamp is NaN (defensive)", () => {
+    const badRow = { ...row, timestamp: Number.NaN };
+    expect(formatThreadRoundBlock(badRow)).toContain(UNKNOWN_TIMESTAMP_LABEL);
+  });
+
+  it("uses unknown label when row timestamp is undefined (defensive)", () => {
+    const badRow = { ...row, timestamp: undefined as unknown as number };
+    expect(formatThreadRoundBlock(badRow)).toContain(UNKNOWN_TIMESTAMP_LABEL);
+  });
 });
 
 describe("buildThreadCommandOutput", () => {
@@ -413,6 +533,25 @@ describe("buildThreadCommandOutput", () => {
     expect(paginationHint).toContain("--budget 400");
   });
 
+  it("formats startRow first (chronologically before role rounds) and consumes budget first", () => {
+    const start: ThreadRoundRow = {
+      round: 0,
+      logId: 1,
+      timestamp: 100,
+      message: { role: "__start__", content: "go", meta: {}, timestamp: 100 },
+    };
+    const desc = [row(2, "bbb"), row(1, "aaa")];
+    const { lines, paginationHint } = buildThreadCommandOutput([], desc, 50_000, "run-s", start);
+    const text = lines.join("");
+    const idxStart = text.indexOf("[#0 __start__]");
+    const idxA = text.indexOf("\naaa\n");
+    const idxB = text.indexOf("\nbbb\n");
+    expect(idxStart).toBeGreaterThan(-1);
+    expect(idxA).toBeGreaterThan(idxStart);
+    expect(idxB).toBeGreaterThan(idxA);
+    expect(paginationHint).toBeNull();
+  });
+
   it("default budget constant matches workflow command default", () => {
     expect(DEFAULT_THREAD_BUDGET_CHARS).toBe(8000);
   });

packages/cli/src/cli-global.ts

@@ -0,0 +1,107 @@
+import { resolveRemote } from "./remotes.js";
+
+let cliDaemonHost: string | null = null;
+let cliDaemonApiToken: string | null = null;
+
+function applyRemoteFlag(argv: string[], i: number): number | null {
+  const read =
+    readEqOrNextFlag(argv, i, "--remote=", "--remote", "--remote requires a remote name") ??
+    readEqOrNextFlag(argv, i, "-r=", "-r", "-r requires a remote name");
+  if (read === null) return null;
+  const resolved = resolveRemote(read.value);
+  if (resolved === null) {
+    throw new Error(`Unknown remote: "${read.value}"`);
+  }
+  if (cliDaemonHost === null) cliDaemonHost = resolved.host;
+  if (cliDaemonApiToken === null && resolved.token !== null) cliDaemonApiToken = resolved.token;
+  return read.lastConsumedIndex;
+}
+
+function readEqOrNextFlag(
+  argv: string[],
+  i: number,
+  flagEq: string,
+  flagWord: string,
+  missingMsg: string,
+): { value: string; lastConsumedIndex: number } | null {
+  const a = argv[i];
+  if (a === undefined) return null;
+  if (a.startsWith(flagEq)) {
+    const value = a.slice(flagEq.length);
+    if (value.length === 0 || value.startsWith("-")) {
+      throw new Error(missingMsg);
+    }
+    return { value, lastConsumedIndex: i };
+  }
+  if (a === flagWord) {
+    const v = argv[i + 1];
+    if (v === undefined || v.length === 0 || v.startsWith("-")) {
+      throw new Error(missingMsg);
+    }
+    return { value: v, lastConsumedIndex: i + 1 };
+  }
+  return null;
+}
+
+/**
+ * Removes `--host` / `--api-token` from argv before citty parses subcommands.
+ * Must run once at process startup (see `cli.ts`).
+ */
+export function consumeGlobalDaemonCliFlags(argv: string[]): string[] {
+  cliDaemonHost = null;
+  cliDaemonApiToken = null;
+  const out: string[] = [];
+
+  for (let i = 0; i < argv.length; i++) {
+    const a = argv[i];
+    if (a === undefined) continue;
+
+    const hostRead = readEqOrNextFlag(
+      argv,
+      i,
+      "--host=",
+      "--host",
+      "--host requires a non-empty value (e.g. 192.168.1.1:9800)",
+    );
+    if (hostRead !== null) {
+      cliDaemonHost = hostRead.value;
+      i = hostRead.lastConsumedIndex;
+      continue;
+    }
+
+    const tokenRead = readEqOrNextFlag(
+      argv,
+      i,
+      "--api-token=",
+      "--api-token",
+      "--api-token requires a value",
+    );
+    if (tokenRead !== null) {
+      cliDaemonApiToken = tokenRead.value.length > 0 ? tokenRead.value : null;
+      i = tokenRead.lastConsumedIndex;
+      continue;
+    }
+
+    const remoteResult = applyRemoteFlag(argv, i);
+    if (remoteResult !== null) {
+      i = remoteResult;
+      continue;
+    }
+
+    out.push(a);
+  }
+
+  return out;
+}
+
+export function isRemoteDaemonCli(): boolean {
+  return cliDaemonHost !== null && cliDaemonHost.length > 0;
+}
+
+export function getCliDaemonHost(): string | null {
+  return cliDaemonHost;
+}
+
+export function getCliDaemonApiToken(): string | null {
+  return cliDaemonApiToken;
+}

packages/cli/src/cli.ts

@@ -1,14 +1,17 @@
+import "@uncaged/nerve-daemon/experimental-warning-suppression.js";
+
 import { defineCommand, runMain } from "citty";
 
+import { consumeGlobalDaemonCliFlags } from "./cli-global.js";
+import { createCommand } from "./commands/create.js";
 import { daemonCommand } from "./commands/daemon.js";
 import { devCommand } from "./commands/dev.js";
 import { initCommand } from "./commands/init.js";
-import { logsCommand } from "./commands/logs.js";
+import { knowledgeCommand } from "./commands/knowledge.js";
+import { remoteCommand } from "./commands/remote.js";
 import { senseCommand } from "./commands/sense.js";
-import { daemonStartCommand } from "./commands/start.js";
-import { statusCommand } from "./commands/status.js";
-import { stopCommand } from "./commands/stop.js";
 import { storeCommand } from "./commands/store.js";
+import { threadCommand } from "./commands/thread.js";
 import { validateCommand } from "./commands/validate.js";
 import { workflowCommand } from "./commands/workflow.js";
 
@@ -35,21 +38,30 @@ function normalizeNerveArgv(argv: string[]): string[] {
 const main = defineCommand({
   meta: {
     name: "nerve",
-    description: "Nerve — an AI agent kernel",
+    description:
+      "Nerve — an AI agent kernel. Global options: --host <host:port> (remote HTTP), --api-token <secret> (Bearer auth).",
   },
   subCommands: {
     init: initCommand,
+    create: createCommand,
     daemon: daemonCommand,
     dev: devCommand,
-    start: daemonStartCommand,
-    stop: stopCommand,
-    status: statusCommand,
-    logs: logsCommand,
     validate: validateCommand,
+    knowledge: knowledgeCommand,
     sense: senseCommand,
     store: storeCommand,
+    remote: remoteCommand,
+    thread: threadCommand,
     workflow: workflowCommand,
   },
 });
 
-runMain(main, { rawArgs: normalizeNerveArgv(process.argv.slice(2)) });
+let cliArgv = process.argv.slice(2);
+try {
+  cliArgv = consumeGlobalDaemonCliFlags(cliArgv);
+} catch (e) {
+  const msg = e instanceof Error ? e.message : String(e);
+  process.stderr.write(`${msg}\n`);
+  process.exit(1);
+}
+runMain(main, { rawArgs: normalizeNerveArgv(cliArgv) });

packages/cli/src/commands/create.ts

@@ -0,0 +1,360 @@
+import { spawn } from "node:child_process";
+import { existsSync, mkdirSync, writeFileSync } from "node:fs";
+import { dirname, join } from "node:path";
+
+import { defineCommand } from "citty";
+
+import { getNerveRoot } from "../workspace.js";
+
+export const RESOURCE_NAME_RE = /^[a-z0-9][a-z0-9-]*[a-z0-9]$|^[a-z0-9]$/;
+
+export function validateResourceName(name: string, type: string): string | null {
+  if (name.length === 0) return `${type} name must not be empty.`;
+  if (name.length > 64) return `${type} name must be 64 characters or fewer.`;
+  if (!RESOURCE_NAME_RE.test(name))
+    return `${type} name must contain only lowercase letters, digits, and hyphens, and must not start or end with a hyphen.`;
+  return null;
+}
+
+export type WorkflowScaffoldFiles = {
+  indexTs: string;
+  roleMainIndexTs: string;
+  roleMainPromptMd: string;
+  packageJson: string;
+};
+
+export function buildWorkflowPackageJson(name: string): string {
+  return `${JSON.stringify(
+    {
+      name: `nerve-workflow-${name}`,
+      private: true,
+      type: "module",
+      scripts: {
+        build:
+          "esbuild index.ts --bundle --platform=node --format=esm --outdir=dist --packages=external",
+      },
+      devDependencies: {
+        esbuild: "^0.27.0",
+      },
+    },
+    null,
+    2,
+  )}\n`;
+}
+
+export function buildWorkflowScaffold(name: string): WorkflowScaffoldFiles {
+  return {
+    indexTs: buildWorkflowIndexTs(name),
+    roleMainIndexTs: buildWorkflowMainRoleIndexTs(name),
+    roleMainPromptMd: buildWorkflowMainRolePromptMd(name),
+    packageJson: buildWorkflowPackageJson(name),
+  };
+}
+
+function buildWorkflowIndexTs(name: string): string {
+  return `import type { WorkflowDefinition } from "@uncaged/nerve-core";
+import { END } from "@uncaged/nerve-core";
+
+import { mainRole } from "./roles/main/index.js";
+
+type MainMeta = Record<string, unknown>;
+
+const workflow: WorkflowDefinition<Record<"main", MainMeta>> = {
+  name: "${name}",
+  roles: {
+    main: mainRole,
+  },
+  moderator({ steps }) {
+    if (steps.length === 0) {
+      return "main";
+    }
+    return END;
+  },
+};
+
+export default workflow;
+`;
+}
+
+function buildWorkflowMainRoleIndexTs(name: string): string {
+  return `import type { RoleResult, StartStep, WorkflowMessage } from "@uncaged/nerve-core";
+
+/**
+ * Main role — implement LLM calls, scripts, HTTP, etc.
+ * Optional: align behavior with \`prompt.md\` in this directory.
+ */
+export async function mainRole(
+  start: StartStep,
+  messages: WorkflowMessage[],
+): Promise<RoleResult<Record<string, unknown>>> {
+  void start;
+  void messages;
+  // TODO: implement your role logic here
+  return {
+    content: "${name} started",
+    meta: {},
+  };
+}
+`;
+}
+
+function buildWorkflowMainRolePromptMd(name: string): string {
+  return `# ${name} — main role
+
+Starter template for this role's system or task instructions.
+
+The scaffolded \`index.ts\` returns a fixed content line; replace that with real logic
+and optionally load this file at runtime if you keep prompts outside code.
+`;
+}
+
+function senseIdToSqlTableName(id: string): string {
+  return id.replaceAll("-", "_");
+}
+
+function senseIdToSchemaExportName(id: string): string {
+  const parts = id.split("-");
+  return parts
+    .map((part, index) =>
+      index === 0 ? part : part.length === 0 ? "" : part.charAt(0).toUpperCase() + part.slice(1),
+    )
+    .join("");
+}
+
+export function buildSenseSchemaTs(senseId: string): string {
+  const table = senseIdToSqlTableName(senseId);
+  const exportName = senseIdToSchemaExportName(senseId);
+  return `import { integer, sqliteTable, text } from "drizzle-orm/sqlite-core";
+
+export const ${exportName} = sqliteTable("${table}", {
+  id: integer("id").primaryKey({ autoIncrement: true }),
+  ts: integer("ts").notNull(),
+  label: text("label").notNull(),
+});
+`;
+}
+
+export function buildSensePackageJson(name: string): string {
+  return `${JSON.stringify(
+    {
+      name: `nerve-sense-${name}`,
+      private: true,
+      type: "module",
+      scripts: {
+        build:
+          "esbuild src/index.ts --bundle --platform=node --format=esm --outdir=. --out-extension:.js=.js --packages=external",
+      },
+      devDependencies: {
+        esbuild: "^0.27.0",
+        "drizzle-orm": "*",
+      },
+    },
+    null,
+    2,
+  )}\n`;
+}
+
+export function buildSenseIndexTs(senseId: string): string {
+  const exportName = senseIdToSchemaExportName(senseId);
+  return `import type { LibSQLDatabase } from "drizzle-orm/libsql";
+
+import { ${exportName} } from "./schema.js";
+
+type SenseResult = {
+  signal: { label: string; ts: number };
+  workflow: null;
+} | null;
+
+/**
+ * ${senseId} — replace this stub with your sampling logic.
+ * Returns non-null to emit a signal, null to stay silent.
+ */
+export async function compute(
+  db: LibSQLDatabase,
+  _peers: Record<string, LibSQLDatabase>,
+  _options: { signal: AbortSignal },
+): Promise<SenseResult> {
+  void ${exportName};
+  return {
+    signal: {
+      label: "${senseId}",
+      ts: Date.now(),
+    },
+    workflow: null,
+  };
+}
+`;
+}
+
+export function buildSenseMigrationSql(senseId: string): string {
+  const table = senseIdToSqlTableName(senseId);
+  return `CREATE TABLE IF NOT EXISTS ${table} (
+  id    INTEGER PRIMARY KEY AUTOINCREMENT,
+  ts    INTEGER NOT NULL,
+  label TEXT    NOT NULL
+);
+`;
+}
+
+function writeFile(filePath: string, content: string): void {
+  mkdirSync(dirname(filePath), { recursive: true });
+  writeFileSync(filePath, content, "utf8");
+}
+
+function spawnAsync(cmd: string, args: string[], cwd: string): Promise<void> {
+  return new Promise<void>((resolve, reject) => {
+    const child = spawn(cmd, args, { cwd, stdio: "inherit" });
+    child.on("close", (code) => {
+      if (code === 0) resolve();
+      else reject(new Error(`${cmd} exited with code ${String(code)}`));
+    });
+    child.on("error", reject);
+  });
+}
+
+const createWorkflowCommand = defineCommand({
+  meta: {
+    name: "workflow",
+    description: "Scaffold a new workflow at ~/.uncaged-nerve/workflows/<name>/",
+  },
+  args: {
+    name: {
+      type: "positional",
+      description: "Workflow name (must match the key in nerve.yaml workflows section)",
+    },
+    force: {
+      type: "boolean",
+      description: "Overwrite if the workflow directory already exists",
+      default: false,
+    },
+  },
+  async run({ args }) {
+    const nerveRoot = getNerveRoot();
+    const workflowDir = join(nerveRoot, "workflows", args.name);
+
+    const nameError = validateResourceName(args.name, "Workflow");
+    if (nameError !== null) {
+      process.stderr.write(`❌ Invalid workflow name: ${nameError}\n`);
+      process.exit(1);
+    }
+
+    if (existsSync(workflowDir) && !args.force) {
+      process.stderr.write(
+        `⚠️ Workflow "${args.name}" already exists at ${workflowDir}. Use --force to overwrite.\n`,
+      );
+      process.exit(1);
+    }
+
+    mkdirSync(workflowDir, { recursive: true });
+    const scaffold = buildWorkflowScaffold(args.name);
+    writeFile(join(workflowDir, "package.json"), scaffold.packageJson);
+    writeFile(join(workflowDir, "index.ts"), scaffold.indexTs);
+    writeFile(join(workflowDir, "roles", "main", "index.ts"), scaffold.roleMainIndexTs);
+    writeFile(join(workflowDir, "roles", "main", "prompt.md"), scaffold.roleMainPromptMd);
+
+    process.stdout.write("✅ Workflow scaffolded:\n");
+    process.stdout.write(`   ${join(workflowDir, "package.json")}\n`);
+    process.stdout.write(`   ${join(workflowDir, "index.ts")}\n`);
+    process.stdout.write(`   ${join(workflowDir, "roles", "main", "index.ts")}\n`);
+    process.stdout.write(`   ${join(workflowDir, "roles", "main", "prompt.md")}\n`);
+    process.stdout.write("\n💡 Next steps:\n");
+    process.stdout.write(
+      `   1. In ${workflowDir}, run \`npm install\` then \`npm run build\` (bundles to dist/index.js).\n`,
+    );
+    process.stdout.write("   2. Add to nerve.yaml:\n");
+    process.stdout.write("         workflows:\n");
+    process.stdout.write(`           ${args.name}:\n`);
+    process.stdout.write("             concurrency: 1\n");
+    process.stdout.write("             overflow: drop\n");
+    process.stdout.write(
+      `   3. Edit ${join(workflowDir, "roles", "main", "index.ts")} (and optional prompt.md).\n`,
+    );
+    process.stdout.write(
+      `   4. Adjust moderator routing in ${join(workflowDir, "index.ts")} if you add roles.\n`,
+    );
+    process.stdout.write("   5. Run `nerve start` to launch the daemon.\n");
+  },
+});
+
+const createSenseCommand = defineCommand({
+  meta: {
+    name: "sense",
+    description: "Scaffold a new sense at ~/.uncaged-nerve/senses/<name>/",
+  },
+  args: {
+    name: {
+      type: "positional",
+      description: "Sense id (must match the key in nerve.yaml senses section)",
+    },
+    force: {
+      type: "boolean",
+      description: "Overwrite if the sense directory already exists",
+      default: false,
+    },
+  },
+  async run({ args }) {
+    const nerveRoot = getNerveRoot();
+    const senseDir = join(nerveRoot, "senses", args.name);
+
+    const nameError = validateResourceName(args.name, "Sense");
+    if (nameError !== null) {
+      process.stderr.write(`❌ Invalid sense name: ${nameError}\n`);
+      process.exit(1);
+    }
+
+    if (existsSync(senseDir) && !args.force) {
+      process.stderr.write(
+        `⚠️ Sense "${args.name}" already exists at ${senseDir}. Use --force to overwrite.\n`,
+      );
+      process.exit(1);
+    }
+
+    mkdirSync(join(senseDir, "src"), { recursive: true });
+    mkdirSync(join(senseDir, "migrations"), { recursive: true });
+    writeFile(join(senseDir, "package.json"), buildSensePackageJson(args.name));
+    writeFile(join(senseDir, "src", "index.ts"), buildSenseIndexTs(args.name));
+    writeFile(join(senseDir, "src", "schema.ts"), buildSenseSchemaTs(args.name));
+    writeFile(join(senseDir, "migrations", "0001_init.sql"), buildSenseMigrationSql(args.name));
+
+    process.stdout.write("✅ Sense scaffolded:\n");
+    process.stdout.write(`   ${join(senseDir, "package.json")}\n`);
+    process.stdout.write(`   ${join(senseDir, "src", "index.ts")}\n`);
+    process.stdout.write(`   ${join(senseDir, "src", "schema.ts")}\n`);
+    process.stdout.write(`   ${join(senseDir, "migrations", "0001_init.sql")}\n`);
+
+    process.stdout.write("\nInstalling sense dependencies and building…\n");
+    try {
+      await spawnAsync("pnpm", ["install", "--no-cache", "--ignore-workspace"], senseDir);
+      await spawnAsync("pnpm", ["run", "build"], senseDir);
+      process.stdout.write("✅ Build complete — index.js ready.\n");
+    } catch {
+      process.stdout.write(
+        `⚠️ Build failed. Run manually:\n   cd ${senseDir} && pnpm install --no-cache --ignore-workspace && pnpm run build\n`,
+      );
+    }
+
+    process.stdout.write("\n💡 Next steps:\n");
+    process.stdout.write("   1. Add to nerve.yaml under senses:\n");
+    process.stdout.write(`         ${args.name}:\n`);
+    process.stdout.write("           group: default\n");
+    process.stdout.write("           throttle: null\n");
+    process.stdout.write("           timeout: 10s\n");
+    process.stdout.write("           grace_period: null\n");
+    process.stdout.write(
+      `   2. Edit ${join(senseDir, "src", "index.ts")} to implement ${args.name}.\n`,
+    );
+    process.stdout.write(`   3. Re-run \`pnpm run build\` in ${senseDir} after edits.\n`);
+    process.stdout.write("   4. Run `nerve start` to launch the daemon.\n");
+  },
+});
+
+export const createCommand = defineCommand({
+  meta: {
+    name: "create",
+    description: "Scaffold a new workflow or sense in the Nerve workspace",
+  },
+  subCommands: {
+    workflow: createWorkflowCommand,
+    sense: createSenseCommand,
+  },
+});

packages/cli/src/commands/dev.ts

@@ -1,6 +1,9 @@
 import { defineCommand } from "citty";
 
-import { runForegroundKernelSession } from "../run-foreground-kernel.js";
+import {
+  type ForegroundSessionOptions,
+  runForegroundKernelSession,
+} from "../run-foreground-kernel.js";
 import { loadDaemonModule } from "../workspace-daemon.js";
 import { getNerveRoot } from "../workspace.js";
 
@@ -9,9 +12,25 @@ export const devCommand = defineCommand({
     name: "dev",
     description: "Run the nerve kernel in the foreground (development mode)",
   },
-  async run() {
+  args: {
+    port: {
+      type: "string",
+      description: "HTTP API port (overrides nerve.yaml api.port). Omit to use YAML / env only.",
+      default: "",
+    },
+  },
+  async run({ args }) {
     const nerveRoot = getNerveRoot();
     const { createKernel } = await loadDaemonModule(nerveRoot);
-    await runForegroundKernelSession(nerveRoot, createKernel);
+    let sessionOpts: ForegroundSessionOptions = {};
+    if (args.port.length > 0) {
+      const n = Number.parseInt(args.port, 10);
+      if (Number.isNaN(n) || n < 1 || n > 65_535) {
+        process.stderr.write(`❌ Invalid --port: ${args.port}\n`);
+        process.exit(1);
+      }
+      sessionOpts = { httpApiPortOverride: n };
+    }
+    await runForegroundKernelSession(nerveRoot, createKernel, sessionOpts);
   },
 });

packages/cli/src/commands/init.ts

@@ -14,13 +14,14 @@ senses:
     throttle: 5s
     timeout: 10s
     grace_period: null
-
-reflexes:
-  - kind: sense
-    sense: cpu-usage
     interval: 10s
 `;
 
+const PNPM_WORKSPACE_YAML = `packages:
+  - 'workflows/*'
+  - 'senses/*'
+`;
+
 const BIOME_JSON = `{
   "$schema": "https://biomejs.dev/schemas/1.9.0/schema.json",
   "formatter": {
@@ -46,28 +47,67 @@ const BIOME_JSON = `{
 }
 `;
 
-const PACKAGE_JSON = `{
-  "name": "my-nerve-workspace",
-  "version": "0.0.1",
-  "private": true,
-  "type": "module",
-  "dependencies": {
-    "@uncaged/nerve-core": "latest",
-    "@uncaged/nerve-daemon": "latest",
-    "drizzle-orm": "latest"
+const PACKAGE_JSON = `${JSON.stringify(
+  {
+    name: "my-nerve-workspace",
+    version: "0.0.1",
+    private: true,
+    type: "module",
+    scripts: {
+      build: "pnpm -r build",
+    },
+    dependencies: {
+      "@uncaged/nerve-core": "latest",
+      "@uncaged/nerve-daemon": "latest",
+      "@uncaged/nerve-skills": "latest",
+      "drizzle-orm": "latest",
+    },
+    devDependencies: {
+      "@biomejs/biome": "latest",
+      "drizzle-kit": "latest",
+    },
+    pnpm: {
+      onlyBuiltDependencies: ["esbuild"],
+    },
   },
-  "devDependencies": {
-    "@biomejs/biome": "latest",
-    "drizzle-kit": "latest"
-  },
-  "pnpm": {
-    "onlyBuiltDependencies": ["esbuild"]
-  }
-}
-`;
+  null,
+  2,
+)}\n`;
 
 const GITIGNORE = `data/
+logs/
+nerve.pid
 node_modules/
+knowledge.db
+`;
+
+const NERVE_SKILLS_MDC = `---
+description: >-
+  Nerve skills package — where bundled Agent Skills live in this workspace and how to use them
+alwaysApply: true
+---
+
+# Nerve skills (\`@uncaged/nerve-skills\`)
+
+This workspace lists **@uncaged/nerve-skills** in \`package.json\`. It ships **Agent Skills** (one directory per skill, each with a \`SKILL.md\`) for Nerve development and related tasks.
+
+## After install
+
+Run your package manager in this workspace (e.g. \`pnpm install\`, \`npm install\` — whatever \`nerve init\` used). Then skills are on disk at:
+
+- \`node_modules/@uncaged/nerve-skills/<skill-id>/SKILL.md\`
+
+Example (current catalog):
+
+- **nerve-dev** — Nerve architecture, CLI, sense/workflow patterns, \`nerve.yaml\`, and conventions: read \`node_modules/@uncaged/nerve-skills/nerve-dev/SKILL.md\`.
+
+## How to use in an agent
+
+1. For tasks that match a skill’s **description** (in the \`SKILL.md\` frontmatter), open that \`SKILL.md\` and follow its structure and checklists.
+2. Prefer the skill as the **source of truth** for Nerve-specific conventions over generic assumptions.
+3. If the catalog grows, new skills appear as new sibling directories under \`node_modules/@uncaged/nerve-skills/\`.
+
+Do not commit \`node_modules\`; the dependency is the supported way to get and update skills to match \`@uncaged/nerve-skills\` on npm.
 `;
 
 const execFileAsync = promisify(execFile);
@@ -82,9 +122,14 @@ export const cpuUsage = sqliteTable("cpu_usage", {
 });
 `;
 
-const CPU_INDEX_JS = `import { cpus } from "node:os";
+const CPU_INDEX_TS = `import { cpus } from "node:os";
 
-export async function compute() {
+type SenseResult = {
+  signal: { model: string; loadPercent: number; ts: number };
+  workflow: null;
+};
+
+export async function compute(): Promise<SenseResult> {
   const cpuList = cpus();
 
   let totalIdle = 0;
@@ -99,13 +144,34 @@ export async function compute() {
   const loadPercent = totalTick === 0 ? 0 : ((totalTick - totalIdle) / totalTick) * 100;
 
   return {
-    model: cpuList[0]?.model ?? "unknown",
-    loadPercent: Math.round(loadPercent * 100) / 100,
-    ts: Date.now(),
+    signal: {
+      model: cpuList[0]?.model ?? "unknown",
+      loadPercent: Math.round(loadPercent * 100) / 100,
+      ts: Date.now(),
+    },
+    workflow: null,
   };
 }
 `;
 
+const CPU_SENSE_PACKAGE_JSON = `${JSON.stringify(
+  {
+    name: "nerve-sense-cpu-usage",
+    private: true,
+    type: "module",
+    scripts: {
+      build:
+        "esbuild src/index.ts --bundle --platform=node --format=esm --outdir=. --out-extension:.js=.js --packages=external",
+    },
+    devDependencies: {
+      esbuild: "^0.27.0",
+      "drizzle-orm": "*",
+    },
+  },
+  null,
+  2,
+)}\n`;
+
 const CPU_MIGRATION_SQL = `CREATE TABLE IF NOT EXISTS cpu_usage (
   id          INTEGER PRIMARY KEY AUTOINCREMENT,
   ts          INTEGER NOT NULL,
@@ -143,90 +209,6 @@ async function detectPackageManager(): Promise<{ cmd: string; installArgs: strin
   return { cmd: "npm", installArgs: ["install"] };
 }
 
-export const WORKFLOW_NAME_RE = /^[a-z0-9][a-z0-9-]*[a-z0-9]$|^[a-z0-9]$/;
-
-export function validateWorkflowName(name: string): string | null {
-  if (name.length === 0) return "Workflow name must not be empty.";
-  if (name.length > 64) return "Workflow name must be 64 characters or fewer.";
-  if (!WORKFLOW_NAME_RE.test(name))
-    return "Workflow name must contain only lowercase letters, digits, and hyphens, and must not start or end with a hyphen.";
-  return null;
-}
-
-export function buildWorkflowTemplate(name: string): string {
-  return `import type { WorkflowDefinition } from "@uncaged/nerve-daemon";
-
-const workflow: WorkflowDefinition = {
-  roles: {
-    main: {
-      async execute(prompt, ctx) {
-        ctx.log("${name} started");
-        // TODO: implement your role logic here
-        return { type: "done" };
-      },
-    },
-  },
-
-  moderate(thread, event) {
-    if (event.type === "thread_start") {
-      return { role: "main", prompt: {} };
-    }
-    return null; // workflow complete
-  },
-};
-
-export default workflow;
-`;
-}
-
-const initWorkflowCommand = defineCommand({
-  meta: {
-    name: "workflow",
-    description: "Scaffold a new workflow template in ~/.uncaged-nerve/workflows/<name>/",
-  },
-  args: {
-    name: {
-      type: "positional",
-      description: "Workflow name (must match the key in nerve.yaml workflows section)",
-    },
-    force: {
-      type: "boolean",
-      description: "Overwrite if the workflow directory already exists",
-      default: false,
-    },
-  },
-  async run({ args }) {
-    const nerveRoot = getNerveRoot();
-    const workflowDir = join(nerveRoot, "workflows", args.name);
-
-    const nameError = validateWorkflowName(args.name);
-    if (nameError !== null) {
-      process.stderr.write(`❌ Invalid workflow name: ${nameError}\n`);
-      process.exit(1);
-    }
-
-    if (existsSync(workflowDir) && !args.force) {
-      process.stderr.write(
-        `⚠️ Workflow "${args.name}" already exists at ${workflowDir}. Use --force to overwrite.\n`,
-      );
-      process.exit(1);
-    }
-
-    mkdirSync(workflowDir, { recursive: true });
-    writeFile(join(workflowDir, "index.ts"), buildWorkflowTemplate(args.name));
-
-    process.stdout.write(`✅ Workflow scaffolded: ${workflowDir}/index.ts\n`);
-    process.stdout.write("\n💡 Next steps:\n");
-    process.stdout.write("   1. Add to nerve.yaml:\n");
-    process.stdout.write("         workflows:\n");
-    process.stdout.write(`           ${args.name}:\n`);
-    process.stdout.write("             concurrency: 1\n");
-    process.stdout.write("             overflow: drop\n");
-    process.stdout.write(`   2. Edit ${workflowDir}/index.ts to implement your roles.\n`);
-    process.stdout.write("   3. Run `nerve start` to launch the daemon.\n");
-  },
-});
-
 const initWorkspaceCommand = defineCommand({
   meta: {
     name: "workspace",
@@ -238,9 +220,14 @@ const initWorkspaceCommand = defineCommand({
       description: "Reinitialize even if workspace already exists (preserves data/)",
       default: false,
     },
+    "skip-install": {
+      type: "boolean",
+      description: "Skip dependency installation (for testing or offline use)",
+      default: false,
+    },
   },
   async run({ args }) {
-    await runInitWorkspace(args.force);
+    await runInitWorkspace(args.force, args["skip-install"]);
   },
 });
 
@@ -332,7 +319,7 @@ async function runInitFromGit(url: string): Promise<void> {
   );
 }
 
-async function runInitWorkspace(force: boolean): Promise<void> {
+async function runInitWorkspace(force: boolean, skipInstall = false): Promise<void> {
   const nerveRoot = getNerveRoot();
 
   if (existsSync(nerveRoot) && !force) {
@@ -342,34 +329,47 @@ async function runInitWorkspace(force: boolean): Promise<void> {
 
   mkdirSync(join(nerveRoot, "data"), { recursive: true });
   mkdirSync(join(nerveRoot, "data", "senses"), { recursive: true });
+  mkdirSync(join(nerveRoot, "senses", "cpu-usage", "src"), { recursive: true });
   mkdirSync(join(nerveRoot, "senses", "cpu-usage", "migrations"), { recursive: true });
 
   writeFile(join(nerveRoot, "nerve.yaml"), NERVE_YAML);
   writeFile(join(nerveRoot, "package.json"), PACKAGE_JSON);
+  writeFile(join(nerveRoot, "pnpm-workspace.yaml"), PNPM_WORKSPACE_YAML);
   writeFile(join(nerveRoot, "biome.json"), BIOME_JSON);
   writeFile(join(nerveRoot, ".gitignore"), GITIGNORE);
-  writeFile(join(nerveRoot, "senses", "cpu-usage", "schema.ts"), CPU_SCHEMA_TS);
-  writeFile(join(nerveRoot, "senses", "cpu-usage", "index.js"), CPU_INDEX_JS);
+  writeFile(join(nerveRoot, "senses", "cpu-usage", "package.json"), CPU_SENSE_PACKAGE_JSON);
+  writeFile(join(nerveRoot, "senses", "cpu-usage", "src", "index.ts"), CPU_INDEX_TS);
+  writeFile(join(nerveRoot, "senses", "cpu-usage", "src", "schema.ts"), CPU_SCHEMA_TS);
   writeFile(
     join(nerveRoot, "senses", "cpu-usage", "migrations", "0001_init.sql"),
     CPU_MIGRATION_SQL,
   );
+  writeFile(join(nerveRoot, ".cursor", "rules", "nerve-skills.mdc"), NERVE_SKILLS_MDC);
 
-  process.stdout.write("Installing dependencies…\n");
-  const { cmd, installArgs } = await detectPackageManager();
-  try {
-    await runCommand(cmd, installArgs, nerveRoot);
-  } catch {
-    process.stdout.write(
-      `⚠️ Install failed. Try manually:\n   cd ${nerveRoot} && ${cmd} ${installArgs.join(" ")}\n`,
-    );
-  }
+  if (!skipInstall) {
+    process.stdout.write("Installing dependencies…\n");
+    const { cmd, installArgs } = await detectPackageManager();
+    try {
+      await runCommand(cmd, installArgs, nerveRoot);
+    } catch {
+      process.stdout.write(
+        `⚠️ Install failed. Try manually:\n   cd ${nerveRoot} && ${cmd} ${installArgs.join(" ")}\n`,
+      );
+    }
 
-  if (!(await verifyNodeSqlite())) {
-    process.stdout.write(
-      "⚠️ Built-in SQLite (node:sqlite) is not available in this Node.js build. " +
-        "The daemon requires Node.js 22.5 or newer with SQLite enabled.\n",
-    );
+    process.stdout.write("Building senses…\n");
+    try {
+      await runCommand("pnpm", ["run", "build"], nerveRoot);
+    } catch {
+      process.stdout.write(`⚠️ Build failed. Try manually:\n   cd ${nerveRoot} && pnpm run build\n`);
+    }
+
+    if (!(await verifyNodeSqlite())) {
+      process.stdout.write(
+        "⚠️ Built-in SQLite (node:sqlite) is not available in this Node.js build. " +
+          "The daemon requires Node.js 22.5 or newer with SQLite enabled.\n",
+      );
+    }
   }
 
   if (!existsSync(join(nerveRoot, ".git"))) {
@@ -391,7 +391,7 @@ export const initCommand = defineCommand({
   meta: {
     name: "init",
     description:
-      "Initialize workspace (nerve init), clone from git (nerve init --from <url>), or scaffold templates (nerve init workflow <name>)",
+      "Initialize workspace (nerve init), clone from git (nerve init --from <url>), or reinit workspace (nerve init workspace)",
   },
   args: {
     force: {
@@ -404,9 +404,13 @@ export const initCommand = defineCommand({
       description: "Clone an existing git repo into ~/.uncaged-nerve instead of scaffolding",
       required: false,
     },
+    "skip-install": {
+      type: "boolean",
+      description: "Skip dependency installation (for testing or offline use)",
+      default: false,
+    },
   },
   subCommands: {
-    workflow: initWorkflowCommand,
     workspace: initWorkspaceCommand,
   },
   async run({ args }) {
@@ -414,6 +418,6 @@ export const initCommand = defineCommand({
       await runInitFromGit(String(args.from));
       return;
     }
-    await runInitWorkspace(args.force);
+    await runInitWorkspace(args.force, args["skip-install"]);
   },
 });

packages/cli/src/commands/knowledge-query-run.ts

@@ -0,0 +1,79 @@
+import { existsSync } from "node:fs";
+import { resolve } from "node:path";
+
+import { KNOWLEDGE_DB } from "../knowledge/paths.js";
+import { queryKnowledgeGlobal, queryKnowledgeRepo } from "../knowledge/query.js";
+import { listRegisteredKnowledgeRoots } from "../knowledge/registry.js";
+import { findKnowledgeRepoRoot } from "../knowledge/repo-root.js";
+
+const DEFAULT_LIMIT = 10;
+
+export function parseKnowledgeQueryLimit(raw: string | undefined): number {
+  if (raw === undefined || raw.trim().length === 0) {
+    return DEFAULT_LIMIT;
+  }
+  const n = Number.parseInt(raw, 10);
+  return Number.isFinite(n) && n > 0 ? n : DEFAULT_LIMIT;
+}
+
+export async function runKnowledgeQueryGlobal(queryText: string, limit: number): Promise<void> {
+  const roots = listRegisteredKnowledgeRoots();
+  if (roots.length === 0) {
+    process.stderr.write(
+      "❌ No registered repos — run `nerve knowledge sync` in each repo first.\n",
+    );
+    process.exit(1);
+  }
+  const hits = await queryKnowledgeGlobal(roots, KNOWLEDGE_DB, queryText, limit);
+  if (hits.length === 0) {
+    process.stdout.write("No results.\n");
+    return;
+  }
+  for (let i = 0; i < hits.length; i++) {
+    const h = hits[i];
+    if (h === undefined) continue;
+    const prefix = h.repoRoot !== null ? `[${h.repoRoot}] ` : "";
+    process.stdout.write(
+      `${String(i + 1)}. score=${h.score.toFixed(4)} ${prefix}${h.path} (${h.slug})\n${h.text}\n---\n`,
+    );
+  }
+}
+
+export async function runKnowledgeQueryScoped(
+  repoFlag: string | undefined,
+  queryText: string,
+  limit: number,
+): Promise<void> {
+  let repoRoot: string | null = null;
+  if (repoFlag !== undefined && String(repoFlag).trim().length > 0) {
+    repoRoot = resolve(String(repoFlag).trim());
+  } else {
+    repoRoot = findKnowledgeRepoRoot(process.cwd());
+  }
+
+  if (repoRoot === null) {
+    process.stderr.write("❌ No knowledge.yaml found — use -r <path> or run from a repo root.\n");
+    process.exit(1);
+  }
+
+  const dbPath = `${repoRoot}/${KNOWLEDGE_DB}`;
+  if (!existsSync(dbPath)) {
+    process.stderr.write(
+      `❌ No ${KNOWLEDGE_DB} in ${repoRoot} — run \`nerve knowledge sync\` first.\n`,
+    );
+    process.exit(1);
+  }
+
+  const hits = await queryKnowledgeRepo(repoRoot, dbPath, queryText, limit);
+  if (hits.length === 0) {
+    process.stdout.write("No results.\n");
+    return;
+  }
+  for (let i = 0; i < hits.length; i++) {
+    const h = hits[i];
+    if (h === undefined) continue;
+    process.stdout.write(
+      `${String(i + 1)}. score=${h.score.toFixed(4)} ${h.path} (${h.slug})\n${h.text}\n---\n`,
+    );
+  }
+}

packages/cli/src/commands/knowledge.ts

@@ -0,0 +1,93 @@
+import { defineCommand } from "citty";
+
+import { knowledgeQueryScopeConflictMessage } from "../knowledge/query-scope.js";
+import { findKnowledgeRepoRoot } from "../knowledge/repo-root.js";
+import { runKnowledgeSync } from "../knowledge/sync.js";
+import {
+  parseKnowledgeQueryLimit,
+  runKnowledgeQueryGlobal,
+  runKnowledgeQueryScoped,
+} from "./knowledge-query-run.js";
+
+const syncCommand = defineCommand({
+  meta: {
+    name: "sync",
+    description: "Chunk matching files from knowledge.yaml and rebuild knowledge.db",
+  },
+  async run() {
+    const repoRoot = findKnowledgeRepoRoot(process.cwd());
+    if (repoRoot === null) {
+      process.stderr.write(
+        "❌ No knowledge.yaml found — run from a repo that contains knowledge.yaml.\n",
+      );
+      process.exit(1);
+    }
+    try {
+      const result = await runKnowledgeSync(repoRoot);
+      process.stdout.write(
+        `✅ Indexed ${String(result.filesIndexed)} file(s), ${String(result.chunksWritten)} chunk(s) → ${result.dbPath}\n`,
+      );
+    } catch (e) {
+      const msg = e instanceof Error ? e.message : String(e);
+      process.stderr.write(`❌ knowledge sync failed: ${msg}\n`);
+      process.exit(1);
+    }
+  },
+});
+
+const queryCommand = defineCommand({
+  meta: {
+    name: "query",
+    description: "Search indexed knowledge (word overlap placeholder until embeddings)",
+  },
+  args: {
+    query: {
+      type: "positional",
+      required: true,
+      description: "Search text",
+    },
+    repo: {
+      type: "string",
+      description: "Use knowledge.db from another repo root (--repo /path)",
+      required: false,
+    },
+    g: {
+      type: "boolean",
+      description: "Search across all repos registered via prior sync",
+      default: false,
+    },
+    limit: {
+      type: "string",
+      description: "Max hits (default 10)",
+      required: false,
+    },
+  },
+  async run({ args }) {
+    const conflict = knowledgeQueryScopeConflictMessage(args.repo, args.g);
+    if (conflict !== null) {
+      process.stderr.write(`${conflict}\n`);
+      process.exit(1);
+    }
+
+    const queryText = args.query;
+    const limit = parseKnowledgeQueryLimit(args.limit);
+
+    if (args.g) {
+      await runKnowledgeQueryGlobal(queryText, limit);
+      return;
+    }
+
+    await runKnowledgeQueryScoped(args.repo as string, queryText, limit);
+  },
+});
+
+export const knowledgeCommand = defineCommand({
+  meta: {
+    name: "knowledge",
+    description: "Project knowledge index (knowledge.yaml + knowledge.db, RFC-003)",
+  },
+  subCommands: {
+    sync: syncCommand,
+    query: queryCommand,
+  },
+});

packages/cli/src/commands/remote.ts

@@ -0,0 +1,160 @@
+import { defineCommand } from "citty";
+import { loadRemotes, resolveRemote, saveRemotes } from "../remotes.js";
+
+const remoteAddCommand = defineCommand({
+  meta: { name: "add", description: "Add a named remote" },
+  args: {
+    name: { type: "positional", description: "Remote name" },
+    host: { type: "positional", description: "host:port" },
+    token: { type: "string", description: "API token", default: "" },
+  },
+  run({ args }) {
+    const config = loadRemotes();
+    if (config.remotes[args.name] !== undefined) {
+      process.stderr.write(`Remote "${args.name}" already exists.\n`);
+      process.exit(1);
+    }
+    config.remotes[args.name] = {
+      host: args.host,
+      token: args.token.length > 0 ? args.token : null,
+    };
+    saveRemotes(config);
+    process.stdout.write(`Added remote "${args.name}" → ${args.host}\n`);
+  },
+});
+
+const remoteListCommand = defineCommand({
+  meta: { name: "list", description: "List all remotes" },
+  run() {
+    const config = loadRemotes();
+    const names = Object.keys(config.remotes);
+    if (names.length === 0) {
+      process.stdout.write("No remotes configured.\n");
+      return;
+    }
+    for (const name of names) {
+      const entry = config.remotes[name];
+      if (entry === undefined) continue;
+      const def = config.default === name ? " (default)" : "";
+      const tok = entry.token !== null ? " token=***" : "";
+      process.stdout.write(`${name}\t${entry.host}${tok}${def}\n`);
+    }
+  },
+});
+
+const remoteShowCommand = defineCommand({
+  meta: { name: "show", description: "Show remote details" },
+  args: {
+    name: { type: "positional", description: "Remote name" },
+  },
+  run({ args }) {
+    const entry = resolveRemote(args.name);
+    if (entry === null) {
+      process.stderr.write(`Remote "${args.name}" not found.\n`);
+      process.exit(1);
+    }
+    process.stdout.write(`name:  ${args.name}\n`);
+    process.stdout.write(`host:  ${entry.host}\n`);
+    process.stdout.write(`token: ${entry.token !== null ? "***" : "(none)"}\n`);
+  },
+});
+
+const remoteSetUrlCommand = defineCommand({
+  meta: { name: "set-url", description: "Update remote host" },
+  args: {
+    name: { type: "positional", description: "Remote name" },
+    host: { type: "positional", description: "New host:port" },
+  },
+  run({ args }) {
+    const config = loadRemotes();
+    const entry = config.remotes[args.name];
+    if (entry === undefined) {
+      process.stderr.write(`Remote "${args.name}" not found.\n`);
+      process.exit(1);
+    }
+    entry.host = args.host;
+    saveRemotes(config);
+    process.stdout.write(`Updated "${args.name}" → ${args.host}\n`);
+  },
+});
+
+const remoteSetTokenCommand = defineCommand({
+  meta: { name: "set-token", description: "Update remote token" },
+  args: {
+    name: { type: "positional", description: "Remote name" },
+    token: { type: "positional", description: "New token" },
+  },
+  run({ args }) {
+    const config = loadRemotes();
+    const entry = config.remotes[args.name];
+    if (entry === undefined) {
+      process.stderr.write(`Remote "${args.name}" not found.\n`);
+      process.exit(1);
+    }
+    entry.token = args.token;
+    saveRemotes(config);
+    process.stdout.write(`Updated token for "${args.name}".\n`);
+  },
+});
+
+const remoteRemoveCommand = defineCommand({
+  meta: { name: "remove", description: "Remove a remote" },
+  args: {
+    name: { type: "positional", description: "Remote name" },
+  },
+  run({ args }) {
+    const config = loadRemotes();
+    if (config.remotes[args.name] === undefined) {
+      process.stderr.write(`Remote "${args.name}" not found.\n`);
+      process.exit(1);
+    }
+    delete config.remotes[args.name];
+    if (config.default === args.name) {
+      config.default = null;
+    }
+    saveRemotes(config);
+    process.stdout.write(`Removed remote "${args.name}".\n`);
+  },
+});
+
+const remoteDefaultCommand = defineCommand({
+  meta: { name: "default", description: "Set or show default remote" },
+  args: {
+    name: {
+      type: "positional",
+      description: "Remote name (omit to show current)",
+      required: false,
+    },
+  },
+  run({ args }) {
+    const config = loadRemotes();
+    if (!args.name || args.name.length === 0) {
+      if (config.default !== null) {
+        process.stdout.write(`${config.default}\n`);
+      } else {
+        process.stdout.write("No default remote set.\n");
+      }
+      return;
+    }
+    if (config.remotes[args.name] === undefined) {
+      process.stderr.write(`Remote "${args.name}" not found.\n`);
+      process.exit(1);
+    }
+    config.default = args.name;
+    saveRemotes(config);
+    process.stdout.write(`Default remote set to "${args.name}".\n`);
+  },
+});
+
+export const remoteCommand = defineCommand({
+  meta: { name: "remote", description: "Manage named remote connections" },
+  subCommands: {
+    add: remoteAddCommand,
+    list: remoteListCommand,
+    show: remoteShowCommand,
+    "set-url": remoteSetUrlCommand,
+    "set-token": remoteSetTokenCommand,
+    remove: remoteRemoveCommand,
+    default: remoteDefaultCommand,
+  },
+});

packages/cli/src/commands/sense.ts

@@ -2,10 +2,16 @@ import { readFileSync } from "node:fs";
 import { join } from "node:path";
 import type { DatabaseSync } from "node:sqlite";
 
-import { type SenseInfo, isPlainRecord, parseNerveConfig } from "@uncaged/nerve-core";
+import {
+  type SenseInfo,
+  isPlainRecord,
+  parseNerveConfig,
+  senseTriggerLabels,
+} from "@uncaged/nerve-core";
 import { defineCommand } from "citty";
 
-import { listSensesViaDaemon, triggerSenseViaDaemon } from "../daemon-client.js";
+import { isRemoteDaemonCli } from "../cli-global.js";
+import { resolveDaemonTransport } from "../daemon-client.js";
 import {
   defaultPreviewSql,
   formatRowsAsAlignedTable,
@@ -14,7 +20,7 @@ import {
   parseSenseQueryArgs,
   pickDefaultPreviewTable,
 } from "../sense-sqlite.js";
-import { getNerveRoot, getSocketPath, isRunning } from "../workspace.js";
+import { getNerveRoot, isRunning } from "../workspace.js";
 
 // ---------------------------------------------------------------------------
 // Formatting helpers (exported for tests)
@@ -43,6 +49,9 @@ export function formatSenseList(senses: SenseInfo[]): string {
     lines.push(`    group:    ${s.group}\n`);
     lines.push(`    throttle: ${formatDuration(s.throttle)}\n`);
     lines.push(`    timeout:  ${formatDuration(s.timeout)}\n`);
+    lines.push(
+      `    trigger schedule: ${s.triggers.length > 0 ? s.triggers.join("; ") : "(none)"}\n`,
+    );
     const lastSignal =
       s.lastSignalTimestamp !== null ? new Date(s.lastSignalTimestamp).toISOString() : "(never)";
     lines.push(`    last signal: ${lastSignal}\n`);
@@ -60,11 +69,13 @@ export function sensesFromConfig(configPath: string): SenseInfo[] {
   }
   const result = parseNerveConfig(raw);
   if (!result.ok) return [];
-  return Object.entries(result.value.senses).map(([name, cfg]) => ({
+  const { senses } = result.value;
+  return Object.entries(senses).map(([name, cfg]) => ({
     name,
     group: cfg.group,
     throttle: cfg.throttle,
     timeout: cfg.timeout,
+    triggers: senseTriggerLabels(name, senses),
     lastSignalTimestamp: null,
   }));
 }
@@ -79,7 +90,7 @@ const senseListCommand = defineCommand({
     description: "List all registered senses and their status",
   },
   async run() {
-    if (!isRunning()) {
+    if (!isRemoteDaemonCli() && !isRunning()) {
       process.stderr.write(
         "⚠️  Daemon is not running — showing static config only (no last signal time).\n\n",
       );
@@ -89,22 +100,17 @@ const senseListCommand = defineCommand({
       return;
     }
 
-    const socketPath = getSocketPath();
-    let response: { ok: true; senses: SenseInfo[] } | { ok: false; error: string };
+    const transport = resolveDaemonTransport();
+    let senses: SenseInfo[];
     try {
-      response = await listSensesViaDaemon(socketPath);
+      senses = await transport.listSenses();
     } catch (e) {
       const msg = e instanceof Error ? e.message : String(e);
       process.stderr.write(`❌ Failed to contact daemon: ${msg}\n`);
       process.exit(1);
     }
 
-    if (!response.ok) {
-      process.stderr.write(`❌ Daemon error: ${response.error}\n`);
-      process.exit(1);
-    }
-
-    process.stdout.write(formatSenseList(response.senses));
+    process.stdout.write(formatSenseList(senses));
   },
 });
 
@@ -124,15 +130,15 @@ const senseTriggerCommand = defineCommand({
     },
   },
   async run({ args }) {
-    if (!isRunning()) {
+    if (!isRemoteDaemonCli() && !isRunning()) {
       process.stderr.write("❌ Nerve daemon is not running. Start it with `nerve start`.\n");
       process.exit(1);
     }
 
-    const socketPath = getSocketPath();
+    const transport = resolveDaemonTransport();
     let response: { ok: true } | { ok: false; error: string };
     try {
-      response = await triggerSenseViaDaemon(socketPath, args.name);
+      response = await transport.triggerSense(args.name);
     } catch (e) {
       const msg = e instanceof Error ? e.message : String(e);
       process.stderr.write(`❌ Failed to contact daemon: ${msg}\n`);
@@ -201,7 +207,7 @@ const senseQueryCommand = defineCommand({
   meta: {
     name: "query",
     description:
-      "Run a read-only SQL query against a sense database (default: last 10 rows of the first data table). Pass optional SQL after the sense name; multiple words are joined.",
+      'Run a read-only SQL query against a sense database (default: last 10 rows of the first data table). Pass optional SQL after the sense name, or use --sql "…".',
   },
   args: {
     name: {

packages/cli/src/commands/start.ts

@@ -1,9 +1,10 @@
 import { spawn } from "node:child_process";
-import { createWriteStream, existsSync } from "node:fs";
+import { createWriteStream, existsSync, readFileSync } from "node:fs";
 import { mkdir } from "node:fs/promises";
 import { dirname, join } from "node:path";
 import { fileURLToPath } from "node:url";
 
+import { parseNerveConfig } from "@uncaged/nerve-core";
 import { defineCommand } from "citty";
 
 import {
@@ -56,7 +57,7 @@ function daemonBootstrapScript(): string {
   );
 }
 
-async function runDaemon(nerveRoot: string): Promise<void> {
+async function runDaemon(nerveRoot: string, cliHttpPort: number | null): Promise<void> {
   if (isRunning()) {
     const pid = readPidFile();
     process.stderr.write(`⚠️ Nerve daemon is already running (pid ${pid}).\n`);
@@ -74,12 +75,27 @@ async function runDaemon(nerveRoot: string): Promise<void> {
 
   const bootstrapPath = daemonBootstrapScript();
 
+  const configPath = join(nerveRoot, "nerve.yaml");
+  let yamlApiPort: number | null = null;
+  try {
+    const raw = readFileSync(configPath, "utf8");
+    const parsed = parseNerveConfig(raw);
+    if (parsed.ok) yamlApiPort = parsed.value.api.port;
+  } catch {
+    // kernel bootstrap will surface a clearer error if config is missing
+  }
+  const resolvedHttpPort = cliHttpPort ?? yamlApiPort;
+  const env: NodeJS.ProcessEnv = { ...process.env, NERVE_ROOT: nerveRoot };
+  if (resolvedHttpPort !== null && resolvedHttpPort > 0) {
+    env.NERVE_API_PORT = String(resolvedHttpPort);
+  }
+
   // After `open`, file-backed WriteStream has a numeric OS fd for spawn stdio; `@types/node` omits `fd` on this WriteStream alias.
   const logFd = (logStream as unknown as { fd: number }).fd;
-  const child = spawn(process.execPath, [bootstrapPath], {
+  const child = spawn(process.execPath, ["--disable-warning=ExperimentalWarning", bootstrapPath], {
     detached: true,
     stdio: ["ignore", logFd, logFd],
-    env: { ...process.env, NERVE_ROOT: nerveRoot },
+    env,
     cwd: nerveRoot,
   });
 
@@ -109,8 +125,8 @@ async function runDaemon(nerveRoot: string): Promise<void> {
 }
 
 /** Background daemon only — use `nerve dev` for foreground mode. */
-export async function runDaemonStartCommand(): Promise<void> {
-  await runDaemon(getNerveRoot());
+export async function runDaemonStartCommand(cliHttpPort: number | null = null): Promise<void> {
+  await runDaemon(getNerveRoot(), cliHttpPort);
 }
 
 export const daemonStartCommand = defineCommand({
@@ -118,7 +134,23 @@ export const daemonStartCommand = defineCommand({
     name: "start",
     description: "Start the nerve daemon in the background",
   },
-  async run() {
-    await runDaemonStartCommand();
+  args: {
+    port: {
+      type: "string",
+      description: "HTTP API port (overrides nerve.yaml api.port). Omit to use YAML / env only.",
+      default: "",
+    },
+  },
+  async run({ args }) {
+    let cliHttpPort: number | null = null;
+    if (args.port.length > 0) {
+      const n = Number.parseInt(args.port, 10);
+      if (Number.isNaN(n) || n < 1 || n > 65_535) {
+        process.stderr.write(`❌ Invalid --port: ${args.port}\n`);
+        process.exit(1);
+      }
+      cliHttpPort = n;
+    }
+    await runDaemonStartCommand(cliHttpPort);
   },
 });

packages/cli/src/commands/status.ts

@@ -4,6 +4,8 @@ import { join } from "node:path";
 import { parseNerveConfig } from "@uncaged/nerve-core";
 import { defineCommand } from "citty";
 
+import { isRemoteDaemonCli } from "../cli-global.js";
+import { resolveDaemonTransport } from "../daemon-client.js";
 import { getNerveRoot, getPidPath, isRunning, readPidFile } from "../workspace.js";
 
 function formatUptime(ms: number): string {
@@ -42,6 +44,23 @@ export const statusCommand = defineCommand({
     description: "Show nerve daemon status",
   },
   async run() {
+    if (isRemoteDaemonCli()) {
+      const transport = resolveDaemonTransport();
+      try {
+        const health = await transport.health();
+        process.stdout.write("✅ Nerve daemon is reachable (remote HTTP).\n");
+        process.stdout.write(`   hostname: ${health.hostname}\n`);
+        process.stdout.write(`   version:  ${health.version}\n`);
+        process.stdout.write(`   uptime:   ${formatUptime(health.uptime * 1000)}\n`);
+        process.stdout.write(`   started:  ${health.startedAt}\n`);
+      } catch (e) {
+        const msg = e instanceof Error ? e.message : String(e);
+        process.stderr.write(`❌ Cannot reach remote daemon: ${msg}\n`);
+        process.exit(1);
+      }
+      return;
+    }
+
     if (!isRunning()) {
       process.stdout.write("😴 Nerve daemon is not running.\n");
       return;

packages/cli/src/commands/thread.ts

@@ -0,0 +1,279 @@
+import { defineCommand } from "citty";
+
+import { isRemoteDaemonCli } from "../cli-global.js";
+import { resolveDaemonTransport } from "../daemon-client.js";
+import { isRunning } from "../workspace.js";
+import {
+  DEFAULT_PAGE_SIZE,
+  DEFAULT_THREAD_BUDGET_CHARS,
+  THREAD_ROUNDS_FETCH_LIMIT,
+  buildInspectOutput,
+  buildListOutput,
+  buildThreadCommandOutput,
+  getAllWorkflowRuns,
+  openStore,
+  parseIntArg,
+} from "./workflow.js";
+
+// ---------------------------------------------------------------------------
+// nerve thread list
+// ---------------------------------------------------------------------------
+
+const threadListCommand = defineCommand({
+  meta: {
+    name: "list",
+    description: "List active (queued/started) workflow runs from logs",
+  },
+  args: {
+    all: {
+      type: "boolean",
+      description: "Include completed/failed/crashed runs",
+      default: false,
+    },
+    workflow: {
+      type: "string",
+      description: "Filter by workflow name",
+      default: "",
+    },
+    limit: {
+      type: "string",
+      description: `Max runs to show (default: ${DEFAULT_PAGE_SIZE})`,
+      default: String(DEFAULT_PAGE_SIZE),
+    },
+    offset: {
+      type: "string",
+      description: "Skip first N runs (for pagination)",
+      default: "0",
+    },
+  },
+  async run({ args }) {
+    const store = await openStore();
+
+    try {
+      const limit = Math.max(1, parseIntArg(args.limit, DEFAULT_PAGE_SIZE));
+      const offset = Math.max(0, parseIntArg(args.offset, 0));
+      const filterWorkflow = args.workflow.length > 0 ? args.workflow : null;
+
+      const runs = args.all
+        ? getAllWorkflowRuns(store, filterWorkflow)
+        : store.getActiveWorkflowRuns(filterWorkflow ?? undefined);
+
+      const { lines, paginationHint } = buildListOutput(
+        runs,
+        offset,
+        limit,
+        args.all,
+        filterWorkflow,
+      );
+
+      for (const line of lines) {
+        process.stdout.write(line);
+      }
+      if (paginationHint !== null) {
+        process.stdout.write(paginationHint);
+      }
+    } finally {
+      store.close();
+    }
+  },
+});
+
+// ---------------------------------------------------------------------------
+// nerve thread show <runId>
+// ---------------------------------------------------------------------------
+
+const threadShowCommand = defineCommand({
+  meta: {
+    name: "show",
+    description: "Print role rounds for a workflow run (agent-oriented, budget-limited)",
+  },
+  args: {
+    runId: {
+      type: "positional",
+      description: "The run ID to dump role rounds for",
+    },
+    before: {
+      type: "string",
+      description:
+        "Exclusive upper bound on 1-based round index (use with hint from prior output to load older rounds)",
+      default: "0",
+    },
+    budget: {
+      type: "string",
+      description: `Max output characters including header (default: ${String(DEFAULT_THREAD_BUDGET_CHARS)})`,
+      default: String(DEFAULT_THREAD_BUDGET_CHARS),
+    },
+  },
+  async run({ args }) {
+    const store = await openStore();
+
+    try {
+      const before = Math.max(0, parseIntArg(args.before, 0));
+      const budgetChars = Math.max(1, parseIntArg(args.budget, DEFAULT_THREAD_BUDGET_CHARS));
+
+      const run = store.getWorkflowRun(args.runId);
+      if (run === null) {
+        process.stderr.write(`❌ No workflow run found with runId: ${args.runId}\n`);
+        process.exit(1);
+      }
+
+      const startRow = before === 0 ? store.getThreadStartMessage(args.runId) : null;
+      const totalRoleRounds = store.getThreadRoundCount(args.runId);
+      if (totalRoleRounds === 0 && startRow === null) {
+        process.stdout.write(
+          `🧵 Workflow thread: ${run.runId}\n   workflow: ${run.workflow}\n   status:   ${run.status}\n\n📭 No role rounds recorded for this run.\n`,
+        );
+        return;
+      }
+
+      const descRows = store.getThreadRounds(args.runId, {
+        before,
+        limit: THREAD_ROUNDS_FETCH_LIMIT,
+      });
+
+      const prefixLines = [
+        "🧵 Role rounds (workflow thread)\n",
+        `   runId:    ${run.runId}\n`,
+        `   workflow: ${run.workflow}\n`,
+        `   status:   ${run.status}\n`,
+        `   rounds:   ${String(totalRoleRounds)} role event(s) total\n\n`,
+      ];
+
+      const { lines, paginationHint } = buildThreadCommandOutput(
+        prefixLines,
+        descRows,
+        budgetChars,
+        args.runId,
+        startRow,
+      );
+
+      for (const line of lines) {
+        process.stdout.write(line);
+      }
+      if (paginationHint !== null) {
+        process.stdout.write(paginationHint);
+      }
+
+      if (descRows.length === 0 && before > 0) {
+        process.stdout.write(`\n📭 No rounds with index < ${String(before)}.\n`);
+      }
+    } finally {
+      store.close();
+    }
+  },
+});
+
+// ---------------------------------------------------------------------------
+// nerve thread inspect <runId>
+// ---------------------------------------------------------------------------
+
+const threadInspectCommand = defineCommand({
+  meta: {
+    name: "inspect",
+    description: "Show details and thread events for a workflow run",
+  },
+  args: {
+    runId: {
+      type: "positional",
+      description: "The run ID to inspect",
+    },
+    limit: {
+      type: "string",
+      description: `Max log entries to show (default: ${DEFAULT_PAGE_SIZE})`,
+      default: String(DEFAULT_PAGE_SIZE),
+    },
+    offset: {
+      type: "string",
+      description: "Skip first N log entries (for pagination)",
+      default: "0",
+    },
+  },
+  async run({ args }) {
+    const store = await openStore();
+
+    try {
+      const limit = Math.max(1, parseIntArg(args.limit, DEFAULT_PAGE_SIZE));
+      const offset = Math.max(0, parseIntArg(args.offset, 0));
+
+      const run = store.getWorkflowRun(args.runId);
+      if (run === null) {
+        process.stderr.write(`❌ No workflow run found with runId: ${args.runId}\n`);
+        process.exit(1);
+      }
+
+      const allLogs = store.query({ source: "workflow", refId: args.runId });
+      const { header, eventLines, paginationHint } = buildInspectOutput(
+        run,
+        allLogs,
+        offset,
+        limit,
+      );
+
+      for (const line of [...header, ...eventLines]) {
+        process.stdout.write(line);
+      }
+      if (paginationHint !== null) {
+        process.stdout.write(paginationHint);
+      }
+    } finally {
+      store.close();
+    }
+  },
+});
+
+// ---------------------------------------------------------------------------
+// nerve thread kill <runId>
+// ---------------------------------------------------------------------------
+
+const threadKillCommand = defineCommand({
+  meta: {
+    name: "kill",
+    description: "Kill a running or queued workflow thread by runId",
+  },
+  args: {
+    runId: {
+      type: "positional",
+      description: "The run ID to kill",
+    },
+  },
+  async run({ args }) {
+    if (!isRemoteDaemonCli() && !isRunning()) {
+      process.stderr.write("❌ Nerve daemon is not running. Start it with `nerve daemon start`.\n");
+      process.exit(1);
+    }
+
+    const transport = resolveDaemonTransport();
+    let response: { ok: true } | { ok: false; error: string };
+    try {
+      response = await transport.killWorkflow(args.runId);
+    } catch (e) {
+      const msg = e instanceof Error ? e.message : String(e);
+      process.stderr.write(`❌ Failed to contact daemon: ${msg}\n`);
+      process.exit(1);
+    }
+
+    if (!response.ok) {
+      process.stderr.write(`❌ Kill failed: ${response.error}\n`);
+      process.exit(1);
+    }
+
+    process.stdout.write(`✅ Kill signal sent for run "${args.runId}".\n`);
+  },
+});
+
+// ---------------------------------------------------------------------------
+// nerve thread (parent command)
+// ---------------------------------------------------------------------------
+
+export const threadCommand = defineCommand({
+  meta: {
+    name: "thread",
+    description: "Inspect and manage workflow threads (runs)",
+  },
+  subCommands: {
+    list: threadListCommand,
+    show: threadShowCommand,
+    inspect: threadInspectCommand,
+    kill: threadKillCommand,
+  },
+});

packages/cli/src/commands/validate.ts

@@ -4,6 +4,7 @@ import { join } from "node:path";
 import { parseNerveConfig } from "@uncaged/nerve-core";
 import { defineCommand } from "citty";
 
+import { validateAgentConfigurationLayer } from "../workflow-agent-validation.js";
 import { getNerveRoot } from "../workspace.js";
 
 export const validateCommand = defineCommand({
@@ -12,7 +13,8 @@ export const validateCommand = defineCommand({
     description: "Validate nerve.yaml configuration",
   },
   async run() {
-    const configPath = join(getNerveRoot(), "nerve.yaml");
+    const nerveRoot = getNerveRoot();
+    const configPath = join(nerveRoot, "nerve.yaml");
     let raw: string;
     try {
       raw = readFileSync(configPath, "utf8");
@@ -29,12 +31,20 @@ export const validateCommand = defineCommand({
     }
 
     const config = result.value;
+    const agentLayer = validateAgentConfigurationLayer(config, nerveRoot);
+    if (!agentLayer.ok) {
+      process.stderr.write(`❌ Config validation failed: ${agentLayer.message}\n`);
+      process.exit(1);
+    }
+
     const senseCount = Object.keys(config.senses).length;
-    const reflexCount = config.reflexes.length;
+    const triggerScheduleCount = Object.values(config.senses).filter(
+      (s) => s.interval !== null || s.on.length > 0,
+    ).length;
     const workflowCount = Object.keys(config.workflows).length;
 
     process.stdout.write(
-      `✅ nerve.yaml is valid — ${senseCount} sense(s), ${reflexCount} reflex(es), ${workflowCount} workflow(s)\n`,
+      `✅ nerve.yaml is valid — ${senseCount} sense(s), ${triggerScheduleCount} sense trigger schedule(s), ${workflowCount} workflow(s)\n`,
     );
   },
 });

packages/cli/src/commands/workflow.ts

@@ -1,19 +1,20 @@
-import { existsSync } from "node:fs";
+import { existsSync, readFileSync } from "node:fs";
 import { join } from "node:path";
 
-import type { DaemonIpcTriggerResponse } from "@uncaged/nerve-core";
-import { DEFAULT_ENGINE_MAX_ROUNDS, isPlainRecord } from "@uncaged/nerve-core";
+import { DEFAULT_ENGINE_MAX_ROUNDS, isPlainRecord, parseNerveConfig } from "@uncaged/nerve-core";
 import { defineCommand } from "citty";
 import { stringify } from "yaml";
 
 import type { LogStore, ThreadRoundRow, WorkflowRun } from "@uncaged/nerve-store";
-import { triggerWorkflowViaDaemon } from "../daemon-client.js";
+import { isRemoteDaemonCli } from "../cli-global.js";
+import { resolveDaemonTransport } from "../daemon-client.js";
+import { formatRowsAsAlignedTable } from "../sense-sqlite.js";
 import { loadDaemonModule } from "../workspace-daemon.js";
-import { getNerveRoot, getSocketPath, isRunning } from "../workspace.js";
+import { getNerveRoot, isRunning } from "../workspace.js";
 
 export const DEFAULT_PAGE_SIZE = 20;
 
-/** Default max characters for `nerve workflow thread` output (including run header). */
+/** Default max characters for `nerve thread show` output (including run header). */
 export const DEFAULT_THREAD_BUDGET_CHARS = 8000;
 
 /** Max role-round rows read from SQLite per invocation (DESC by round). */
@@ -28,11 +29,28 @@ export function getDbPath(): string {
   return join(getNerveRoot(), "data", "logs.db");
 }
 
-export function formatTs(timestampMs: number): string {
-  return new Date(timestampMs).toISOString();
+/** Human-readable placeholder when a timestamp is missing or not representable as ISO 8601. */
+export const UNKNOWN_TIMESTAMP_LABEL = "(unknown)";
+
+/**
+ * Format epoch milliseconds as UTC ISO 8601, or {@link UNKNOWN_TIMESTAMP_LABEL} when the value
+ * is nullish, not a finite number, or cannot be converted (defensive against bad DB / test data).
+ */
+export function formatTs(timestampMs: number | null | undefined): string {
+  if (timestampMs === null || timestampMs === undefined) {
+    return UNKNOWN_TIMESTAMP_LABEL;
+  }
+  if (typeof timestampMs !== "number" || !Number.isFinite(timestampMs)) {
+    return UNKNOWN_TIMESTAMP_LABEL;
+  }
+  try {
+    return new Date(timestampMs).toISOString();
+  } catch {
+    return UNKNOWN_TIMESTAMP_LABEL;
+  }
 }
 
-async function openStore(): Promise<LogStore> {
+export async function openStore(): Promise<LogStore> {
   const nerveRoot = getNerveRoot();
   const dbPath = getDbPath();
   if (!existsSync(dbPath)) {
@@ -59,6 +77,8 @@ export function statusIcon(status: WorkflowRun["status"]): string {
       return "🗑";
     case "interrupted":
       return "⚠️";
+    case "killed":
+      return "🛑";
     default: {
       const _exhaustive: never = status;
       return `?(${_exhaustive})`;
@@ -79,7 +99,8 @@ export function getAllWorkflowRuns(store: LogStore, filterWorkflow: string | nul
  */
 export function formatRunLine(run: WorkflowRun): string {
   const icon = statusIcon(run.status);
-  return `  ${icon} ${run.runId}  workflow=${run.workflow}  status=${run.status}  timestamp=${formatTs(run.timestamp)}\n`;
+  const exitCodeStr = run.exitCode !== null ? `  exit_code=${run.exitCode}` : "";
+  return `  ${icon} ${run.runId}  workflow=${run.workflow}  status=${run.status}${exitCodeStr}  timestamp=${formatTs(run.timestamp)}\n`;
 }
 
 /**
@@ -122,7 +143,7 @@ export function buildListOutput(
     const allFlagStr = allFlag ? " --all" : "";
     paginationHint =
       `\n⏩ ${remaining} more run(s) not shown. Fetch next page:\n` +
-      `   nerve workflow list --offset ${offset + limit}${allFlagStr}${wfFlag}\n`;
+      `   nerve thread list --offset ${offset + limit}${allFlagStr}${wfFlag}\n`;
   }
 
   return { lines, paginationHint };
@@ -175,14 +196,14 @@ export function buildInspectOutput(
   if (remaining > 0) {
     paginationHint =
       `\n⏩ ${remaining} more event(s) not shown. Fetch next page:\n` +
-      `   nerve workflow inspect ${run.runId} --offset ${offset + limit}\n`;
+      `   nerve thread inspect ${run.runId} --offset ${offset + limit}\n`;
   }
 
   return { header, eventLines, paginationHint };
 }
 
 // ---------------------------------------------------------------------------
-// nerve workflow thread <runId> — agent-oriented role rounds
+// nerve thread show <runId> — agent-oriented role rounds
 // ---------------------------------------------------------------------------
 
 export type PartitionedMessage = {
@@ -203,12 +224,12 @@ export function partitionWorkflowMessage(msg: {
 }): PartitionedMessage {
   const roleStr = msg.role;
   const contentBody = msg.content;
-  const meta: Record<string, unknown> =
+  const meta =
     msg.meta !== null && msg.meta !== undefined && typeof msg.meta === "object"
       ? isPlainRecord(msg.meta)
         ? msg.meta
         : (msg.meta as Record<string, unknown>)
-      : {};
+      : ({} as Record<string, unknown>);
   return { roleStr, contentBody, meta };
 }
 
@@ -249,28 +270,42 @@ function buildTruncatedSingleRound(
     lines: [...prefixLines, single],
     paginationHint:
       hintRound > 1
-        ? `\n⏩ Older rounds exist. Fetch with:\n   nerve workflow thread ${runId} --before ${String(hintRound)}${budgetFlag}\n`
+        ? `\n⏩ Older rounds exist. Fetch with:\n   nerve thread show ${runId} --before ${String(hintRound)}${budgetFlag}\n`
         : null,
   };
 }
 
 /**
- * Build stdout lines for `nerve workflow thread`: newest-first selection from
+ * Build stdout lines for `nerve thread show`: newest-first selection from
  * `descRows` until `budgetChars` (including `prefixLines`), then chronological order.
+ * When `startRow` is set (typically the persisted `__start__` frame on the first page only),
+ * it is formatted first and its length is subtracted from the budget before consuming `descRows`.
  */
 export function buildThreadCommandOutput(
   prefixLines: string[],
   descRows: ThreadRoundRow[],
   budgetChars: number,
   runId: string,
+  startRow: ThreadRoundRow | null = null,
 ): ThreadCommandOutput {
   const prefixText = prefixLines.join("");
   let remaining = Math.max(0, budgetChars - prefixText.length);
-  const picked: ThreadRoundRow[] = [];
+  const leadingRoundBlocks: string[] = [];
 
   const budgetFlag =
     budgetChars === DEFAULT_THREAD_BUDGET_CHARS ? "" : ` --budget ${String(budgetChars)}`;
 
+  if (startRow !== null) {
+    const startBlock = formatThreadRoundBlock(startRow);
+    if (startBlock.length <= remaining) {
+      leadingRoundBlocks.push(startBlock);
+      remaining -= startBlock.length;
+    } else {
+      return buildTruncatedSingleRound(startRow, remaining, prefixLines, runId, budgetFlag);
+    }
+  }
+
+  const picked: ThreadRoundRow[] = [];
   for (const row of descRows) {
     const block = formatThreadRoundBlock(row);
     if (block.length <= remaining) {
@@ -279,7 +314,13 @@ export function buildThreadCommandOutput(
       continue;
     }
     if (picked.length === 0) {
-      return buildTruncatedSingleRound(row, remaining, prefixLines, runId, budgetFlag);
+      return buildTruncatedSingleRound(
+        row,
+        remaining,
+        [...prefixLines, ...leadingRoundBlocks],
+        runId,
+        budgetFlag,
+      );
     }
     break;
   }
@@ -288,213 +329,98 @@ export function buildThreadCommandOutput(
   const shownMinRound = picked.length === 0 ? null : Math.min(...picked.map((r) => r.round));
   let paginationHint: string | null = null;
   if (shownMinRound !== null && shownMinRound > 1) {
-    paginationHint = `\n⏩ Older rounds not shown. Fetch with:\n   nerve workflow thread ${runId} --before ${String(shownMinRound)}${budgetFlag}\n`;
+    paginationHint = `\n⏩ Older rounds not shown. Fetch with:\n   nerve thread show ${runId} --before ${String(shownMinRound)}${budgetFlag}\n`;
   }
 
-  return { lines: [...prefixLines, ...blocksAsc], paginationHint };
+  return { lines: [...prefixLines, ...leadingRoundBlocks, ...blocksAsc], paginationHint };
 }
 
 // ---------------------------------------------------------------------------
-// nerve workflow list
+// nerve workflow list (reads workflow definitions from workspace YAML)
 // ---------------------------------------------------------------------------
 
 const workflowListCommand = defineCommand({
   meta: {
     name: "list",
-    description: "List active (queued/started) workflow runs",
+    description: "List workflow definitions from nerve.yaml",
   },
-  args: {
-    all: {
-      type: "boolean",
-      description: "Include completed/failed/crashed runs",
-      default: false,
-    },
-    workflow: {
-      type: "string",
-      description: "Filter by workflow name",
-      default: "",
-    },
-    limit: {
-      type: "string",
-      description: `Max runs to show (default: ${DEFAULT_PAGE_SIZE})`,
-      default: String(DEFAULT_PAGE_SIZE),
-    },
-    offset: {
-      type: "string",
-      description: "Skip first N runs (for pagination)",
-      default: "0",
-    },
-  },
-  async run({ args }) {
-    const store = await openStore();
-
+  async run() {
+    const configPath = join(getNerveRoot(), "nerve.yaml");
+    let raw: string;
     try {
-      const limit = Math.max(1, parseIntArg(args.limit, DEFAULT_PAGE_SIZE));
-      const offset = Math.max(0, parseIntArg(args.offset, 0));
-      const filterWorkflow = args.workflow.length > 0 ? args.workflow : null;
-
-      const runs = args.all
-        ? getAllWorkflowRuns(store, filterWorkflow)
-        : store.getActiveWorkflowRuns(filterWorkflow ?? undefined);
-
-      const { lines, paginationHint } = buildListOutput(
-        runs,
-        offset,
-        limit,
-        args.all,
-        filterWorkflow,
-      );
-
-      for (const line of lines) {
-        process.stdout.write(line);
-      }
-      if (paginationHint !== null) {
-        process.stdout.write(paginationHint);
-      }
-    } finally {
-      store.close();
+      raw = readFileSync(configPath, "utf8");
+    } catch {
+      process.stderr.write(`❌ Could not read ${configPath}\n`);
+      process.exit(1);
     }
+
+    const result = parseNerveConfig(raw);
+    if (!result.ok) {
+      process.stderr.write(`❌ Config validation failed: ${result.error.message}\n`);
+      process.exit(1);
+    }
+
+    const config = result.value;
+    const workflowEntries = Object.entries(config.workflows);
+
+    if (workflowEntries.length === 0) {
+      process.stdout.write("📭 No workflows defined in nerve.yaml.\n");
+      return;
+    }
+
+    const rows = workflowEntries.map(([name, wf]) => ({
+      name,
+      concurrency: wf.concurrency,
+      overflow: wf.overflow,
+      ...(wf.overflow === "queue" ? { maxQueue: wf.maxQueue } : {}),
+    }));
+
+    process.stdout.write(`📋 Workflow definitions (${String(rows.length)}):\n\n`);
+    process.stdout.write(formatRowsAsAlignedTable(rows));
   },
 });
 
 // ---------------------------------------------------------------------------
-// nerve workflow inspect <runId>
+// nerve workflow status (daemon — registered workflows + queue depth)
 // ---------------------------------------------------------------------------
 
-const workflowInspectCommand = defineCommand({
+const workflowStatusCommand = defineCommand({
   meta: {
-    name: "inspect",
-    description: "Show details and thread events for a workflow run",
+    name: "status",
+    description: "Show live workflow status from the running daemon (concurrency, active, queued)",
   },
-  args: {
-    runId: {
-      type: "positional",
-      description: "The run ID to inspect",
-    },
-    limit: {
-      type: "string",
-      description: `Max log entries to show (default: ${DEFAULT_PAGE_SIZE})`,
-      default: String(DEFAULT_PAGE_SIZE),
-    },
-    offset: {
-      type: "string",
-      description: "Skip first N log entries (for pagination)",
-      default: "0",
-    },
-  },
-  async run({ args }) {
-    const store = await openStore();
-
-    try {
-      const limit = Math.max(1, parseIntArg(args.limit, DEFAULT_PAGE_SIZE));
-      const offset = Math.max(0, parseIntArg(args.offset, 0));
-
-      const run = store.getWorkflowRun(args.runId);
-      if (run === null) {
-        process.stderr.write(`❌ No workflow run found with runId: ${args.runId}\n`);
-        process.exit(1);
-      }
-
-      const allLogs = store.query({ source: "workflow", refId: args.runId });
-      const { header, eventLines, paginationHint } = buildInspectOutput(
-        run,
-        allLogs,
-        offset,
-        limit,
-      );
-
-      for (const line of [...header, ...eventLines]) {
-        process.stdout.write(line);
-      }
-      if (paginationHint !== null) {
-        process.stdout.write(paginationHint);
-      }
-    } finally {
-      store.close();
+  async run() {
+    if (!isRemoteDaemonCli() && !isRunning()) {
+      process.stderr.write("❌ Nerve daemon is not running. Start it with `nerve daemon start`.\n");
+      process.exit(1);
     }
-  },
-});
-
-// ---------------------------------------------------------------------------
-// nerve workflow thread <runId>
-// ---------------------------------------------------------------------------
-
-const workflowThreadCommand = defineCommand({
-  meta: {
-    name: "thread",
-    description: "Print role rounds for a workflow run (agent-oriented, budget-limited)",
-  },
-  args: {
-    runId: {
-      type: "positional",
-      description: "The run ID to dump role rounds for",
-    },
-    before: {
-      type: "string",
-      description:
-        "Exclusive upper bound on 1-based round index (use with hint from prior output to load older rounds)",
-      default: "0",
-    },
-    budget: {
-      type: "string",
-      description: `Max output characters including header (default: ${String(DEFAULT_THREAD_BUDGET_CHARS)})`,
-      default: String(DEFAULT_THREAD_BUDGET_CHARS),
-    },
-  },
-  async run({ args }) {
-    const store = await openStore();
 
+    const transport = resolveDaemonTransport();
+    let workflows: Awaited<ReturnType<typeof transport.listWorkflows>>;
     try {
-      const before = Math.max(0, parseIntArg(args.before, 0));
-      const budgetChars = Math.max(1, parseIntArg(args.budget, DEFAULT_THREAD_BUDGET_CHARS));
-
-      const run = store.getWorkflowRun(args.runId);
-      if (run === null) {
-        process.stderr.write(`❌ No workflow run found with runId: ${args.runId}\n`);
-        process.exit(1);
-      }
-
-      const totalRoleRounds = store.getThreadRoundCount(args.runId);
-      if (totalRoleRounds === 0) {
-        process.stdout.write(
-          `🧵 Workflow thread: ${run.runId}\n   workflow: ${run.workflow}\n   status:   ${run.status}\n\n📭 No role rounds recorded for this run.\n`,
-        );
-        return;
-      }
-
-      const descRows = store.getThreadRounds(args.runId, {
-        before,
-        limit: THREAD_ROUNDS_FETCH_LIMIT,
-      });
-
-      const prefixLines = [
-        "🧵 Role rounds (workflow thread)\n",
-        `   runId:    ${run.runId}\n`,
-        `   workflow: ${run.workflow}\n`,
-        `   status:   ${run.status}\n`,
-        `   rounds:   ${String(totalRoleRounds)} role event(s) total\n\n`,
-      ];
-
-      const { lines, paginationHint } = buildThreadCommandOutput(
-        prefixLines,
-        descRows,
-        budgetChars,
-        args.runId,
-      );
-
-      for (const line of lines) {
-        process.stdout.write(line);
-      }
-      if (paginationHint !== null) {
-        process.stdout.write(paginationHint);
-      }
-
-      if (descRows.length === 0 && before > 0) {
-        process.stdout.write(`\n📭 No rounds with index < ${String(before)}.\n`);
-      }
-    } finally {
-      store.close();
+      workflows = await transport.listWorkflows();
+    } catch (e) {
+      const msg = e instanceof Error ? e.message : String(e);
+      process.stderr.write(`❌ Failed to contact daemon: ${msg}\n`);
+      process.exit(1);
     }
+
+    const rows = workflows.map((w) => ({
+      name: w.name,
+      active: w.activeThreads,
+      runIds: w.activeRunIds.length > 0 ? w.activeRunIds.join(", ") : "—",
+      queued: w.queuedThreads,
+      concurrency: w.config.concurrency,
+      overflow: w.config.overflow,
+    }));
+
+    if (rows.length === 0) {
+      process.stdout.write("📭 No workflows in nerve.yaml (or empty registry).\n");
+      return;
+    }
+
+    process.stdout.write(`📋 Workflows (${String(rows.length)}):\n\n`);
+    process.stdout.write(formatRowsAsAlignedTable(rows));
   },
 });
 
@@ -502,6 +428,21 @@ const workflowThreadCommand = defineCommand({
 // nerve workflow trigger <name>
 // ---------------------------------------------------------------------------
 
+function readWorkspaceDefaultMaxRounds(): number {
+  const configPath = join(getNerveRoot(), "nerve.yaml");
+  let raw: string;
+  try {
+    raw = readFileSync(configPath, "utf8");
+  } catch {
+    return DEFAULT_ENGINE_MAX_ROUNDS;
+  }
+  const result = parseNerveConfig(raw);
+  if (!result.ok) {
+    return DEFAULT_ENGINE_MAX_ROUNDS;
+  }
+  return result.value.maxRounds;
+}
+
 const workflowTriggerCommand = defineCommand({
   meta: {
     name: "trigger",
@@ -512,41 +453,38 @@ const workflowTriggerCommand = defineCommand({
       type: "positional",
       description: "The workflow name to trigger",
     },
-    payload: {
+    maxRounds: {
       type: "string",
-      description:
-        'JSON with optional "prompt" (string), "maxRounds" (number), and "dryRun" (boolean) for the workflow run (default: {})',
-      default: "{}",
+      description: "Max moderator rounds (default: nerve.yaml maxRounds)",
+      default: "",
+    },
+    prompt: {
+      type: "string",
+      description: "Initial prompt for the workflow run",
+      default: "",
+    },
+    dryRun: {
+      type: "boolean",
+      description: "Run the workflow in dry-run mode",
+      default: false,
     },
   },
   async run({ args }) {
-    let triggerPayload: unknown = {};
-    try {
-      triggerPayload = JSON.parse(args.payload) as unknown;
-    } catch {
-      process.stderr.write(`❌ --payload must be valid JSON. Got: ${args.payload}\n`);
+    const prompt = args.prompt;
+    const defaultMax = readWorkspaceDefaultMaxRounds();
+    const maxRounds =
+      args.maxRounds.length > 0 ? parseIntArg(args.maxRounds, defaultMax) : defaultMax;
+    const dryRun = args.dryRun;
+
+    if (!isRemoteDaemonCli() && !isRunning()) {
+      process.stderr.write("❌ Nerve daemon is not running. Start it with `nerve daemon start`.\n");
       process.exit(1);
     }
 
-    let prompt = "";
-    let maxRounds = DEFAULT_ENGINE_MAX_ROUNDS;
-    let dryRun = false;
-    if (isPlainRecord(triggerPayload)) {
-      const p = triggerPayload;
-      if (typeof p.prompt === "string") prompt = p.prompt;
-      if (typeof p.maxRounds === "number") maxRounds = p.maxRounds;
-      if (typeof p.dryRun === "boolean") dryRun = p.dryRun;
-    }
-
-    if (!isRunning()) {
-      process.stderr.write("❌ Nerve daemon is not running. Start it with `nerve start`.\n");
-      process.exit(1);
-    }
-
-    const socketPath = getSocketPath();
-    let response: DaemonIpcTriggerResponse;
+    const transport = resolveDaemonTransport();
+    let response: { ok: true } | { ok: false; error: string };
     try {
-      response = await triggerWorkflowViaDaemon(socketPath, args.name, prompt, maxRounds, dryRun);
+      response = await transport.triggerWorkflow(args.name, { prompt, maxRounds, dryRun });
     } catch (e) {
       const msg = e instanceof Error ? e.message : String(e);
       process.stderr.write(`❌ Failed to contact daemon: ${msg}\n`);
@@ -559,7 +497,7 @@ const workflowTriggerCommand = defineCommand({
     }
 
     process.stdout.write(`✅ Triggered workflow "${args.name}" via daemon.\n`);
-    process.stdout.write("\n💡 Inspect active runs with: nerve workflow list\n");
+    process.stdout.write("\n💡 Inspect active runs with: nerve thread list\n");
   },
 });
 
@@ -570,12 +508,11 @@ const workflowTriggerCommand = defineCommand({
 export const workflowCommand = defineCommand({
   meta: {
     name: "workflow",
-    description: "Manage and inspect workflow runs",
+    description: "Manage workflow definitions and trigger workflows",
   },
   subCommands: {
     list: workflowListCommand,
-    inspect: workflowInspectCommand,
-    thread: workflowThreadCommand,
+    status: workflowStatusCommand,
     trigger: workflowTriggerCommand,
   },
 });

packages/cli/src/daemon-bootstrap.ts

@@ -1,3 +1,5 @@
+import "@uncaged/nerve-daemon/experimental-warning-suppression.js";
+
 import { runForegroundKernelSession } from "./run-foreground-kernel.js";
 import { loadDaemonModule } from "./workspace-daemon.js";
 

packages/cli/src/daemon-client.ts

@@ -10,28 +10,32 @@ import type { Socket } from "node:net";
 
 import type {
   DaemonIpcListSensesResponse,
+  DaemonIpcListWorkflowsResponse,
   DaemonIpcRequest,
   DaemonIpcTriggerResponse,
+  DaemonTransport,
+  DaemonTransportTriggerResult,
+  DaemonTransportWorkflowLaunch,
+  HealthInfo,
   SenseInfo,
+  WorkflowStatus,
 } from "@uncaged/nerve-core";
-import { isPlainRecord } from "@uncaged/nerve-core";
+import {
+  DEFAULT_ENGINE_MAX_ROUNDS,
+  isPlainRecord,
+  isSenseInfo,
+  isWorkflowStatus,
+} from "@uncaged/nerve-core";
+
+import { getCliDaemonApiToken, getCliDaemonHost } from "./cli-global.js";
+import { HttpTransport } from "./http-transport.js";
+import { getSocketPath } from "./workspace.js";
 
 const CONNECT_TIMEOUT_MS = 3_000;
 const RESPONSE_TIMEOUT_MS = 5_000;
 
 export type { SenseInfo };
 
-function isSenseInfo(value: unknown): value is SenseInfo {
-  if (!isPlainRecord(value)) return false;
-  return (
-    typeof value.name === "string" &&
-    typeof value.group === "string" &&
-    (value.throttle === null || typeof value.throttle === "number") &&
-    (value.timeout === null || typeof value.timeout === "number") &&
-    (value.lastSignalTimestamp === null || typeof value.lastSignalTimestamp === "number")
-  );
-}
-
 function parseDaemonResponse(line: string): DaemonIpcTriggerResponse {
   try {
     const obj: unknown = JSON.parse(line);
@@ -62,6 +66,51 @@ function parseListSensesResponse(line: string): DaemonIpcListSensesResponse {
   return { ok: false, error: `Unexpected daemon response: ${line}` };
 }
 
+function parseListWorkflowsResponse(line: string): DaemonIpcListWorkflowsResponse {
+  try {
+    const obj: unknown = JSON.parse(line);
+    if (isPlainRecord(obj)) {
+      const r = obj;
+      if (r.ok === false && typeof r.error === "string") return { ok: false, error: r.error };
+      if (r.ok === true && Array.isArray(r.workflows) && r.workflows.every(isWorkflowStatus)) {
+        return { ok: true, workflows: r.workflows };
+      }
+    }
+  } catch {
+    // fall through
+  }
+  return { ok: false, error: `Unexpected daemon response: ${line}` };
+}
+
+function parseHealthResponse(line: string): HealthInfo | null {
+  try {
+    const obj: unknown = JSON.parse(line);
+    if (!isPlainRecord(obj)) return null;
+    const r = obj;
+    if (r.ok === true && isPlainRecord(r.health)) {
+      const h = r.health;
+      if (
+        typeof h.ok === "boolean" &&
+        typeof h.version === "string" &&
+        typeof h.uptime === "number" &&
+        typeof h.startedAt === "string" &&
+        typeof h.hostname === "string"
+      ) {
+        return {
+          ok: h.ok,
+          version: h.version,
+          uptime: h.uptime,
+          startedAt: h.startedAt,
+          hostname: h.hostname,
+        };
+      }
+    }
+  } catch {
+    // fall through
+  }
+  return null;
+}
+
 /**
  * Connect to the daemon socket, send one JSON request (newline-terminated),
  * and resolve with the first non-empty line parsed by `parseFirstLine`.
@@ -126,6 +175,78 @@ function sendAndReceive<T>(
   });
 }
 
+/** Unix-socket implementation of {@link DaemonTransport} (local daemon). */
+export class UnixTransport implements DaemonTransport {
+  readonly socketPath: string;
+  constructor(socketPath: string) {
+    this.socketPath = socketPath;
+  }
+
+  async health(): Promise<HealthInfo> {
+    const parsed = await sendAndReceive(this.socketPath, { type: "health" }, (line) =>
+      parseHealthResponse(line),
+    );
+    if (parsed === null) {
+      throw new Error("Unexpected daemon response for health");
+    }
+    return parsed;
+  }
+
+  async listSenses(): Promise<SenseInfo[]> {
+    const r = await sendAndReceive(
+      this.socketPath,
+      { type: "list-senses" },
+      parseListSensesResponse,
+    );
+    if (!r.ok) {
+      throw new Error(r.error);
+    }
+    return r.senses;
+  }
+
+  async listWorkflows(): Promise<WorkflowStatus[]> {
+    const r = await sendAndReceive(
+      this.socketPath,
+      { type: "list-workflows" },
+      parseListWorkflowsResponse,
+    );
+    if (!r.ok) {
+      throw new Error(r.error);
+    }
+    return r.workflows;
+  }
+
+  async triggerSense(name: string): Promise<DaemonTransportTriggerResult> {
+    return sendAndReceive(
+      this.socketPath,
+      { type: "trigger-sense", sense: name },
+      parseDaemonResponse,
+    );
+  }
+
+  async triggerWorkflow(
+    name: string,
+    launch: DaemonTransportWorkflowLaunch | null,
+  ): Promise<DaemonTransportTriggerResult> {
+    const prompt = launch !== null ? launch.prompt : "";
+    const maxRounds = launch !== null ? launch.maxRounds : DEFAULT_ENGINE_MAX_ROUNDS;
+    const dryRun = launch !== null ? launch.dryRun : false;
+    const message: DaemonIpcRequest = {
+      type: "trigger-workflow",
+      workflow: name,
+      prompt,
+      maxRounds,
+      dryRun,
+    };
+    return sendAndReceive(this.socketPath, message, parseDaemonResponse);
+  }
+
+  async killWorkflow(runId: string): Promise<DaemonTransportTriggerResult> {
+    const message: DaemonIpcRequest = { type: "kill-workflow", runId };
+    return sendAndReceive(this.socketPath, message, parseDaemonResponse);
+  }
+}
+
 /**
  * Send a trigger-workflow message to the running daemon via its Unix socket.
  * Resolves with the daemon's response or rejects on connection/timeout errors.
@@ -167,3 +288,39 @@ export function listSensesViaDaemon(socketPath: string): Promise<DaemonIpcListSe
   const message: DaemonIpcRequest = { type: "list-senses" };
   return sendAndReceive(socketPath, message, parseListSensesResponse);
 }
+
+/**
+ * Send a list-workflows message to the running daemon via its Unix socket.
+ */
+export function listWorkflowsViaDaemon(
+  socketPath: string,
+): Promise<DaemonIpcListWorkflowsResponse> {
+  const message: DaemonIpcRequest = { type: "list-workflows" };
+  return sendAndReceive(socketPath, message, parseListWorkflowsResponse);
+}
+
+/**
+ * Send a kill-workflow message to the running daemon via its Unix socket.
+ * Resolves with the daemon's response or rejects on connection/timeout errors.
+ */
+export function killWorkflowViaDaemon(
+  socketPath: string,
+  runId: string,
+): Promise<DaemonIpcTriggerResponse> {
+  const message: DaemonIpcRequest = { type: "kill-workflow", runId };
+  return sendAndReceive(socketPath, message, parseDaemonResponse);
+}
+
+/** Unix socket when no `--host`; otherwise {@link HttpTransport} for remote HTTP API. */
+export function resolveDaemonTransport(): DaemonTransport {
+  const host = getCliDaemonHost();
+  if (host !== null && host.length > 0) {
+    const tok = getCliDaemonApiToken();
+    return tok !== null && tok.length > 0
+      ? new HttpTransport({ host, token: tok })
+      : new HttpTransport({ host });
+  }
+  return new UnixTransport(getSocketPath());
+}
+
+export { HttpTransport } from "./http-transport.js";

packages/cli/src/http-transport.ts

@@ -0,0 +1,185 @@
+import type {
+  DaemonTransport,
+  DaemonTransportTriggerResult,
+  DaemonTransportWorkflowLaunch,
+  HealthInfo,
+  SenseInfo,
+  WorkflowStatus,
+} from "@uncaged/nerve-core";
+import {
+  DEFAULT_ENGINE_MAX_ROUNDS,
+  isPlainRecord,
+  isSenseInfo,
+  isWorkflowStatus,
+} from "@uncaged/nerve-core";
+
+function normalizeBaseUrl(host: string): string {
+  const t = host.trim();
+  const withScheme = t.startsWith("http://") || t.startsWith("https://") ? t : `http://${t}`;
+  return withScheme.endsWith("/") ? withScheme.slice(0, -1) : withScheme;
+}
+
+function isHealthInfo(value: unknown): value is HealthInfo {
+  if (!isPlainRecord(value)) return false;
+  return (
+    typeof value.ok === "boolean" &&
+    typeof value.version === "string" &&
+    typeof value.uptime === "number" &&
+    typeof value.startedAt === "string" &&
+    typeof value.hostname === "string"
+  );
+}
+
+async function readJsonBody(res: Response): Promise<unknown> {
+  const text = await res.text();
+  if (text.trim().length === 0) return null;
+  try {
+    return JSON.parse(text) as unknown;
+  } catch {
+    return null;
+  }
+}
+
+function httpErrorMessage(status: number, body: unknown): string {
+  if (isPlainRecord(body) && body.ok === false && typeof body.error === "string") {
+    return body.error;
+  }
+  return `HTTP ${String(status)}`;
+}
+
+/** Remote daemon control plane via JSON HTTP API (Phase 2). */
+export class HttpTransport implements DaemonTransport {
+  private readonly baseUrl: string;
+  private readonly token: string | null;
+
+  constructor(opts: { host: string; token?: string | null }) {
+    this.baseUrl = normalizeBaseUrl(opts.host);
+    this.token =
+      opts.token !== undefined && opts.token !== null && opts.token.length > 0 ? opts.token : null;
+  }
+
+  private baseHeaders(): Record<string, string> {
+    const h: Record<string, string> = { Accept: "application/json" };
+    if (this.token !== null) {
+      h.Authorization = `Bearer ${this.token}`;
+    }
+    return h;
+  }
+
+  async health(): Promise<HealthInfo> {
+    const res = await fetch(`${this.baseUrl}/api/health`, {
+      headers: this.baseHeaders(),
+    });
+    const body = await readJsonBody(res);
+    if (res.status === 401) {
+      throw new Error(httpErrorMessage(res.status, body));
+    }
+    if (!res.ok || !isHealthInfo(body)) {
+      throw new Error(httpErrorMessage(res.status, body));
+    }
+    return body;
+  }
+
+  async listSenses(): Promise<SenseInfo[]> {
+    const res = await fetch(`${this.baseUrl}/api/senses`, {
+      headers: this.baseHeaders(),
+    });
+    const body = await readJsonBody(res);
+    if (res.status === 401) {
+      throw new Error(httpErrorMessage(res.status, body));
+    }
+    if (!res.ok || !isPlainRecord(body) || !Array.isArray(body.senses)) {
+      throw new Error(httpErrorMessage(res.status, body));
+    }
+    if (!body.senses.every(isSenseInfo)) {
+      throw new Error("Unexpected senses payload from daemon HTTP API");
+    }
+    return body.senses;
+  }
+
+  async listWorkflows(): Promise<WorkflowStatus[]> {
+    const res = await fetch(`${this.baseUrl}/api/workflows`, {
+      headers: this.baseHeaders(),
+    });
+    const body = await readJsonBody(res);
+    if (res.status === 401) {
+      throw new Error(httpErrorMessage(res.status, body));
+    }
+    if (!res.ok || !isPlainRecord(body) || !Array.isArray(body.workflows)) {
+      throw new Error(httpErrorMessage(res.status, body));
+    }
+    if (!body.workflows.every(isWorkflowStatus)) {
+      throw new Error("Unexpected workflows payload from daemon HTTP API");
+    }
+    return body.workflows;
+  }
+
+  async triggerSense(name: string): Promise<DaemonTransportTriggerResult> {
+    const res = await fetch(`${this.baseUrl}/api/trigger-sense`, {
+      method: "POST",
+      headers: { ...this.baseHeaders(), "Content-Type": "application/json" },
+      body: JSON.stringify({ name }),
+    });
+    const body = await readJsonBody(res);
+    if (res.status === 401) {
+      return { ok: false, error: httpErrorMessage(res.status, body) };
+    }
+    if (!isPlainRecord(body)) {
+      return { ok: false, error: httpErrorMessage(res.status, body) };
+    }
+    if (body.ok === true) return { ok: true };
+    if (body.ok === false && typeof body.error === "string")
+      return { ok: false, error: body.error };
+    return { ok: false, error: httpErrorMessage(res.status, body) };
+  }
+
+  async triggerWorkflow(
+    name: string,
+    launch: DaemonTransportWorkflowLaunch | null,
+  ): Promise<DaemonTransportTriggerResult> {
+    const L =
+      launch !== null
+        ? launch
+        : { prompt: "", maxRounds: DEFAULT_ENGINE_MAX_ROUNDS, dryRun: false };
+    const res = await fetch(`${this.baseUrl}/api/trigger-workflow`, {
+      method: "POST",
+      headers: { ...this.baseHeaders(), "Content-Type": "application/json" },
+      body: JSON.stringify({
+        name,
+        prompt: L.prompt,
+        maxRounds: L.maxRounds,
+        dryRun: L.dryRun,
+      }),
+    });
+    const body = await readJsonBody(res);
+    if (res.status === 401) {
+      return { ok: false, error: httpErrorMessage(res.status, body) };
+    }
+    if (!isPlainRecord(body)) {
+      return { ok: false, error: httpErrorMessage(res.status, body) };
+    }
+    if (body.ok === true) return { ok: true };
+    if (body.ok === false && typeof body.error === "string")
+      return { ok: false, error: body.error };
+    return { ok: false, error: httpErrorMessage(res.status, body) };
+  }
+
+  async killWorkflow(runId: string): Promise<DaemonTransportTriggerResult> {
+    const res = await fetch(`${this.baseUrl}/api/kill-workflow`, {
+      method: "POST",
+      headers: { ...this.baseHeaders(), "Content-Type": "application/json" },
+      body: JSON.stringify({ runId }),
+    });
+    const body = await readJsonBody(res);
+    if (res.status === 401) {
+      return { ok: false, error: httpErrorMessage(res.status, body) };
+    }
+    if (!isPlainRecord(body)) {
+      return { ok: false, error: httpErrorMessage(res.status, body) };
+    }
+    if (body.ok === true) return { ok: true };
+    if (body.ok === false && typeof body.error === "string")
+      return { ok: false, error: body.error };
+    return { ok: false, error: httpErrorMessage(res.status, body) };
+  }
+}

packages/cli/src/knowledge/chunk-markdown.ts

@@ -0,0 +1,88 @@
+const HEADING_RE = /^(#{1,6})\s+(.+)$/;
+
+export type MarkdownChunk = {
+  slug: string;
+  text: string;
+};
+
+function slugPart(title: string): string {
+  const t = title.trim().toLowerCase().replace(/\s+/g, "-");
+  const safe = t.replace(/[^a-z0-9_-]+/g, "");
+  return safe.length > 0 ? safe : "section";
+}
+
+function splitLargeMarkdownChunk(slugBase: string, text: string): MarkdownChunk[] {
+  const maxParagraphs = 24;
+  const paragraphs = text.split(/\n\s*\n/).filter((p) => p.trim().length > 0);
+  if (paragraphs.length <= maxParagraphs) {
+    return [{ slug: slugBase, text }];
+  }
+  const chunks: MarkdownChunk[] = [];
+  let part = 0;
+  for (let i = 0; i < paragraphs.length; i += maxParagraphs) {
+    const slice = paragraphs.slice(i, i + maxParagraphs).join("\n\n");
+    chunks.push({ slug: `${slugBase}-part${String(part)}`, text: slice });
+    part += 1;
+  }
+  return chunks;
+}
+
+function headingLineIndices(lines: string[]): number[] {
+  const headingIdx: number[] = [];
+  for (let i = 0; i < lines.length; i++) {
+    const line = lines[i];
+    if (line !== undefined && HEADING_RE.test(line)) {
+      headingIdx.push(i);
+    }
+  }
+  return headingIdx;
+}
+
+function chunksFromHeadings(
+  lines: string[],
+  headingIdx: number[],
+  baseSlug: string,
+): MarkdownChunk[] {
+  const chunks: MarkdownChunk[] = [];
+  const firstHead = headingIdx[0] ?? 0;
+  if (firstHead > 0) {
+    const preamble = lines.slice(0, firstHead).join("\n").trim();
+    if (preamble.length > 0) {
+      chunks.push(...splitLargeMarkdownChunk(`${baseSlug}#preamble`, preamble));
+    }
+  }
+
+  for (let h = 0; h < headingIdx.length; h++) {
+    const start = headingIdx[h] ?? 0;
+    const end = h + 1 < headingIdx.length ? (headingIdx[h + 1] ?? lines.length) : lines.length;
+    const block = lines.slice(start, end).join("\n").trim();
+    if (block.length === 0) {
+      continue;
+    }
+    const titleLine = lines[start] ?? "";
+    const ht = HEADING_RE.exec(titleLine);
+    const suffix = ht !== null ? slugPart(ht[2] ?? "h") : `h${String(h)}`;
+    chunks.push(...splitLargeMarkdownChunk(`${baseSlug}#${suffix}-${String(h)}`, block));
+  }
+  return chunks;
+}
+
+/**
+ * Split Markdown by headings; long sections are split further by blank-line paragraphs.
+ */
+export function chunkMarkdown(relativePath: string, source: string): MarkdownChunk[] {
+  const lines = source.split(/\r?\n/);
+  const headingIdx = headingLineIndices(lines);
+  const baseSlug = relativePath.replace(/\//g, "-");
+
+  if (headingIdx.length === 0) {
+    const text = source.trim();
+    if (text.length === 0) {
+      return [];
+    }
+    return splitLargeMarkdownChunk(`${baseSlug}#doc`, text);
+  }
+
+  const chunks = chunksFromHeadings(lines, headingIdx, baseSlug);
+  return chunks;
+}

packages/cli/src/knowledge/chunk-typescript.ts

@@ -0,0 +1,87 @@
+export type TsJsChunk = {
+  slug: string;
+  text: string;
+};
+
+/**
+ * Line starts a function-like declaration (heuristic, no full TS parse).
+ */
+function isFunctionStartLine(line: string): boolean {
+  const t = line.trimStart();
+  if (/^(export\s+)?declare\s+/.test(t)) {
+    return false;
+  }
+  if (/^(export\s+)?(async\s+)?function\s+[A-Za-z_$][\w$]*\s*\(/.test(t)) {
+    return true;
+  }
+  if (/^(export\s+)?const\s+[A-Za-z_$][\w$]*\s*=\s*(async\s*)?\(/.test(t)) {
+    return true;
+  }
+  if (/^(export\s+)?const\s+[A-Za-z_$][\w$]*\s*=\s*async\s+function/.test(t)) {
+    return true;
+  }
+  return false;
+}
+
+function slugPart(name: string): string {
+  const safe = name.replace(/[^\w$-]+/g, "-").toLowerCase();
+  return safe.length > 0 ? safe : "block";
+}
+
+function extractRoughName(firstLine: string): string {
+  const m =
+    /function\s+([A-Za-z_$][\w$]*)/.exec(firstLine) ?? /const\s+([A-Za-z_$][\w$]*)/.exec(firstLine);
+  return m !== null && m[1] !== undefined ? m[1] : "fn";
+}
+
+/**
+ * Split `.ts` / `.js` by top-level function-like lines; falls back to paragraph chunks.
+ */
+export function chunkTypeScriptOrJavaScript(relativePath: string, source: string): TsJsChunk[] {
+  const baseSlug = relativePath.replace(/\./g, "-").replace(/\//g, "-");
+  const lines = source.split(/\r?\n/);
+  const starts: number[] = [];
+  for (let i = 0; i < lines.length; i++) {
+    const line = lines[i];
+    if (line !== undefined && isFunctionStartLine(line)) {
+      starts.push(i);
+    }
+  }
+
+  if (starts.length === 0) {
+    return paragraphFallbackChunks(baseSlug, source);
+  }
+
+  const chunks: TsJsChunk[] = [];
+  for (let s = 0; s < starts.length; s++) {
+    const start = starts[s] ?? 0;
+    const end = s + 1 < starts.length ? (starts[s + 1] ?? lines.length) : lines.length;
+    const block = lines.slice(start, end).join("\n").trim();
+    if (block.length === 0) {
+      continue;
+    }
+    const first = lines[start] ?? "";
+    const name = extractRoughName(first);
+    chunks.push({
+      slug: `${baseSlug}#${slugPart(name)}-${String(s)}`,
+      text: block,
+    });
+  }
+
+  return chunks.length > 0 ? chunks : paragraphFallbackChunks(baseSlug, source);
+}
+
+function paragraphFallbackChunks(baseSlug: string, source: string): TsJsChunk[] {
+  const text = source.trim();
+  if (text.length === 0) {
+    return [];
+  }
+  const parts = text.split(/\n\s*\n/).filter((p) => p.trim().length > 0);
+  if (parts.length === 0) {
+    return [{ slug: `${baseSlug}#0`, text }];
+  }
+  return parts.map((p, i) => ({
+    slug: `${baseSlug}#para-${String(i)}`,
+    text: p.trim(),
+  }));
+}

packages/cli/src/knowledge/chunk.ts

@@ -0,0 +1,23 @@
+import { chunkMarkdown } from "./chunk-markdown.js";
+import { chunkTypeScriptOrJavaScript } from "./chunk-typescript.js";
+
+export type KnowledgeChunk = {
+  slug: string;
+  text: string;
+};
+
+export function chunkKnowledgeFile(relativePath: string, source: string): KnowledgeChunk[] {
+  const lower = relativePath.toLowerCase();
+  if (lower.endsWith(".md")) {
+    return chunkMarkdown(relativePath, source);
+  }
+  if (
+    lower.endsWith(".ts") ||
+    lower.endsWith(".tsx") ||
+    lower.endsWith(".js") ||
+    lower.endsWith(".jsx")
+  ) {
+    return chunkTypeScriptOrJavaScript(relativePath, source);
+  }
+  return [{ slug: `${relativePath.replace(/\//g, "-")}#0`, text: source.trim() }];
+}

packages/cli/src/knowledge/embed-service.ts

@@ -0,0 +1,101 @@
+/**
+ * Remote embedding service client — calls embed.shazhou.workers.dev
+ * for real vector embeddings. Falls back to fake hash-based embeddings
+ * if credentials are not configured.
+ */
+
+type EmbedResponse = {
+  embeddings: number[][];
+  model: string;
+  dimensions: number;
+  cached: boolean[];
+};
+
+export type EmbedServiceConfig = {
+  url: string;
+  token: string;
+};
+
+/**
+ * Resolve embed service config from environment or cfg.
+ * Returns null if not configured (will fall back to placeholder).
+ */
+export function resolveEmbedConfig(): EmbedServiceConfig | null {
+  const url = process.env.EMBED_SERVICE_URL ?? null;
+  const token = process.env.EMBED_AUTH_TOKEN ?? null;
+  if (url === null || token === null) {
+    return null;
+  }
+  return { url, token };
+}
+
+const BATCH_SIZE = 100;
+
+/**
+ * Call remote embedding service. Batches texts in groups of 100.
+ * Returns Float32Array per text (stored as Buffer for SQLite BLOB).
+ */
+export async function embedTexts(config: EmbedServiceConfig, texts: string[]): Promise<Buffer[]> {
+  const results: Buffer[] = [];
+
+  for (let i = 0; i < texts.length; i += BATCH_SIZE) {
+    const batch = texts.slice(i, i + BATCH_SIZE);
+    const resp = await fetch(`${config.url}/embed`, {
+      method: "POST",
+      headers: {
+        "Content-Type": "application/json",
+        Authorization: `Bearer ${config.token}`,
+      },
+      body: JSON.stringify({ texts: batch }),
+    });
+
+    if (!resp.ok) {
+      const body = await resp.text();
+      throw new Error(`Embed service error ${String(resp.status)}: ${body}`);
+    }
+
+    const data = (await resp.json()) as EmbedResponse;
+
+    for (const vec of data.embeddings) {
+      const buf = Buffer.alloc(vec.length * 4);
+      for (let j = 0; j < vec.length; j++) {
+        buf.writeFloatLE(vec[j] as number, j * 4);
+      }
+      results.push(buf);
+    }
+  }
+
+  return results;
+}
+
+/**
+ * Embed a single text (for query). Returns Float32Array as Buffer.
+ */
+export async function embedQuery(config: EmbedServiceConfig, text: string): Promise<Buffer> {
+  const results = await embedTexts(config, [text]);
+  const first = results[0];
+  if (first === undefined) {
+    throw new Error("Embed service returned empty result");
+  }
+  return first;
+}
+
+/**
+ * Cosine similarity between two embedding buffers (Float32LE encoded).
+ */
+export function cosineSimilarity(a: Buffer, b: Buffer): number {
+  const len = Math.min(a.length, b.length) / 4;
+  let dot = 0;
+  let normA = 0;
+  let normB = 0;
+  for (let i = 0; i < len; i++) {
+    const va = a.readFloatLE(i * 4);
+    const vb = b.readFloatLE(i * 4);
+    dot += va * vb;
+    normA += va * va;
+    normB += vb * vb;
+  }
+  const denom = Math.sqrt(normA) * Math.sqrt(normB);
+  if (denom === 0) return 0;
+  return dot / denom;
+}

packages/cli/src/knowledge/exclude-match.ts

@@ -0,0 +1,19 @@
+import picomatch from "picomatch";
+
+const PICOMATCH_OPTS = { dot: true } as const;
+
+/**
+ * True if `relativePosixPath` matches any exclude glob (POSIX slashes).
+ */
+export function matchesKnowledgeExclude(
+  relativePosixPath: string,
+  excludePatterns: ReadonlyArray<string>,
+): boolean {
+  for (const pattern of excludePatterns) {
+    const isMatch = picomatch(pattern, PICOMATCH_OPTS);
+    if (isMatch(relativePosixPath)) {
+      return true;
+    }
+  }
+  return false;
+}

packages/cli/src/knowledge/fake-embedding.ts

@@ -0,0 +1,7 @@
+import { createHash } from "node:crypto";
+
+/** Deterministic placeholder embedding bytes until a remote embedding service exists (RFC-003). */
+export function fakeEmbeddingBytes(text: string): Buffer {
+  const hash = createHash("sha256").update(text, "utf8").digest();
+  return Buffer.concat([hash, hash, hash, hash]);
+}

packages/cli/src/knowledge/glob-files.ts

@@ -0,0 +1,39 @@
+import { globSync, statSync } from "node:fs";
+import { join } from "node:path";
+
+import type { KnowledgeConfig } from "@uncaged/nerve-core";
+
+import { matchesKnowledgeExclude } from "./exclude-match.js";
+
+function toPosix(rel: string): string {
+  return rel.split("\\").join("/");
+}
+
+function isFileUnderRoot(repoRoot: string, rel: string): boolean {
+  try {
+    return statSync(join(repoRoot, rel)).isFile();
+  } catch {
+    return false;
+  }
+}
+
+/**
+ * Files matched by `include` globs minus `exclude` globs, relative POSIX paths, sorted.
+ */
+export function listKnowledgeFiles(repoRoot: string, config: KnowledgeConfig): string[] {
+  const matched = new Set<string>();
+  for (const pattern of config.include) {
+    const paths = globSync(pattern, { cwd: repoRoot });
+    for (const rel of paths) {
+      const posix = toPosix(rel);
+      if (!isFileUnderRoot(repoRoot, posix)) {
+        continue;
+      }
+      if (matchesKnowledgeExclude(posix, config.exclude)) {
+        continue;
+      }
+      matched.add(posix);
+    }
+  }
+  return [...matched].sort();
+}

packages/cli/src/knowledge/knowledge-db.ts

@@ -0,0 +1,95 @@
+import { createHash } from "node:crypto";
+import { DatabaseSync } from "node:sqlite";
+
+export type KnowledgeChunkRow = {
+  path: string;
+  slug: string;
+  chunkIndex: number;
+  text: string;
+  embedding: Buffer;
+  contentHash: string;
+};
+
+export type KnowledgeChunkInsert = {
+  path: string;
+  slug: string;
+  chunkIndex: number;
+  text: string;
+  contentHash: string;
+  embedding: Buffer;
+};
+
+const SCHEMA = `
+CREATE TABLE IF NOT EXISTS chunks (
+  id INTEGER PRIMARY KEY AUTOINCREMENT,
+  path TEXT NOT NULL,
+  chunk_index INTEGER NOT NULL,
+  slug TEXT NOT NULL,
+  text TEXT NOT NULL,
+  embedding BLOB NOT NULL,
+  content_hash TEXT NOT NULL,
+  UNIQUE(path, chunk_index)
+);
+
+CREATE INDEX IF NOT EXISTS idx_chunks_path ON chunks(path);
+`;
+
+export function openKnowledgeDb(dbPath: string): DatabaseSync {
+  const db = new DatabaseSync(dbPath);
+  db.exec(SCHEMA);
+  return db;
+}
+
+export function contentHash(text: string): string {
+  return createHash("sha256").update(text, "utf8").digest("hex");
+}
+
+export function replaceAllChunks(db: DatabaseSync, rows: KnowledgeChunkInsert[]): void {
+  db.exec("BEGIN IMMEDIATE");
+  try {
+    db.prepare("DELETE FROM chunks").run();
+    const insert = db.prepare(
+      `INSERT INTO chunks (path, chunk_index, slug, text, embedding, content_hash)
+       VALUES (@path, @chunk_index, @slug, @text, @embedding, @content_hash)`,
+    );
+    for (let i = 0; i < rows.length; i++) {
+      const row = rows[i];
+      if (row === undefined) continue;
+      const emb = row.embedding;
+      insert.run({
+        path: row.path,
+        chunk_index: row.chunkIndex,
+        slug: row.slug,
+        text: row.text,
+        embedding: emb,
+        content_hash: row.contentHash,
+      });
+    }
+    db.exec("COMMIT");
+  } catch (e) {
+    db.exec("ROLLBACK");
+    throw e;
+  }
+}
+
+export function loadAllChunks(db: DatabaseSync): KnowledgeChunkRow[] {
+  const stmt = db.prepare(
+    "SELECT path, chunk_index, slug, text, embedding, content_hash FROM chunks ORDER BY path, chunk_index",
+  );
+  const rows = stmt.all() as Array<{
+    path: string;
+    chunk_index: number;
+    slug: string;
+    text: string;
+    embedding: Buffer | Uint8Array;
+    content_hash: string;
+  }>;
+  return rows.map((r) => ({
+    path: r.path,
+    slug: r.slug,
+    chunkIndex: r.chunk_index,
+    text: r.text,
+    embedding: Buffer.from(r.embedding),
+    contentHash: r.content_hash,
+  }));
+}

packages/cli/src/knowledge/paths.ts

@@ -0,0 +1,2 @@
+export const KNOWLEDGE_YAML = "knowledge.yaml";
+export const KNOWLEDGE_DB = "knowledge.db";

packages/cli/src/knowledge/query-scope.ts

@@ -0,0 +1,13 @@
+/**
+ * `-r` and `-g` are mutually exclusive for `nerve knowledge query`.
+ */
+export function knowledgeQueryScopeConflictMessage(
+  repoFlag: string | null | undefined,
+  globalFlag: boolean,
+): string | null {
+  const hasR = repoFlag !== undefined && repoFlag !== null && String(repoFlag).trim().length > 0;
+  if (hasR && globalFlag) {
+    return "❌ Use either -r <path> or -g, not both.";
+  }
+  return null;
+}

packages/cli/src/knowledge/query.ts

@@ -0,0 +1,116 @@
+import { existsSync } from "node:fs";
+import { join } from "node:path";
+
+import {
+  type EmbedServiceConfig,
+  cosineSimilarity,
+  embedQuery,
+  resolveEmbedConfig,
+} from "./embed-service.js";
+import type { KnowledgeChunkRow } from "./knowledge-db.js";
+import { loadAllChunks, openKnowledgeDb } from "./knowledge-db.js";
+import { wordOverlapScore } from "./word-overlap.js";
+
+export type KnowledgeQueryHit = {
+  repoRoot: string | null;
+  path: string;
+  slug: string;
+  text: string;
+  score: number;
+};
+
+function rankChunksByCosine(
+  queryEmbedding: Buffer,
+  chunks: KnowledgeChunkRow[],
+  limit: number,
+): Array<{ chunk: KnowledgeChunkRow; score: number }> {
+  const scored = chunks.map((chunk) => ({
+    chunk,
+    score: cosineSimilarity(queryEmbedding, chunk.embedding),
+  }));
+  scored.sort((a, b) => b.score - a.score);
+  return scored.slice(0, limit);
+}
+
+function rankChunksByWordOverlap(
+  query: string,
+  chunks: KnowledgeChunkRow[],
+  limit: number,
+): Array<{ chunk: KnowledgeChunkRow; score: number }> {
+  const scored = chunks.map((chunk) => ({
+    chunk,
+    score: wordOverlapScore(query, `${chunk.text}\n${chunk.path}`),
+  }));
+  scored.sort((a, b) => b.score - a.score);
+  return scored.slice(0, limit);
+}
+
+async function rankChunks(
+  queryText: string,
+  chunks: KnowledgeChunkRow[],
+  limit: number,
+  embedConfig: EmbedServiceConfig | null,
+): Promise<Array<{ chunk: KnowledgeChunkRow; score: number }>> {
+  if (embedConfig !== null) {
+    const queryVec = await embedQuery(embedConfig, queryText);
+    return rankChunksByCosine(queryVec, chunks, limit);
+  }
+  return rankChunksByWordOverlap(queryText, chunks, limit);
+}
+
+export async function queryKnowledgeRepo(
+  repoRoot: string,
+  dbPath: string,
+  queryText: string,
+  limit: number,
+): Promise<KnowledgeQueryHit[]> {
+  const embedConfig = resolveEmbedConfig();
+  const db = openKnowledgeDb(dbPath);
+  try {
+    const rows = loadAllChunks(db);
+    const ranked = await rankChunks(queryText, rows, limit, embedConfig);
+    return ranked.map((r) => ({
+      repoRoot,
+      path: r.chunk.path,
+      slug: r.chunk.slug,
+      text: r.chunk.text,
+      score: r.score,
+    }));
+  } finally {
+    db.close();
+  }
+}
+
+export async function queryKnowledgeGlobal(
+  repoRoots: ReadonlyArray<string>,
+  dbFileName: string,
+  queryText: string,
+  limit: number,
+): Promise<KnowledgeQueryHit[]> {
+  const embedConfig = resolveEmbedConfig();
+  const combined: KnowledgeQueryHit[] = [];
+  for (const root of repoRoots) {
+    const dbPath = join(root, dbFileName);
+    if (!existsSync(dbPath)) {
+      continue;
+    }
+    const db = openKnowledgeDb(dbPath);
+    try {
+      const rows = loadAllChunks(db);
+      const ranked = await rankChunks(queryText, rows, limit, embedConfig);
+      for (const r of ranked) {
+        combined.push({
+          repoRoot: root,
+          path: r.chunk.path,
+          slug: r.chunk.slug,
+          text: r.chunk.text,
+          score: r.score,
+        });
+      }
+    } finally {
+      db.close();
+    }
+  }
+  combined.sort((a, b) => b.score - a.score);
+  return combined.slice(0, limit);
+}

packages/cli/src/knowledge/registry.ts

@@ -0,0 +1,60 @@
+import { mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import { dirname, join } from "node:path";
+
+import { getNerveRoot } from "../workspace.js";
+
+export type KnowledgeRepoRegistry = {
+  roots: ReadonlyArray<string>;
+};
+
+const FILE_NAME = "knowledge-repos.json";
+
+/** When `nerveHome` is omitted, uses `~/.uncaged-nerve`. */
+export function getKnowledgeRegistryPath(nerveHome: string | null = null): string {
+  const root = nerveHome ?? getNerveRoot();
+  return join(root, "data", FILE_NAME);
+}
+
+function defaultRegistry(): KnowledgeRepoRegistry {
+  return { roots: [] };
+}
+
+export function readKnowledgeRegistry(nerveHome: string | null = null): KnowledgeRepoRegistry {
+  const path = getKnowledgeRegistryPath(nerveHome);
+  try {
+    const raw = readFileSync(path, "utf8");
+    const parsed: unknown = JSON.parse(raw);
+    if (
+      typeof parsed === "object" &&
+      parsed !== null &&
+      "roots" in parsed &&
+      Array.isArray(parsed.roots)
+    ) {
+      const roots = parsed.roots.filter((x): x is string => typeof x === "string");
+      return { roots: [...new Set(roots)].sort() };
+    }
+  } catch {
+    // missing or invalid — treat as empty
+  }
+  return defaultRegistry();
+}
+
+export function registerKnowledgeRepoRoot(
+  repoRootAbsolute: string,
+  nerveHome: string | null = null,
+): void {
+  const resolved = repoRootAbsolute.trim();
+  if (resolved.length === 0) {
+    return;
+  }
+  const prev = readKnowledgeRegistry(nerveHome);
+  const nextRoots = [...new Set([...prev.roots, resolved])].sort();
+  const next: KnowledgeRepoRegistry = { roots: nextRoots };
+  const path = getKnowledgeRegistryPath(nerveHome);
+  mkdirSync(dirname(path), { recursive: true });
+  writeFileSync(path, `${JSON.stringify(next, null, 2)}\n`, "utf8");
+}
+
+export function listRegisteredKnowledgeRoots(nerveHome: string | null = null): string[] {
+  return [...readKnowledgeRegistry(nerveHome).roots];
+}

packages/cli/src/knowledge/repo-root.ts

@@ -0,0 +1,21 @@
+import { existsSync } from "node:fs";
+import { dirname, join, resolve } from "node:path";
+
+import { KNOWLEDGE_YAML } from "./paths.js";
+
+/**
+ * Walk upward from `startDir` until `knowledge.yaml` exists.
+ */
+export function findKnowledgeRepoRoot(startDir: string): string | null {
+  let dir = resolve(startDir);
+  while (true) {
+    if (existsSync(join(dir, KNOWLEDGE_YAML))) {
+      return dir;
+    }
+    const parent = dirname(dir);
+    if (parent === dir) {
+      return null;
+    }
+    dir = parent;
+  }
+}

packages/cli/src/knowledge/sync.ts

@@ -0,0 +1,111 @@
+import { readFileSync } from "node:fs";
+import { join } from "node:path";
+
+import { type KnowledgeConfig, parseKnowledgeYaml } from "@uncaged/nerve-core";
+
+import { chunkKnowledgeFile } from "./chunk.js";
+import { type EmbedServiceConfig, embedTexts, resolveEmbedConfig } from "./embed-service.js";
+import { fakeEmbeddingBytes } from "./fake-embedding.js";
+import { listKnowledgeFiles } from "./glob-files.js";
+import type { KnowledgeChunkInsert } from "./knowledge-db.js";
+import { contentHash, openKnowledgeDb, replaceAllChunks } from "./knowledge-db.js";
+import { KNOWLEDGE_DB, KNOWLEDGE_YAML } from "./paths.js";
+import { registerKnowledgeRepoRoot } from "./registry.js";
+
+export type KnowledgeSyncResult = {
+  repoRoot: string;
+  dbPath: string;
+  filesIndexed: number;
+  chunksWritten: number;
+  embeddingSource: "remote" | "placeholder";
+};
+
+function loadConfig(repoRoot: string): KnowledgeConfig {
+  const raw = readFileSync(join(repoRoot, KNOWLEDGE_YAML), "utf8");
+  const parsed = parseKnowledgeYaml(raw);
+  if (!parsed.ok) {
+    throw parsed.error;
+  }
+  return parsed.value;
+}
+
+async function computeEmbeddings(
+  texts: string[],
+  embedConfig: EmbedServiceConfig | null,
+): Promise<{ buffers: Buffer[]; source: "remote" | "placeholder" }> {
+  if (embedConfig !== null) {
+    const buffers = await embedTexts(embedConfig, texts);
+    return { buffers, source: "remote" };
+  }
+  // Fallback to placeholder when embed service is not configured
+  const buffers = texts.map((t) => fakeEmbeddingBytes(t));
+  return { buffers, source: "placeholder" };
+}
+
+/**
+ * @param nerveHomeForRegistry — when set, registers this repo under that Nerve home (for tests); default writes `~/.uncaged-nerve/data/knowledge-repos.json`.
+ */
+export async function runKnowledgeSync(
+  repoRoot: string,
+  nerveHomeForRegistry: string | null = null,
+): Promise<KnowledgeSyncResult> {
+  const config = loadConfig(repoRoot);
+  const relFiles = listKnowledgeFiles(repoRoot, config);
+
+  const preInserts: Array<{
+    path: string;
+    slug: string;
+    chunkIndex: number;
+    text: string;
+    hash: string;
+  }> = [];
+
+  for (const rel of relFiles) {
+    const abs = join(repoRoot, rel);
+    const source = readFileSync(abs, "utf8");
+    const chunks = chunkKnowledgeFile(rel, source);
+    for (let i = 0; i < chunks.length; i++) {
+      const ch = chunks[i];
+      if (ch === undefined) continue;
+      preInserts.push({
+        path: rel,
+        slug: ch.slug,
+        chunkIndex: i,
+        text: ch.text,
+        hash: contentHash(ch.text),
+      });
+    }
+  }
+
+  // Compute embeddings (remote or placeholder)
+  const embedConfig = resolveEmbedConfig();
+  const texts = preInserts.map((p) => p.text);
+  const { buffers, source } = await computeEmbeddings(texts, embedConfig);
+
+  const inserts: KnowledgeChunkInsert[] = preInserts.map((p, idx) => ({
+    path: p.path,
+    slug: p.slug,
+    chunkIndex: p.chunkIndex,
+    text: p.text,
+    contentHash: p.hash,
+    embedding: buffers[idx] ?? fakeEmbeddingBytes(p.text),
+  }));
+
+  const dbPath = join(repoRoot, KNOWLEDGE_DB);
+  const db = openKnowledgeDb(dbPath);
+  try {
+    replaceAllChunks(db, inserts);
+  } finally {
+    db.close();
+  }
+
+  registerKnowledgeRepoRoot(repoRoot, nerveHomeForRegistry);
+
+  return {
+    repoRoot,
+    dbPath,
+    filesIndexed: relFiles.length,
+    chunksWritten: inserts.length,
+    embeddingSource: source,
+  };
+}

packages/cli/src/knowledge/word-overlap.ts

@@ -0,0 +1,26 @@
+function tokenize(s: string): Set<string> {
+  const parts = s
+    .toLowerCase()
+    .split(/[^\w]+/)
+    .filter((x) => x.length > 0);
+  return new Set(parts);
+}
+
+/**
+ * Jaccard-like score over word sets (placeholder until real embeddings; RFC-003).
+ */
+export function wordOverlapScore(query: string, document: string): number {
+  const q = tokenize(query);
+  const d = tokenize(document);
+  if (q.size === 0) {
+    return 0;
+  }
+  let inter = 0;
+  for (const w of q) {
+    if (d.has(w)) {
+      inter += 1;
+    }
+  }
+  const union = q.size + d.size - inter;
+  return union === 0 ? 0 : inter / union;
+}