feat: thread root node + workflowAsAgent returns root hash

- Engine generates step Merkle nodes (type: step) after each role step
- Engine generates thread root Merkle node (type: thread) on completion
- WorkflowResult gains rootHash field
- WorkflowFn returns WorkflowCompletion (no rootHash), engine wraps with rootHash
- workflowAsAgent returns rootHash instead of summary
- Full DAG traversal: root → steps → content
- 151 tests passing

Fixes #42

docs/plans/2025-05-07-workflow-as-agent.md

@@ -0,0 +1,315 @@
+# Workflow-as-Agent Implementation Plan
+
+> **For Hermes:** Use subagent-driven-development skill to implement this plan task-by-task.
+
+**Goal:** Enable workflows to invoke other workflows as agents, backed by global CAS and refs tracking.
+
+**Architecture:** Migrate CAS from thread-local to global (`~/.uncaged/workflow/cas/`), add `refs` to RoleStep for GC traceability, then build `workflowAsAgent(name)` factory that resolves workflow name → bundle via registry and spawns a child thread.
+
+**Tech Stack:** TypeScript, Bun, Zod v4, monorepo with `packages/`
+
+**Issue:** https://git.shazhou.work/uncaged/workflow/issues/25
+
+---
+
+## Phase 1: Global CAS Migration
+
+Move CAS storage from `<threadDir>/<threadId>.cas/` to `~/.uncaged/workflow/cas/` (global, content-addressed, immutable). This is a **breaking change** — thread-local `.cas/` directories are abandoned.
+
+### Task 1.1: Add `globalCasDir` helper to `storage-root.ts`
+
+**Objective:** Provide a single function that returns the global CAS directory path.
+
+**Files:**
+- Modify: `packages/workflow/src/storage-root.ts`
+- Test: `packages/workflow/__tests__/storage-root.test.ts`
+
+**Implementation:**
+
+```typescript
+// storage-root.ts — add export
+export function getGlobalCasDir(storageRoot?: string): string {
+  const root = storageRoot ?? getDefaultWorkflowStorageRoot();
+  return join(root, "cas");
+}
+```
+
+Export from `packages/workflow/src/index.ts`.
+
+### Task 1.2: Update `cmd-cas.ts` to use global CAS
+
+**Objective:** CLI `cas get/put/list/rm` no longer needs threadId for storage location — CAS is global. But keep threadId in CLI for backward compat of planner/coder prompts (they pass threadId).
+
+**Files:**
+- Modify: `packages/cli-workflow/src/cmd-cas.ts`
+
+**Changes:**
+- `resolveCasDir` → use `getGlobalCasDir(storageRoot)` instead of deriving from thread data path
+- `cmdCasPut` / `cmdCasGet` / `cmdCasList` / `cmdCasRm`: threadId is still accepted (prompts pass it) but storage goes to global dir
+- Remove the `resolveThreadDataPath` dependency for CAS operations — thread doesn't need to exist to read CAS
+
+```typescript
+import { createThreadCas, getGlobalCasDir } from "@uncaged/workflow";
+
+export async function cmdCasGet(
+  storageRoot: string,
+  _threadId: string, // kept for CLI compat, not used for path
+  hash: string,
+): Promise<Result<string, string>> {
+  const cas = createThreadCas(getGlobalCasDir(storageRoot));
+  const content = await cas.get(hash);
+  if (content === null) {
+    return err(`cas entry not found: ${hash}`);
+  }
+  return ok(content);
+}
+// ... same pattern for put/list/rm
+```
+
+### Task 1.3: Update `cmd-thread.ts` — thread rm no longer deletes `.cas/`
+
+**Objective:** Since CAS is global, `thread rm` should NOT delete CAS entries. CAS cleanup is GC's job.
+
+**Files:**
+- Modify: `packages/cli-workflow/src/cmd-thread.ts`
+- Check: remove any `rmdir` / `unlink` of `<threadId>.cas/` directory
+
+### Task 1.4: Rename `createThreadCas` → `createCasStore`
+
+**Objective:** The name `createThreadCas` is misleading now. Rename to `createCasStore`.
+
+**Files:**
+- Modify: `packages/workflow/src/cas.ts` — rename function
+- Modify: `packages/workflow/src/index.ts` — update export (keep `createThreadCas` as deprecated alias for one release)
+- Modify: all consumers (`cmd-cas.ts`)
+
+### Task 1.5: Update tests
+
+**Objective:** All CAS-related tests use global dir instead of thread-local.
+
+**Files:**
+- Modify: `packages/cli-workflow/__tests__/commands.test.ts`
+- Verify: `bun test` passes
+
+### Task 1.6: Clean up old thread-local `.cas/` references
+
+**Objective:** Remove dead code that creates/reads thread-local `.cas/` directories.
+
+**Files:**
+- Search all `*.ts` for `.cas` path construction patterns
+- Remove orphaned helpers
+
+---
+
+## Phase 2: RoleStep `refs` Tracking
+
+Add `refs: string[]` to persisted role steps so GC can trace which CAS entries are alive.
+
+### Task 2.1: Add `refs` to `RoleOutput` and engine persistence
+
+**Objective:** Every role step can declare which CAS hashes it produced or consumed.
+
+**Files:**
+- Modify: `packages/workflow/src/types.ts`
+- Modify: `packages/workflow/src/engine.ts`
+
+**Changes to `types.ts`:**
+
+```typescript
+export type RoleOutput = {
+  role: string;
+  content: string;
+  meta: Record<string, unknown>;
+  refs: string[];  // CAS hashes produced/consumed by this step
+};
+```
+
+**Changes to `engine.ts`:**
+- `appendDataLine` for role steps: include `refs` field (default `[]` if not provided)
+
+### Task 2.2: Auto-populate refs from meta hashes
+
+**Objective:** The engine should automatically extract CAS hashes from `meta` to populate `refs`, so roles don't need to manually track them.
+
+**Strategy:** After meta extraction, walk the meta object and collect any string that looks like a CAS hash (Crockford Base32, 13 chars). This is a heuristic but works because CAS hashes are distinctive.
+
+Alternative (simpler): Let each `RoleDefinition` optionally declare a `extractRefs(meta: M) => string[]` function. For planner, this returns `meta.phases.map(p => p.hash)`. For coder, `[meta.completedPhase]`.
+
+**Recommended:** The explicit `extractRefs` approach — no magic, no false positives.
+
+**Files:**
+- Modify: `packages/workflow/src/types.ts` — add optional `extractRefs` to `RoleDefinition`
+- Modify: `packages/workflow/src/create-workflow.ts` — call `extractRefs` after meta extraction, set on `RoleOutput.refs`
+- Modify: `packages/workflow-role-planner/src/planner.ts` — implement `extractRefs`
+- Modify: `packages/workflow-role-coder/src/coder.ts` — implement `extractRefs`
+
+```typescript
+// types.ts — RoleDefinition addition
+export type RoleDefinition<Meta extends Record<string, unknown>> = {
+  description: string;
+  systemPrompt: string;
+  extractPrompt: string;
+  schema: z.ZodType<Meta>;
+  extractRefs?: (meta: Meta) => string[];  // CAS hashes to track
+};
+
+// planner.ts
+extractRefs: (meta) => meta.phases.map(p => p.hash),
+
+// coder.ts
+extractRefs: (meta) => [meta.completedPhase],
+```
+
+### Task 2.3: Update fork logic to preserve refs
+
+**Objective:** When forking a thread, `refs` from historical steps must be carried over.
+
+**Files:**
+- Modify: `packages/workflow/src/fork-thread.ts`
+- Verify: `ForkHistoricalStep` / `PrefilledDiskStep` include `refs`
+
+### Task 2.4: Tests for refs tracking
+
+**Files:**
+- Add: `packages/workflow/__tests__/refs-tracking.test.ts`
+- Verify: refs appear in `.data.jsonl` output
+
+---
+
+## Phase 3: CAS Garbage Collection
+
+### Task 3.1: Implement `gc.ts` in `@uncaged/workflow`
+
+**Objective:** Mark-and-sweep GC — scan all thread `.data.jsonl` files, collect `refs`, delete orphaned CAS entries.
+
+**Files:**
+- Create: `packages/workflow/src/gc.ts`
+- Export from: `packages/workflow/src/index.ts`
+
+```typescript
+export type GcResult = {
+  scannedThreads: number;
+  activeRefs: number;
+  deletedEntries: number;
+  deletedHashes: string[];
+};
+
+export async function garbageCollectCas(storageRoot: string): Promise<GcResult> {
+  // 1. Find all .data.jsonl files under storageRoot
+  // 2. Parse each, flatMap step.refs → Set<string>
+  // 3. List all CAS entries via createCasStore(globalCasDir).list()
+  // 4. Delete entries not in active set
+  // 5. Return stats
+}
+```
+
+### Task 3.2: Add `uncaged-workflow gc` CLI command
+
+**Files:**
+- Create: `packages/cli-workflow/src/cmd-gc.ts`
+- Modify: `packages/cli-workflow/src/cli-dispatch.ts` — add `gc` subcommand
+
+### Task 3.3: Run GC on `thread rm`
+
+**Files:**
+- Modify: `packages/cli-workflow/src/cmd-thread.ts` — after deleting thread data, optionally run GC
+
+### Task 3.4: Tests for GC
+
+**Files:**
+- Create: `packages/cli-workflow/__tests__/gc-cli.test.ts`
+
+---
+
+## Phase 4: `workflowAsAgent` Factory
+
+### Task 4.1: Create `workflowAsAgent` in `@uncaged/workflow`
+
+**Objective:** Factory function that takes a workflow name, resolves to bundle, returns an `AgentFn`.
+
+**Files:**
+- Create: `packages/workflow/src/workflow-as-agent.ts`
+- Export from: `packages/workflow/src/index.ts`
+
+```typescript
+import type { AgentFn } from "./types.js";
+
+export type WorkflowAsAgentOptions = {
+  storageRoot?: string;
+};
+
+export function workflowAsAgent(
+  workflowName: string,
+  options?: WorkflowAsAgentOptions,
+): AgentFn {
+  return async (ctx) => {
+    const storageRoot = options?.storageRoot ?? getDefaultWorkflowStorageRoot();
+
+    // 1. Read registry → resolve name to bundle hash + path
+    const registry = await readWorkflowRegistry(storageRoot);
+    const entry = getRegisteredWorkflow(registry, workflowName);
+    if (entry === null) {
+      return `ERROR: workflow "${workflowName}" not found in registry`;
+    }
+
+    // 2. Load bundle
+    const bundlePath = join(storageRoot, "bundles", `${entry.hash}.esm.js`);
+    const bundleExports = await extractBundleExports(bundlePath);
+
+    // 3. Create child thread input from ctx.start.content (parent prompt)
+    const input: ThreadInput = {
+      prompt: ctx.start.content,
+      steps: [],
+    };
+
+    // 4. Generate child threadId
+    const childThreadId = generateUlid();
+
+    // 5. Execute — collect all yields, return final content
+    const io: ExecuteThreadIo = { ... };
+    const result = await executeThread(bundleExports.run, workflowName, input, ...);
+
+    // 6. Return summary as agent content
+    return result.summary;
+  };
+}
+```
+
+### Task 4.2: System-level depth limit
+
+**Objective:** Prevent infinite recursion. Track depth via thread metadata, enforce a global max (default 3, configurable in `workflow.yaml`).
+
+**Files:**
+- Modify: `packages/workflow/src/types.ts` — add `depth` to `WorkflowFnOptions`
+- Modify: `packages/workflow/src/workflow-as-agent.ts` — increment depth, check limit
+- Modify: registry or config types for `maxDepth` setting
+
+### Task 4.3: Tests for workflowAsAgent
+
+**Files:**
+- Create: `packages/workflow/__tests__/workflow-as-agent.test.ts`
+- Test: name resolution, depth limit, child thread execution
+
+### Task 4.4: Integration test — nested workflow
+
+**Objective:** Create a minimal test workflow that calls another workflow via `workflowAsAgent`.
+
+**Files:**
+- Create: `packages/workflow/__tests__/workflow-as-agent-integration.test.ts`
+
+---
+
+## Execution Order
+
+```
+Phase 1 (Global CAS) → Phase 2 (refs) → Phase 3 (GC) → Phase 4 (workflowAsAgent)
+```
+
+Each phase is independently mergeable. Phase 3 depends on Phase 2 (needs refs to know what's alive). Phase 4 depends on Phase 1 (global CAS for cross-thread sharing).
+
+## Breaking Changes
+
+- CAS storage location moves from `<thread>.cas/` to `~/.uncaged/workflow/cas/`
+- `RoleOutput` gains required `refs: string[]` field
+- Existing threads with thread-local CAS will lose access to old CAS data (acceptable — those are short-lived workflow artifacts)
+- `createThreadCas` renamed to `createCasStore` (alias kept temporarily)

examples/hello-world.ts

@@ -28,6 +28,7 @@ const greeter: RoleDefinition<Roles["greeter"]> = {
   systemPrompt: "You greet the user briefly.",
   extractPrompt: "Extract the greeting string produced for the user.",
   schema: greeterMetaSchema,
+  extractRefs: null,
 };
 
 const extract = createExtract({

packages/cli-workflow/__tests__/commands.test.ts

@@ -3,8 +3,9 @@ import { mkdir, mkdtemp, readFile, rm, unlink, writeFile } from "node:fs/promise
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 
-import { getRegisteredWorkflow, readWorkflowRegistry } from "@uncaged/workflow";
+import { getGlobalCasDir, getRegisteredWorkflow, readWorkflowRegistry } from "@uncaged/workflow";
 import { cmdAdd } from "../src/cmd-add.js";
+import { cmdCasGet, cmdCasList, cmdCasPut, cmdCasRm } from "../src/cmd-cas.js";
 import { cmdHistory } from "../src/cmd-history.js";
 import { cmdList, formatListLines } from "../src/cmd-list.js";
 import { cmdRemove } from "../src/cmd-remove.js";
@@ -15,6 +16,9 @@ import { addCliArgs } from "./bundle-fixture.js";
 const fixtureDescriptor = `export const descriptor = { description: "fixture", roles: {} };
 `;
 
+const wfPutImport = `import { putContentMerkleNode } from "@uncaged/workflow";
+`;
+
 describe("cli workflow commands", () => {
   let prevEnv: string | undefined;
   let storageRoot: string;
@@ -40,11 +44,13 @@ describe("cli workflow commands", () => {
     const bundlePath = join(bundleDir, "demo.esm.js");
     await writeFile(
       bundlePath,
-      `${fixtureDescriptor}import fs from "node:fs";
+      `${fixtureDescriptor}${wfPutImport}import fs from "node:fs";
 
-export const run = async function* (input) {
+export const run = async function* (input, options) {
   fs.existsSync(".");
-  yield { role: "noop", content: input.prompt, meta: { done: true } };
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, input.prompt);
+  yield { role: "noop", contentHash: h, meta: { done: true }, refs: [h] };
   return { returnCode: 0, summary: "done" };
 }
 `,
@@ -111,8 +117,8 @@ export const run = async function* (input) { return { returnCode: 0, summary: in
     const bundlePath = join(storageRoot, "solo.esm.js");
     await writeFile(
       bundlePath,
-      `export const run = async function* (input) {
-  yield { role: "x", content: input.prompt, meta: {} };
+      `export const run = async function* () {
+  yield { role: "x", contentHash: "STUBHASH00000000000000001", meta: {}, refs: [] };
   return { returnCode: 0, summary: "ok" };
 }
 `,
@@ -140,8 +146,11 @@ export const run = async function* (input) { return { returnCode: 0, summary: in
     },
   },
 };
-export const run = async function* (input) {
-  yield { role: "greeter", content: input.prompt, meta: { greeting: "hi" } };
+${wfPutImport}
+export const run = async function* (input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, input.prompt);
+  yield { role: "greeter", contentHash: h, meta: { greeting: "hi" }, refs: [h] };
   return { returnCode: 0, summary: "ok" };
 };
 `,
@@ -179,8 +188,10 @@ export const run = async function* (input) {
     const bundlePath = join(bundleDir, "demo.esm.js");
     await writeFile(
       bundlePath,
-      `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "x", meta: {} };
+      `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "x");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "x" };
 }
 `,
@@ -208,8 +219,10 @@ export const run = async function* (input) {
     const dtsPath = join(bundleDir, "types.d.ts");
     await writeFile(
       bundlePath,
-      `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "x", meta: {} };
+      `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "x");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "x" };
 }
 `,
@@ -239,8 +252,10 @@ export const run = async function* (input) {
     const bundlePath = join(bundleDir, "demo.esm.js");
     await writeFile(
       bundlePath,
-      `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "x", meta: {} };
+      `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "x");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "x" };
 }
 `,
@@ -260,13 +275,17 @@ export const run = async function* (input) {
     const bundleDir = join(storageRoot, "src");
     await mkdir(bundleDir, { recursive: true });
     const bundlePath = join(bundleDir, "demo.esm.js");
-    const v1 = `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "v1", meta: {} };
+    const v1 = `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "v1");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "v1" };
 }
 `;
-    const v2 = `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "v2", meta: {} };
+    const v2 = `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "v2");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "v2" };
 }
 `;
@@ -298,13 +317,17 @@ export const run = async function* (input) {
     const bundleDir = join(storageRoot, "src");
     await mkdir(bundleDir, { recursive: true });
     const bundlePath = join(bundleDir, "demo.esm.js");
-    const v1 = `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "v1", meta: {} };
+    const v1 = `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "v1");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "v1" };
 }
 `;
-    const v2 = `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "v2", meta: {} };
+    const v2 = `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "v2");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "v2" };
 }
 `;
@@ -346,8 +369,10 @@ export const run = async function* (input) {
     const bundlePath = join(bundleDir, "demo.esm.js");
     await writeFile(
       bundlePath,
-      `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "x", meta: {} };
+      `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "x");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "x" };
 }
 `,
@@ -357,8 +382,10 @@ export const run = async function* (input) {
     expect(add1.ok).toBe(true);
     await writeFile(
       bundlePath,
-      `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "y", meta: {} };
+      `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "y");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "y" };
 }
 `,
@@ -371,14 +398,47 @@ export const run = async function* (input) {
     expect(bad.ok).toBe(false);
   });
 
+  test("cas put/get/list/rm use global cas dir (thread id not required for storage)", async () => {
+    const put = await cmdCasPut(storageRoot, "nonexistent-thread-id", "phase doc");
+    expect(put.ok).toBe(true);
+    if (!put.ok) {
+      return;
+    }
+    const hash = put.value;
+    const blobPath = join(getGlobalCasDir(storageRoot), `${hash}.txt`);
+    expect(await readFile(blobPath, "utf8")).toBe("phase doc");
+
+    const got = await cmdCasGet(storageRoot, "other-thread", hash);
+    expect(got.ok).toBe(true);
+    if (!got.ok) {
+      return;
+    }
+    expect(got.value).toBe("phase doc");
+
+    const listed = await cmdCasList(storageRoot, "another-thread");
+    expect(listed.ok).toBe(true);
+    if (!listed.ok) {
+      return;
+    }
+    expect(listed.value).toContain(hash);
+
+    const removed = await cmdCasRm(storageRoot, "rm-thread", hash);
+    expect(removed.ok).toBe(true);
+
+    const missing = await cmdCasGet(storageRoot, "after-rm", hash);
+    expect(missing.ok).toBe(false);
+  });
+
   test("rollback rejects missing bundle file for target hash", async () => {
     const bundleDir = join(storageRoot, "src");
     await mkdir(bundleDir, { recursive: true });
     const bundlePath = join(bundleDir, "demo.esm.js");
     await writeFile(
       bundlePath,
-      `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "x", meta: {} };
+      `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "x");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "x" };
 }
 `,
@@ -392,8 +452,10 @@ export const run = async function* (input) {
     const hash1 = add1.value.hash;
     await writeFile(
       bundlePath,
-      `${fixtureDescriptor}export const run = async function* (input) {
-  yield { role: "a", content: "y", meta: {} };
+      `${fixtureDescriptor}${wfPutImport}export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "y");
+  yield { role: "a", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "y" };
 }
 `,

packages/cli-workflow/__tests__/fork-cli.test.ts

@@ -2,6 +2,7 @@ import { afterEach, beforeEach, describe, expect, test } from "bun:test";
 import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
+import { createCasStore, getContentMerklePayload, getGlobalCasDir } from "@uncaged/workflow";
 import { cmdAdd } from "../src/cmd-add.js";
 import { cmdFork } from "../src/cmd-fork.js";
 import { cmdRun } from "../src/cmd-run.js";
@@ -9,7 +10,9 @@ import { pathExists } from "../src/fs-utils.js";
 import { addCliArgs } from "./bundle-fixture.js";
 
 /** Three-role workflow that respects `input.steps` for fork/resume. */
-const threeRoleBundleSource = `export const descriptor = {
+const threeRoleBundleSource = `import { putContentMerkleNode } from "@uncaged/workflow";
+
+export const descriptor = {
   description: "fork-cli",
   roles: {
     planner: { description: "planner", schema: {} },
@@ -17,20 +20,21 @@ const threeRoleBundleSource = `export const descriptor = {
     reviewer: { description: "reviewer", schema: {} },
   },
 };
-export const run = async function* (input) {
+export const run = async function* (input, options) {
+  const cas = options.cas;
   const has = (r) => input.steps.some((s) => s.role === r);
   if (!has("planner")) {
-    yield { role: "planner", content: "p1", meta: { k: "planner" } };
+    const h = await putContentMerkleNode(cas, "p1");
+    yield { role: "planner", contentHash: h, meta: { k: "planner" }, refs: [h] };
   }
   if (!has("coder")) {
-    yield { role: "coder", content: "c1", meta: { k: "coder" } };
+    const h = await putContentMerkleNode(cas, "c1");
+    yield { role: "coder", contentHash: h, meta: { k: "coder" }, refs: [h] };
   }
   if (!has("reviewer")) {
-    yield {
-      role: "reviewer",
-      content: "rev-" + String(input.steps.length),
-      meta: { k: "reviewer" },
-    };
+    const body = "rev-" + String(input.steps.length);
+    const h = await putContentMerkleNode(cas, body);
+    yield { role: "reviewer", contentHash: h, meta: { k: "reviewer" }, refs: [h] };
   }
   return { returnCode: 0, summary: "done" };
 };
@@ -132,7 +136,8 @@ describe("cli fork", () => {
 
     const last = JSON.parse(lines[lines.length - 1] ?? "{}") as Record<string, unknown>;
     expect(last.role).toBe("reviewer");
-    expect(last.content).toBe("rev-1");
+    const cas = createCasStore(getGlobalCasDir(storageRoot));
+    expect(await getContentMerklePayload(cas, String(last.contentHash))).toBe("rev-1");
   });
 
   test("fork without --from-role retries last role", async () => {
@@ -179,11 +184,12 @@ describe("cli fork", () => {
 
     const replayCoder = JSON.parse(lines[2] ?? "{}") as Record<string, unknown>;
     expect(replayCoder.role).toBe("coder");
-    expect(replayCoder.content).toBe("c1");
+    const cas = createCasStore(getGlobalCasDir(storageRoot));
+    expect(await getContentMerklePayload(cas, String(replayCoder.contentHash))).toBe("c1");
 
     const last = JSON.parse(lines[lines.length - 1] ?? "{}") as Record<string, unknown>;
     expect(last.role).toBe("reviewer");
-    expect(last.content).toBe("rev-2");
+    expect(await getContentMerklePayload(cas, String(last.contentHash))).toBe("rev-2");
   });
 
   test("fork rejects unknown role with available names", async () => {

packages/cli-workflow/__tests__/gc-cli.test.ts

@@ -0,0 +1,162 @@
+import { afterEach, beforeEach, describe, expect, test } from "bun:test";
+import { spawnSync } from "node:child_process";
+import { mkdir, mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { fileURLToPath } from "node:url";
+import {
+  createCasStore,
+  garbageCollectCas,
+  getGlobalCasDir,
+  putContentMerkleNode,
+} from "@uncaged/workflow";
+import { cmdThreadRemove } from "../src/cmd-thread.js";
+import { pathExists } from "../src/fs-utils.js";
+
+const cliEntryPath = fileURLToPath(new URL("../src/cli.ts", import.meta.url));
+
+async function writeDemoDataJsonl(params: {
+  path: string;
+  threadId: string;
+  bundleHash: string;
+  cas: ReturnType<typeof createCasStore>;
+  activeHash: string;
+}): Promise<void> {
+  const bodyHash = await putContentMerkleNode(params.cas, "p");
+  const text = [
+    JSON.stringify({
+      name: "demo",
+      hash: params.bundleHash,
+      threadId: params.threadId,
+      parameters: { prompt: "hi", options: { maxRounds: 5 } },
+      timestamp: 100,
+    }),
+    JSON.stringify({
+      role: "planner",
+      contentHash: bodyHash,
+      meta: {},
+      refs: [params.activeHash, bodyHash],
+      timestamp: 101,
+    }),
+    "",
+  ].join("\n");
+  await writeFile(params.path, text, "utf8");
+}
+
+describe("gc cli and garbageCollectCas", () => {
+  let prevEnv: string | undefined;
+  let storageRoot: string;
+
+  beforeEach(async () => {
+    prevEnv = process.env.UNCAGED_WORKFLOW_STORAGE_ROOT;
+    storageRoot = await mkdtemp(join(tmpdir(), "uncaged-wf-gc-"));
+    process.env.UNCAGED_WORKFLOW_STORAGE_ROOT = storageRoot;
+  });
+
+  afterEach(async () => {
+    if (prevEnv === undefined) {
+      delete process.env.UNCAGED_WORKFLOW_STORAGE_ROOT;
+    } else {
+      process.env.UNCAGED_WORKFLOW_STORAGE_ROOT = prevEnv;
+    }
+    await rm(storageRoot, { recursive: true, force: true });
+  });
+
+  test("garbageCollectCas keeps CAS entries referenced by thread refs", async () => {
+    const bundleHash = "C9NMV6V2TQT81";
+    const threadId = "01AAA1111111111111111111";
+    const logsDir = join(storageRoot, "logs", bundleHash);
+    await mkdir(logsDir, { recursive: true });
+
+    const cas = createCasStore(getGlobalCasDir(storageRoot));
+    const activeHash = await cas.put("active-blob");
+    const orphanHash = await cas.put("orphan-blob");
+
+    await writeDemoDataJsonl({
+      path: join(logsDir, `${threadId}.data.jsonl`),
+      threadId,
+      bundleHash,
+      cas,
+      activeHash,
+    });
+
+    const gc = await garbageCollectCas(storageRoot);
+    expect(gc.ok).toBe(true);
+    if (!gc.ok) {
+      return;
+    }
+    expect(gc.value.scannedThreads).toBe(1);
+    expect(gc.value.activeRefs).toBe(2);
+    expect(gc.value.deletedEntries).toBe(1);
+    expect(gc.value.deletedHashes).toEqual([orphanHash]);
+
+    expect(await pathExists(join(getGlobalCasDir(storageRoot), `${activeHash}.txt`))).toBe(true);
+    expect(await pathExists(join(getGlobalCasDir(storageRoot), `${orphanHash}.txt`))).toBe(false);
+  });
+
+  test("garbageCollectCas deletes orphaned CAS when no threads reference them", async () => {
+    const cas = createCasStore(getGlobalCasDir(storageRoot));
+    const orphanHash = await cas.put("lonely");
+
+    const gc = await garbageCollectCas(storageRoot);
+    expect(gc.ok).toBe(true);
+    if (!gc.ok) {
+      return;
+    }
+    expect(gc.value.scannedThreads).toBe(0);
+    expect(gc.value.activeRefs).toBe(0);
+    expect(gc.value.deletedEntries).toBe(1);
+    expect(gc.value.deletedHashes).toEqual([orphanHash]);
+    expect(await pathExists(join(getGlobalCasDir(storageRoot), `${orphanHash}.txt`))).toBe(false);
+  });
+
+  test("cli gc prints stats", async () => {
+    const bundleHash = "C9NMV6V2TQT81";
+    const threadId = "01BBB2222222222222222222";
+    const logsDir = join(storageRoot, "logs", bundleHash);
+    await mkdir(logsDir, { recursive: true });
+
+    const cas = createCasStore(getGlobalCasDir(storageRoot));
+    const activeHash = await cas.put("keep-me");
+    await cas.put("drop-me");
+
+    await writeDemoDataJsonl({
+      path: join(logsDir, `${threadId}.data.jsonl`),
+      threadId,
+      bundleHash,
+      cas,
+      activeHash,
+    });
+
+    const env = { ...process.env, UNCAGED_WORKFLOW_STORAGE_ROOT: storageRoot };
+    const proc = spawnSync(process.execPath, [cliEntryPath, "gc"], { env, encoding: "utf8" });
+    expect(proc.status).toBe(0);
+    expect(String(proc.stdout).trim()).toBe("scanned 1 threads, 2 active refs, deleted 1 entries");
+  });
+
+  test("thread rm triggers gc so unreferenced CAS is removed", async () => {
+    const bundleHash = "C9NMV6V2TQT81";
+    const threadId = "01CCC3333333333333333333";
+    const logsDir = join(storageRoot, "logs", bundleHash);
+    await mkdir(logsDir, { recursive: true });
+
+    const cas = createCasStore(getGlobalCasDir(storageRoot));
+    const activeHash = await cas.put("pinned-by-ref");
+    await writeDemoDataJsonl({
+      path: join(logsDir, `${threadId}.data.jsonl`),
+      threadId,
+      bundleHash,
+      cas,
+      activeHash,
+    });
+
+    const orphanHash = await cas.put("orphan-after-rm");
+    const orphanPath = join(getGlobalCasDir(storageRoot), `${orphanHash}.txt`);
+
+    const removed = await cmdThreadRemove(storageRoot, threadId);
+    expect(removed.ok).toBe(true);
+
+    expect(await pathExists(orphanPath)).toBe(false);
+    expect(await pathExists(join(getGlobalCasDir(storageRoot), `${activeHash}.txt`))).toBe(false);
+  });
+});

packages/cli-workflow/__tests__/thread-cli.test.ts

@@ -4,7 +4,9 @@ import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { dirname, join } from "node:path";
 import { fileURLToPath } from "node:url";
+import { getGlobalCasDir } from "@uncaged/workflow";
 import { cmdAdd } from "../src/cmd-add.js";
+import { cmdCasPut } from "../src/cmd-cas.js";
 import { cmdKill } from "../src/cmd-kill.js";
 import { cmdPause } from "../src/cmd-pause.js";
 import { cmdPs } from "../src/cmd-ps.js";
@@ -12,9 +14,12 @@ import { cmdResume } from "../src/cmd-resume.js";
 import { cmdRun } from "../src/cmd-run.js";
 import { cmdThreadRemove, cmdThreadShow } from "../src/cmd-thread.js";
 import { cmdThreads } from "../src/cmd-threads.js";
-import { pathExists } from "../src/fs-utils.js";
+import { pathExists, readTextFileIfExists } from "../src/fs-utils.js";
 import { addCliArgs } from "./bundle-fixture.js";
 
+const wfPutImport = `import { putContentMerkleNode } from "@uncaged/workflow";
+`;
+
 const threadFixtureDescriptor = `export const descriptor = {
   description: "thread-cli",
   roles: {
@@ -29,18 +34,26 @@ const threadFixtureDescriptor = `export const descriptor = {
 `;
 
 const fastBundleSource = `${threadFixtureDescriptor}
-export const run = async function* (input) {
-  yield { role: "planner", content: "plan", meta: { plan: input.prompt } };
-  yield { role: "coder", content: "code", meta: { diff: "y" } };
+${wfPutImport}
+export const run = async function* (input, options) {
+  const cas = options.cas;
+  let h = await putContentMerkleNode(cas, "plan");
+  yield { role: "planner", contentHash: h, meta: { plan: input.prompt }, refs: [h] };
+  h = await putContentMerkleNode(cas, "code");
+  yield { role: "coder", contentHash: h, meta: { diff: "y" }, refs: [h] };
   return { returnCode: 0, summary: "done" };
 };
 `;
 
 const slowPlannerBundleSource = `${threadFixtureDescriptor}
-export const run = async function* (input) {
+${wfPutImport}
+export const run = async function* (input, options) {
   await new Promise((r) => setTimeout(r, 400));
-  yield { role: "planner", content: "plan", meta: { plan: input.prompt } };
-  yield { role: "coder", content: "code", meta: { diff: "y" } };
+  const cas = options.cas;
+  let h = await putContentMerkleNode(cas, "plan");
+  yield { role: "planner", contentHash: h, meta: { plan: input.prompt }, refs: [h] };
+  h = await putContentMerkleNode(cas, "code");
+  yield { role: "coder", contentHash: h, meta: { diff: "y" }, refs: [h] };
   return { returnCode: 0, summary: "done" };
 };
 `;
@@ -48,27 +61,38 @@ export const run = async function* (input) {
 const cliEntryPath = fileURLToPath(new URL("../src/cli.ts", import.meta.url));
 
 const abortablePlannerBundleSource = `${threadFixtureDescriptor}
-export const run = async function* (input) {
+${wfPutImport}
+export const run = async function* (input, options) {
   await new Promise((r) => setTimeout(r, 600));
-  yield { role: "planner", content: "plan", meta: { plan: input.prompt } };
-  yield { role: "coder", content: "code", meta: { diff: "y" } };
+  const cas = options.cas;
+  let h = await putContentMerkleNode(cas, "plan");
+  yield { role: "planner", contentHash: h, meta: { plan: input.prompt }, refs: [h] };
+  h = await putContentMerkleNode(cas, "code");
+  yield { role: "coder", contentHash: h, meta: { diff: "y" }, refs: [h] };
   return { returnCode: 0, summary: "done" };
 };
 `;
 
 const pauseResumeBundleSource = `${threadFixtureDescriptor}
-export const run = async function* (input) {
-  yield { role: "first", content: "f", meta: {} };
+${wfPutImport}
+export const run = async function* (_input, options) {
+  const cas = options.cas;
+  let h = await putContentMerkleNode(cas, "f");
+  yield { role: "first", contentHash: h, meta: {}, refs: [h] };
   await new Promise((r) => setTimeout(r, 1500));
-  yield { role: "second", content: "s", meta: {} };
+  h = await putContentMerkleNode(cas, "s");
+  yield { role: "second", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "done" };
 };
 `;
 
 const delayedFirstYieldBundleSource = `${threadFixtureDescriptor}
-export const run = async function* (input) {
+${wfPutImport}
+export const run = async function* (_input, options) {
   await new Promise((r) => setTimeout(r, 900));
-  yield { role: "only", content: "x", meta: {} };
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "x");
+  yield { role: "only", contentHash: h, meta: {}, refs: [h] };
   return { returnCode: 0, summary: "done" };
 };
 `;
@@ -175,6 +199,55 @@ describe("cli thread commands", () => {
     expect(await pathExists(dataPath)).toBe(false);
   });
 
+  test("thread rm runs GC and removes CAS blobs not referenced by any remaining thread", async () => {
+    const bundleDir = join(storageRoot, "src");
+    await mkdir(bundleDir, { recursive: true });
+    const bundlePath = join(bundleDir, "demo.esm.js");
+    await writeFile(bundlePath, fastBundleSource, "utf8");
+
+    const added = await cmdAdd(storageRoot, addCliArgs("solve-issue", bundlePath));
+    expect(added.ok).toBe(true);
+    if (!added.ok) {
+      return;
+    }
+
+    const ran = await cmdRun(storageRoot, "solve-issue", "hello", 5);
+    expect(ran.ok).toBe(true);
+    if (!ran.ok) {
+      return;
+    }
+
+    const threadId = ran.value.threadId;
+
+    let threads = await cmdThreads(storageRoot, []);
+    for (
+      let attempt = 0;
+      attempt < 50 && threads.ok && !threads.value.some((l) => l.includes(threadId));
+      attempt++
+    ) {
+      await new Promise((r) => setTimeout(r, 20));
+      threads = await cmdThreads(storageRoot, []);
+    }
+
+    const dataPath = join(storageRoot, "logs", added.value.hash, `${threadId}.data.jsonl`);
+    const runningPath = join(dirname(dataPath), `${threadId}.running`);
+    await waitUntilRunningFileAbsent(runningPath, 120);
+
+    const put = await cmdCasPut(storageRoot, threadId, "keep-after-thread-rm");
+    expect(put.ok).toBe(true);
+    if (!put.ok) {
+      return;
+    }
+    const hash = put.value;
+    const casBlob = join(getGlobalCasDir(storageRoot), `${hash}.txt`);
+
+    const removed = await cmdThreadRemove(storageRoot, threadId);
+    expect(removed.ok).toBe(true);
+
+    const stillThere = await readTextFileIfExists(casBlob);
+    expect(stillThere).toBeNull();
+  });
+
   test("cli entrypoint dispatches threads / ps (spawn)", () => {
     const env = { ...process.env, UNCAGED_WORKFLOW_STORAGE_ROOT: storageRoot };
     const threads = spawnSync(process.execPath, [cliEntryPath, "threads"], {

packages/cli-workflow/src/cli-dispatch.ts

@@ -2,6 +2,7 @@ import { printCliError, printCliLine, printCliWarn } from "./cli-output.js";
 import { cmdAdd, formatAddSuccess, parseAddArgv } from "./cmd-add.js";
 import { cmdCasGet, cmdCasList, cmdCasPut, cmdCasRm } from "./cmd-cas.js";
 import { cmdFork, parseForkArgv } from "./cmd-fork.js";
+import { cmdGc } from "./cmd-gc.js";
 import { cmdHistory } from "./cmd-history.js";
 import { cmdKill } from "./cmd-kill.js";
 import { cmdList, formatListLines } from "./cmd-list.js";
@@ -34,6 +35,7 @@ function usage(): string {
     "  uncaged-workflow thread <id>",
     "  uncaged-workflow thread rm <id>",
     "  uncaged-workflow fork <thread-id> [--from-role <role>]",
+    "  uncaged-workflow gc",
     "  uncaged-workflow cas get <thread-id> <hash>",
     "  uncaged-workflow cas put <thread-id> <content>",
     "  uncaged-workflow cas list <thread-id>",
@@ -266,6 +268,23 @@ async function dispatchThreadBranch(storageRoot: string, rest: string[]): Promis
   return dispatchThread(storageRoot, rest);
 }
 
+async function dispatchGc(storageRoot: string, argv: string[]): Promise<number> {
+  if (argv.length > 0) {
+    printCliError(`${usage()}\n\nerror: gc takes no arguments`);
+    return 1;
+  }
+  const result = await cmdGc(storageRoot);
+  if (!result.ok) {
+    printCliError(result.error);
+    return 1;
+  }
+  const stats = result.value;
+  printCliLine(
+    `scanned ${stats.scannedThreads} threads, ${stats.activeRefs} active refs, deleted ${stats.deletedEntries} entries`,
+  );
+  return 0;
+}
+
 async function dispatchFork(storageRoot: string, argv: string[]): Promise<number> {
   const parsed = parseForkArgv(argv);
   if (!parsed.ok) {
@@ -387,6 +406,7 @@ const COMMAND_TABLE: Record<string, DispatchFn> = {
   threads: dispatchThreads,
   thread: dispatchThreadBranch,
   fork: dispatchFork,
+  gc: dispatchGc,
   cas: dispatchCas,
 };
 

packages/cli-workflow/src/cmd-add.ts

@@ -192,7 +192,7 @@ export async function cmdAdd(
     return validated;
   }
 
-  const extracted = await extractBundleExports(resolvedPath);
+  const extracted = await extractBundleExports(resolvedPath, { storageRoot });
   if (!extracted.ok) {
     return extracted;
   }

packages/cli-workflow/src/cmd-cas.ts

@@ -1,23 +1,11 @@
-import { dirname, join } from "node:path";
-
-import { createThreadCas, err, ok, type Result } from "@uncaged/workflow";
-
-import { resolveThreadDataPath } from "./thread-scan.js";
-
-function resolveCasDir(threadDataPath: string, threadId: string): string {
-  return join(dirname(threadDataPath), `${threadId}.cas`);
-}
+import { createCasStore, err, getGlobalCasDir, ok, type Result } from "@uncaged/workflow";
 
 export async function cmdCasGet(
   storageRoot: string,
-  threadId: string,
+  _threadId: string,
   hash: string,
 ): Promise<Result<string, string>> {
-  const dataPath = await resolveThreadDataPath(storageRoot, threadId);
-  if (dataPath === null) {
-    return err(`thread not found: ${threadId}`);
-  }
-  const cas = createThreadCas(resolveCasDir(dataPath, threadId));
+  const cas = createCasStore(getGlobalCasDir(storageRoot));
   const content = await cas.get(hash);
   if (content === null) {
     return err(`cas entry not found: ${hash}`);
@@ -27,41 +15,29 @@ export async function cmdCasGet(
 
 export async function cmdCasPut(
   storageRoot: string,
-  threadId: string,
+  _threadId: string,
   content: string,
 ): Promise<Result<string, string>> {
-  const dataPath = await resolveThreadDataPath(storageRoot, threadId);
-  if (dataPath === null) {
-    return err(`thread not found: ${threadId}`);
-  }
-  const cas = createThreadCas(resolveCasDir(dataPath, threadId));
+  const cas = createCasStore(getGlobalCasDir(storageRoot));
   const hash = await cas.put(content);
   return ok(hash);
 }
 
 export async function cmdCasList(
   storageRoot: string,
-  threadId: string,
+  _threadId: string,
 ): Promise<Result<string[], string>> {
-  const dataPath = await resolveThreadDataPath(storageRoot, threadId);
-  if (dataPath === null) {
-    return err(`thread not found: ${threadId}`);
-  }
-  const cas = createThreadCas(resolveCasDir(dataPath, threadId));
+  const cas = createCasStore(getGlobalCasDir(storageRoot));
   const hashes = await cas.list();
   return ok(hashes);
 }
 
 export async function cmdCasRm(
   storageRoot: string,
-  threadId: string,
+  _threadId: string,
   hash: string,
 ): Promise<Result<void, string>> {
-  const dataPath = await resolveThreadDataPath(storageRoot, threadId);
-  if (dataPath === null) {
-    return err(`thread not found: ${threadId}`);
-  }
-  const cas = createThreadCas(resolveCasDir(dataPath, threadId));
+  const cas = createCasStore(getGlobalCasDir(storageRoot));
   await cas.delete(hash);
   return ok(undefined);
 }

packages/cli-workflow/src/cmd-fork.ts

@@ -65,8 +65,9 @@ export async function cmdFork(
   const newThreadId = generateUlid(Date.now());
   const stepsOnWire = plan.value.historicalSteps.map((s) => ({
     role: s.role,
-    content: s.content,
+    contentHash: s.contentHash,
     meta: s.meta,
+    refs: s.refs,
     timestamp: s.timestamp,
   }));
 

packages/cli-workflow/src/cmd-gc.ts

@@ -0,0 +1,5 @@
+import { type GcResult, garbageCollectCas, type Result } from "@uncaged/workflow";
+
+export async function cmdGc(storageRoot: string): Promise<Result<GcResult, string>> {
+  return garbageCollectCas(storageRoot);
+}

packages/cli-workflow/src/cmd-run.ts

@@ -46,7 +46,7 @@ export async function cmdRun(
       threadId,
       workflowName: name,
       prompt,
-      options: { maxRounds },
+      options: { maxRounds, depth: 0 },
     },
     { awaitResponseLine: false },
   );

packages/cli-workflow/src/cmd-thread.ts

@@ -1,7 +1,7 @@
-import { rm, unlink } from "node:fs/promises";
+import { unlink } from "node:fs/promises";
 import { dirname, join } from "node:path";
 
-import { err, ok, type Result } from "@uncaged/workflow";
+import { err, garbageCollectCas, ok, type Result } from "@uncaged/workflow";
 
 import { readTextFileIfExists } from "./fs-utils.js";
 import { resolveThreadDataPath } from "./thread-scan.js";
@@ -33,12 +33,12 @@ export async function cmdThreadRemove(
   const dir = dirname(dataPath);
   const infoPath = join(dir, `${threadId}.info.jsonl`);
   const runningPath = join(dir, `${threadId}.running`);
-  const casPath = join(dir, `${threadId}.cas`);
 
   await unlink(dataPath);
   await unlink(infoPath).catch(() => {});
   await unlink(runningPath).catch(() => {});
-  await rm(casPath, { recursive: true, force: true });
+
+  await garbageCollectCas(storageRoot);
 
   return ok(undefined);
 }

packages/workflow-agent-cursor/src/index.ts

@@ -54,7 +54,7 @@ export function createCursorAgent(config: CursorAgentConfig): AgentFn {
       "From the thread context, determine the absolute filesystem path where the project/repository is located.",
       extractCtx,
     );
-    const fullPrompt = buildAgentPrompt(ctx);
+    const fullPrompt = await buildAgentPrompt(ctx);
     const args = [
       "-p",
       fullPrompt,

packages/workflow-agent-hermes/src/index.ts

@@ -35,7 +35,7 @@ export function createHermesAgent(config: HermesAgentConfig): AgentFn {
   const timeoutMs = config.timeout;
 
   return async (ctx) => {
-    const fullPrompt = buildAgentPrompt(ctx);
+    const fullPrompt = await buildAgentPrompt(ctx);
     const args = [
       "chat",
       "-q",

packages/workflow-agent-llm/__tests__/create-llm-adapter.test.ts

@@ -1,8 +1,14 @@
 import { describe, expect, test } from "bun:test";
-import { START, type ThreadContext } from "@uncaged/workflow";
+import { mkdtempSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { createCasStore, START, type ThreadContext } from "@uncaged/workflow";
 
 import { createLlmAdapter } from "../src/create-llm-adapter.js";
 
+const casDir = mkdtempSync(join(tmpdir(), "wf-llm-adapter-cas-"));
+const testCas = createCasStore(casDir);
+
 function makeCtx(userContent: string): ThreadContext {
   return {
     start: {
@@ -11,9 +17,11 @@ function makeCtx(userContent: string): ThreadContext {
       meta: { maxRounds: 10 },
       timestamp: 1,
     },
+    depth: 0,
     steps: [],
     threadId: "01TEST000000000000000000TR",
     currentRole: { name: "planner", systemPrompt: "system instructions" },
+    cas: testCas,
   };
 }
 

packages/workflow-role-coder/src/coder.ts

@@ -38,4 +38,5 @@ export const coderRole: RoleDefinition<CoderMeta> = {
   extractPrompt:
     "Extract completedPhase: the planner phase hash finished this round (exact hash string from the plan). If multiple phases were finished in one round, use the last finished phase hash. Extract filesChanged and a summary of the work.",
   schema: coderMetaSchema,
+  extractRefs: (meta) => [meta.completedPhase],
 };

packages/workflow-role-committer/src/committer.ts

@@ -31,4 +31,5 @@ export const committerRole: RoleDefinition<CommitterMeta> = {
   extractPrompt:
     "Extract the commit result: committed (with branch and SHA), recoverable failure, or unrecoverable failure. Include error details and log references if applicable.",
   schema: committerMetaSchema,
+  extractRefs: null,
 };

packages/workflow-role-planner/src/planner.ts

@@ -49,4 +49,5 @@ export const plannerRole: RoleDefinition<PlannerMeta> = {
   extractPrompt:
     "Extract the implementation phases from the agent's output. Each phase has a hash (the CAS content-hash returned by the cas put command) and a title (one-line summary).",
   schema: plannerMetaSchema,
+  extractRefs: (meta) => meta.phases.map((p) => p.hash),
 };

packages/workflow-role-preparer/src/preparer.ts

@@ -47,4 +47,5 @@ export const preparerRole: RoleDefinition<PreparerMeta> = {
   extractPrompt:
     "Extract repoPath (absolute path), defaultBranch, conventions (summary string or null), and toolchain (packageManager, testCommand, lintCommand, buildCommand — each string or null).",
   schema: preparerMetaSchema,
+  extractRefs: null,
 };

packages/workflow-role-reviewer/src/reviewer.ts

@@ -21,4 +21,5 @@ export const reviewerRole: RoleDefinition<ReviewerMeta> = {
   extractPrompt:
     "Extract the review verdict: approved or rejected. If rejected, list the blocking issues.",
   schema: reviewerMetaSchema,
+  extractRefs: null,
 };

packages/workflow-template-solve-issue/__tests__/solve-issue-template.test.ts

@@ -1,5 +1,9 @@
 import { afterEach, describe, expect, test } from "bun:test";
+import { mkdtemp, rm } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
 import {
+  createCasStore,
   createExtract,
   END,
   type ModeratorContext,
@@ -104,6 +108,7 @@ function makeCtx(
 ): ModeratorContext<SolveIssueMeta> {
   return {
     threadId: "01TEST000000000000000000TR",
+    depth: 0,
     start: makeStart(maxRounds),
     steps,
   };
@@ -112,7 +117,7 @@ function makeCtx(
 function preparerStep(): RoleStep<SolveIssueMeta> {
   return {
     role: "preparer",
-    content: "prepared",
+    contentHash: "STUBHASHPREPARER01",
     meta: {
       repoPath: "/home/user/repos/test",
       defaultBranch: "main",
@@ -124,6 +129,7 @@ function preparerStep(): RoleStep<SolveIssueMeta> {
         buildCommand: "bun run build",
       },
     },
+    refs: [],
     timestamp: 0,
   };
 }
@@ -131,8 +137,9 @@ function preparerStep(): RoleStep<SolveIssueMeta> {
 function plannerStep(phases: PlannerMeta["phases"] = DEFAULT_PHASES): RoleStep<SolveIssueMeta> {
   return {
     role: "planner",
-    content: "plan",
+    contentHash: "STUBHASHPLANNER001",
     meta: { phases },
+    refs: phases.map((p) => p.hash),
     timestamp: 1,
   };
 }
@@ -140,8 +147,9 @@ function plannerStep(phases: PlannerMeta["phases"] = DEFAULT_PHASES): RoleStep<S
 function coderStep(completedPhase = "4KNMR2PX"): RoleStep<SolveIssueMeta> {
   return {
     role: "coder",
-    content: "code",
+    contentHash: "STUBHASHCODER00001",
     meta: { completedPhase, filesChanged: ["a.ts"], summary: "fixed" },
+    refs: [completedPhase],
     timestamp: 2,
   };
 }
@@ -149,10 +157,11 @@ function coderStep(completedPhase = "4KNMR2PX"): RoleStep<SolveIssueMeta> {
 function reviewerStep(approved: boolean): RoleStep<SolveIssueMeta> {
   return {
     role: "reviewer",
-    content: "rev",
+    contentHash: "STUBHASHREVIEWER01",
     meta: approved
       ? { status: "approved" as const }
       : { status: "rejected" as const, issues: ["needs fix"] },
+    refs: [],
     timestamp: 3,
   };
 }
@@ -160,8 +169,9 @@ function reviewerStep(approved: boolean): RoleStep<SolveIssueMeta> {
 function committerStep(): RoleStep<SolveIssueMeta> {
   return {
     role: "committer",
-    content: "commit",
+    contentHash: "STUBHASHCOMMITTER1",
     meta: { status: "committed", branch: "feat/issue-1", commitSha: "abc1234" },
+    refs: [],
     timestamp: 4,
   };
 }
@@ -275,10 +285,15 @@ describe("solveIssueModerator", () => {
 
 describe("createSolveIssueRun", () => {
   let restoreFetch: (() => void) | null = null;
+  let casDir: string | undefined;
 
-  afterEach(() => {
+  afterEach(async () => {
     restoreFetch?.();
     restoreFetch = null;
+    if (casDir !== undefined) {
+      await rm(casDir, { recursive: true, force: true }).catch(() => {});
+      casDir = undefined;
+    }
   });
 
   test("structured extraction yields preparer then planner meta from mocked chat completions", async () => {
@@ -295,10 +310,13 @@ describe("createSolveIssueRun", () => {
     };
     restoreFetch = installMockChatCompletions([EXPECT_PREPARER_META, EXPECT_PLANNER_META]);
 
+    casDir = await mkdtemp(join(tmpdir(), "solve-issue-cas-"));
+    const cas = createCasStore(casDir);
+
     const run = createSolveIssueRun({ agent: async () => "" }, stubExtract);
     const gen = run(
       { prompt: "task", steps: [] },
-      { threadId: "01TEST000000000000000000TR", maxRounds: 20 },
+      { threadId: "01TEST000000000000000000TR", maxRounds: 20, depth: 0, cas },
     );
     const first = await gen.next();
     expect(first.done).toBe(false);
@@ -330,6 +348,9 @@ describe("createSolveIssueRun", () => {
       EXPECT_CODER_META,
     ]);
 
+    casDir = await mkdtemp(join(tmpdir(), "solve-issue-cas-"));
+    const cas = createCasStore(casDir);
+
     const calls: string[] = [];
     const run = createSolveIssueRun(
       {
@@ -356,7 +377,7 @@ describe("createSolveIssueRun", () => {
     );
     const gen = run(
       { prompt: "task", steps: [] },
-      { threadId: "01TEST000000000000000000TR", maxRounds: 20 },
+      { threadId: "01TEST000000000000000000TR", maxRounds: 20, depth: 0, cas },
     );
     await gen.next();
     expect(calls).toEqual(["preparer"]);

packages/workflow-util-agent/__tests__/build-agent-prompt.test.ts

@@ -1,5 +1,8 @@
-import { describe, expect, test } from "bun:test";
-import { START, type ThreadContext } from "@uncaged/workflow";
+import { afterEach, beforeEach, describe, expect, test } from "bun:test";
+import { mkdtemp, rm } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { createCasStore, putContentMerkleNode, START, type ThreadContext } from "@uncaged/workflow";
 
 import { buildAgentPrompt } from "../src/index.js";
 
@@ -13,35 +16,53 @@ function startTask(content: string): ThreadContext["start"] {
 }
 
 describe("buildAgentPrompt", () => {
-  test("includes system prompt and full task; omits tools when there are no steps", () => {
+  let casRoot: string;
+
+  beforeEach(async () => {
+    casRoot = await mkdtemp(join(tmpdir(), "wf-build-prompt-cas-"));
+  });
+
+  afterEach(async () => {
+    await rm(casRoot, { recursive: true, force: true });
+  });
+
+  test("includes system prompt and full task; omits tools when there are no steps", async () => {
+    const cas = createCasStore(casRoot);
     const ctx: ThreadContext = {
       start: startTask("fix the bug"),
+      depth: 0,
       steps: [],
       threadId: "01TEST000000000000000000TR",
       currentRole: { name: START, systemPrompt: "You are an agent." },
+      cas,
     };
-    const text = buildAgentPrompt(ctx);
+    const text = await buildAgentPrompt(ctx);
     expect(text).toContain("You are an agent.");
     expect(text).toContain("## Task");
     expect(text).toContain("fix the bug");
     expect(text).not.toContain("## Tools");
   });
 
-  test("single step shows full content and meta, and includes tools", () => {
+  test("single step shows full content and meta, and includes tools", async () => {
+    const cas = createCasStore(casRoot);
+    const onlyHash = await putContentMerkleNode(cas, "only step full body");
     const ctx: ThreadContext = {
       start: startTask("user task"),
+      depth: 0,
       threadId: "01TEST000000000000000000TR",
       currentRole: { name: "coder", systemPrompt: "Be helpful." },
+      cas,
       steps: [
         {
           role: "coder",
-          content: "only step full body",
+          contentHash: onlyHash,
           meta: { files: ["a.ts"] },
+          refs: [onlyHash],
           timestamp: 2,
         },
       ],
     };
-    const text = buildAgentPrompt(ctx);
+    const text = await buildAgentPrompt(ctx);
     expect(text).toContain("## Task");
     expect(text).toContain("user task");
     expect(text).toContain("## Step: coder");
@@ -51,27 +72,34 @@ describe("buildAgentPrompt", () => {
     expect(text).toContain("uncaged-workflow thread 01TEST000000000000000000TR");
   });
 
-  test("two or more steps: previous steps are meta-only; latest step is full", () => {
+  test("two or more steps: previous steps are meta-only; latest step is full", async () => {
+    const cas = createCasStore(casRoot);
+    const plannerHash = await putContentMerkleNode(cas, "PLANNER_SECRET_FULL_TEXT");
+    const coderHash = await putContentMerkleNode(cas, "last step full content");
     const ctx: ThreadContext = {
       start: startTask("first message full: task content here"),
+      depth: 0,
       threadId: "01TEST000000000000000000TR",
       currentRole: { name: "coder", systemPrompt: "System." },
+      cas,
       steps: [
         {
           role: "planner",
-          content: "PLANNER_SECRET_FULL_TEXT",
+          contentHash: plannerHash,
           meta: { plan: "short" },
+          refs: [plannerHash],
           timestamp: 2,
         },
         {
           role: "coder",
-          content: "last step full content",
+          contentHash: coderHash,
           meta: { done: true },
+          refs: [coderHash],
           timestamp: 3,
         },
       ],
     };
-    const text = buildAgentPrompt(ctx);
+    const text = await buildAgentPrompt(ctx);
     expect(text).toContain("first message full: task content here");
     expect(text).toContain("## Previous Steps");
     expect(text).toContain("### Step 1: planner");
@@ -84,33 +112,42 @@ describe("buildAgentPrompt", () => {
     expect(text).toContain("uncaged-workflow thread 01TEST000000000000000000TR");
   });
 
-  test("middle steps show meta summary only, not full content", () => {
+  test("middle steps show meta summary only, not full content", async () => {
+    const cas = createCasStore(casRoot);
+    const ha = await putContentMerkleNode(cas, "HIDDEN_A");
+    const hb = await putContentMerkleNode(cas, "HIDDEN_B_MIDDLE");
+    const hc = await putContentMerkleNode(cas, "VISIBLE_LAST");
     const ctx: ThreadContext = {
       start: startTask("start"),
+      depth: 0,
       threadId: "01TEST000000000000000000TR",
       currentRole: { name: "c", systemPrompt: "S" },
+      cas,
       steps: [
         {
           role: "a",
-          content: "HIDDEN_A",
+          contentHash: ha,
           meta: { n: 1 },
+          refs: [ha],
           timestamp: 2,
         },
         {
           role: "b",
-          content: "HIDDEN_B_MIDDLE",
+          contentHash: hb,
           meta: { n: 2 },
+          refs: [hb],
           timestamp: 3,
         },
         {
           role: "c",
-          content: "VISIBLE_LAST",
+          contentHash: hc,
           meta: { n: 3 },
+          refs: [hc],
           timestamp: 4,
         },
       ],
     };
-    const text = buildAgentPrompt(ctx);
+    const text = await buildAgentPrompt(ctx);
     expect(text).not.toContain("HIDDEN_A");
     expect(text).not.toContain("HIDDEN_B_MIDDLE");
     expect(text).toContain('Summary: {"n":1}');

packages/workflow-util-agent/src/build-agent-prompt.ts

@@ -1,7 +1,16 @@
 import type { AgentContext } from "@uncaged/workflow";
+import { getContentMerklePayload } from "@uncaged/workflow";
+
+async function resolveStepText(ctx: AgentContext, contentHash: string): Promise<string> {
+  const text = await getContentMerklePayload(ctx.cas, contentHash);
+  if (text === null) {
+    throw new Error(`buildAgentPrompt: missing CAS blob for ${contentHash}`);
+  }
+  return text;
+}
 
 /** Builds the full agent prompt: system instructions plus summarized thread history. */
-export function buildAgentPrompt(ctx: AgentContext): string {
+export async function buildAgentPrompt(ctx: AgentContext): Promise<string> {
   const lines: string[] = [];
   lines.push(ctx.currentRole.systemPrompt);
   lines.push("");
@@ -15,10 +24,11 @@ export function buildAgentPrompt(ctx: AgentContext): string {
 
   if (steps.length === 1) {
     const s = steps[0];
+    const body = await resolveStepText(ctx, s.contentHash);
     lines.push("");
     lines.push(`## Step: ${s.role}`);
     lines.push("");
-    lines.push(s.content);
+    lines.push(body);
     lines.push("");
     lines.push(`Meta: ${JSON.stringify(s.meta)}`);
   } else {
@@ -31,10 +41,11 @@ export function buildAgentPrompt(ctx: AgentContext): string {
       lines.push(`Summary: ${JSON.stringify(s.meta)}`);
     }
     const last = steps[steps.length - 1];
+    const lastBody = await resolveStepText(ctx, last.contentHash);
     lines.push("");
     lines.push(`## Latest Step: ${last.role}`);
     lines.push("");
-    lines.push(last.content);
+    lines.push(lastBody);
     lines.push("");
     lines.push(`Meta: ${JSON.stringify(last.meta)}`);
   }

packages/workflow/__tests__/build-descriptor.test.ts

@@ -22,6 +22,7 @@ describe("buildDescriptor", () => {
           systemPrompt: "You are an analyst.",
           extractPrompt: "Extract title and count from the analysis.",
           schema,
+          extractRefs: null,
         },
       },
       moderator: () => END,

packages/workflow/__tests__/bundle-validator.test.ts

@@ -26,6 +26,19 @@ export const run = async function* (input) {
     expect(r.ok).toBe(true);
   });
 
+  test("allows static import of @uncaged/workflow", () => {
+    const source = `${minimalDescriptor}import { putContentMerkleNode } from "@uncaged/workflow";
+
+export const run = async function* (_input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "x");
+  return { returnCode: 0, summary: h };
+};
+`;
+    const r = validateWorkflowBundle({ filePath: "/tmp/w.esm.js", source });
+    expect(r.ok).toBe(true);
+  });
+
   test("rejects wrong filename suffix", () => {
     const r = validateWorkflowBundle({
       filePath: "/tmp/w.js",

packages/workflow/__tests__/cas.test.ts

@@ -3,10 +3,16 @@ import { mkdtemp, rm } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 
-import { createThreadCas } from "../src/cas.js";
+import { createCasStore, createThreadCas } from "../src/cas.js";
 import { hashString } from "../src/hash.js";
 
-describe("createThreadCas", () => {
+describe("cas module exports", () => {
+  test("createThreadCas is a deprecated alias of createCasStore", () => {
+    expect(createThreadCas).toBe(createCasStore);
+  });
+});
+
+describe("createCasStore", () => {
   let casDir: string;
 
   beforeEach(async () => {
@@ -18,7 +24,7 @@ describe("createThreadCas", () => {
   });
 
   test("put returns consistent hash for same content", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     const h1 = await cas.put("hello world");
     const h2 = await cas.put("hello world");
     expect(h1).toBe(h2);
@@ -26,14 +32,14 @@ describe("createThreadCas", () => {
   });
 
   test("put returns hash matching hashString", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     const content = "some content to store";
     const h = await cas.put(content);
     expect(h).toBe(hashString(content));
   });
 
   test("get returns stored content", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     const content = "line1\nline2\nline3";
     const h = await cas.put(content);
     const retrieved = await cas.get(h);
@@ -41,13 +47,13 @@ describe("createThreadCas", () => {
   });
 
   test("get returns null for missing hash", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     const result = await cas.get("0000000000000");
     expect(result).toBeNull();
   });
 
   test("delete removes entry", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     const h = await cas.put("to be deleted");
     await cas.delete(h);
     const result = await cas.get(h);
@@ -55,12 +61,12 @@ describe("createThreadCas", () => {
   });
 
   test("delete on missing hash does not throw", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     await cas.delete("0000000000000");
   });
 
   test("list returns all stored hashes", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     const h1 = await cas.put("aaa");
     const h2 = await cas.put("bbb");
     const h3 = await cas.put("ccc");
@@ -69,13 +75,13 @@ describe("createThreadCas", () => {
   });
 
   test("list returns empty array when cas dir does not exist", async () => {
-    const cas = createThreadCas(join(casDir, "nonexistent"));
+    const cas = createCasStore(join(casDir, "nonexistent"));
     const hashes = await cas.list();
     expect(hashes).toEqual([]);
   });
 
   test("put is idempotent — same content written twice causes no error", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     const h1 = await cas.put("idempotent");
     const h2 = await cas.put("idempotent");
     expect(h1).toBe(h2);
@@ -84,7 +90,7 @@ describe("createThreadCas", () => {
   });
 
   test("different content produces different hashes", async () => {
-    const cas = createThreadCas(casDir);
+    const cas = createCasStore(casDir);
     const h1 = await cas.put("alpha");
     const h2 = await cas.put("beta");
     expect(h1).not.toBe(h2);

packages/workflow/__tests__/engine.test.ts

@@ -4,10 +4,17 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import * as z from "zod/v4";
 
+import { createCasStore } from "../src/cas.js";
 import { createWorkflow } from "../src/create-workflow.js";
 import { executeThread } from "../src/engine.js";
 import { createExtract } from "../src/extract-fn.js";
 import { createLogger } from "../src/logger.js";
+import {
+  createContentMerkleNode,
+  getContentMerklePayload,
+  parseMerkleNode,
+  serializeMerkleNode,
+} from "../src/merkle.js";
 import { END } from "../src/types.js";
 
 const plannerMetaSchema = z.object({
@@ -89,12 +96,14 @@ const demoWorkflow = createWorkflow<DemoMeta>(
         systemPrompt: "You are a planner.",
         extractPrompt: "Extract plan text and affected files list.",
         schema: plannerMetaSchema,
+        extractRefs: null,
       },
       coder: {
         description: "Demo coder",
         systemPrompt: "You are a coder.",
         extractPrompt: "Extract the code diff summary.",
         schema: coderMetaSchema,
+        extractRefs: null,
       },
     },
     moderator: (ctx) => {
@@ -138,6 +147,7 @@ describe("executeThread", () => {
       const dataPath = join(root, "logs", hash, `${threadId}.data.jsonl`);
       const infoPath = join(root, "logs", hash, `${threadId}.info.jsonl`);
       await mkdir(join(root, "logs", hash), { recursive: true });
+      const cas = createCasStore(join(root, "cas"));
 
       const logger = createLogger({ sink: { kind: "file", path: infoPath } });
       const ac = new AbortController();
@@ -148,16 +158,30 @@ describe("executeThread", () => {
         { prompt: "Fix the login redirect bug in #3", steps: [] },
         {
           maxRounds: 5,
+          depth: 0,
           signal: ac.signal,
           awaitAfterEachYield: async () => {},
           forkSourceThreadId: null,
           prefilledDiskSteps: null,
         },
-        { threadId, hash, dataJsonlPath: dataPath, infoJsonlPath: infoPath },
+        { threadId, hash, dataJsonlPath: dataPath, infoJsonlPath: infoPath, cas },
         logger,
       );
 
       expect(result.returnCode).toBe(0);
+      expect(typeof result.rootHash).toBe("string");
+      expect(result.rootHash.length).toBeGreaterThan(0);
+
+      const rootYaml = await cas.get(result.rootHash);
+      expect(rootYaml).not.toBeNull();
+      const rootNode = parseMerkleNode(rootYaml ?? "");
+      expect(rootNode.type).toBe("thread");
+      const rootPayload = rootNode.payload as Record<string, unknown>;
+      expect(rootPayload.workflow).toBe("demo-flow");
+      expect(rootPayload.threadId).toBe(threadId);
+      const rootResult = rootPayload.result as Record<string, unknown>;
+      expect(rootResult.returnCode).toBe(0);
+      expect(rootNode.children.length).toBe(2);
 
       const dataText = await readFile(dataPath, "utf8");
       const lines = dataText
@@ -176,16 +200,34 @@ describe("executeThread", () => {
       expect(params.prompt).toBe("Fix the login redirect bug in #3");
       const opts = params.options as Record<string, unknown>;
       expect(opts.maxRounds).toBe(5);
-      expect(Object.keys(opts).sort()).toEqual(["maxRounds"]);
+      expect(opts.depth).toBe(0);
+      expect(Object.keys(opts).sort()).toEqual(["depth", "maxRounds"]);
 
       const role1 = JSON.parse(lines[1] ?? "{}") as Record<string, unknown>;
       expect(role1.role).toBe("planner");
-      expect(role1.content).toBe("plan-body");
+      expect(typeof role1.contentHash).toBe("string");
+      expect(await getContentMerklePayload(cas, String(role1.contentHash))).toBe("plan-body");
       expect(role1.meta).toEqual({ plan: "do-it", files: ["a.ts"] });
+      expect(role1.refs).toEqual([role1.contentHash]);
       expect(typeof role1.timestamp).toBe("number");
 
       const role2 = JSON.parse(lines[2] ?? "{}") as Record<string, unknown>;
       expect(role2.role).toBe("coder");
+      expect(role2.refs).toEqual([role2.contentHash]);
+
+      const step1Yaml = await cas.get(rootNode.children[0] ?? "");
+      const step2Yaml = await cas.get(rootNode.children[1] ?? "");
+      expect(step1Yaml).not.toBeNull();
+      expect(step2Yaml).not.toBeNull();
+      const step1Node = parseMerkleNode(step1Yaml ?? "");
+      const step2Node = parseMerkleNode(step2Yaml ?? "");
+      expect(step1Node.type).toBe("step");
+      expect(step2Node.type).toBe("step");
+      expect(step1Node.children).toEqual([String(role1.contentHash)]);
+      expect(step2Node.children).toEqual([String(role2.contentHash)]);
+      const step1Payload = step1Node.payload as Record<string, unknown>;
+      expect(step1Payload.role).toBe("planner");
+      expect(step1Payload.meta).toEqual({ plan: "do-it", files: ["a.ts"] });
 
       const infoText = await readFile(infoPath, "utf8");
       const infoLines = infoText
@@ -213,11 +255,14 @@ describe("executeThread", () => {
       const dataPath = join(root, "logs", hash, `${threadId}.data.jsonl`);
       const infoPath = join(root, "logs", hash, `${threadId}.info.jsonl`);
       await mkdir(join(root, "logs", hash), { recursive: true });
+      const cas = createCasStore(join(root, "cas"));
+      const plannerHash = await cas.put(serializeMerkleNode(createContentMerkleNode("plan-body")));
 
       const logger = createLogger({ sink: { kind: "file", path: infoPath } });
       const ac = new AbortController();
 
       const histTs = 9_000_000;
+      const mergedPlannerRefs = ["CAS111AAAAAAA", plannerHash];
       const result = await executeThread(
         demoWorkflow,
         "demo-flow",
@@ -226,30 +271,38 @@ describe("executeThread", () => {
           steps: [
             {
               role: "planner",
-              content: "plan-body",
+              contentHash: plannerHash,
               meta: { plan: "do-it", files: ["a.ts"] },
+              refs: mergedPlannerRefs,
             },
           ],
         },
         {
           maxRounds: 5,
+          depth: 0,
           signal: ac.signal,
           awaitAfterEachYield: async () => {},
           forkSourceThreadId: "01SRC1111111111111111111",
           prefilledDiskSteps: [
             {
               role: "planner",
-              content: "plan-body",
+              contentHash: plannerHash,
               meta: { plan: "do-it", files: ["a.ts"] },
+              refs: mergedPlannerRefs,
               timestamp: histTs,
             },
           ],
         },
-        { threadId, hash, dataJsonlPath: dataPath, infoJsonlPath: infoPath },
+        { threadId, hash, dataJsonlPath: dataPath, infoJsonlPath: infoPath, cas },
         logger,
       );
 
       expect(result.returnCode).toBe(0);
+      expect(typeof result.rootHash).toBe("string");
+
+      const rootYaml = await cas.get(result.rootHash);
+      const rootNode = parseMerkleNode(rootYaml ?? "");
+      expect(rootNode.children.length).toBe(2);
 
       const dataText = await readFile(dataPath, "utf8");
       const lines = dataText
@@ -264,10 +317,11 @@ describe("executeThread", () => {
       const role0 = JSON.parse(lines[1] ?? "{}") as Record<string, unknown>;
       expect(role0.role).toBe("planner");
       expect(role0.timestamp).toBe(histTs);
+      expect(role0.refs).toEqual(mergedPlannerRefs);
 
       const role1 = JSON.parse(lines[2] ?? "{}") as Record<string, unknown>;
       expect(role1.role).toBe("coder");
-      expect(role1.content).toBe("code-body");
+      expect(await getContentMerklePayload(cas, String(role1.contentHash))).toBe("code-body");
     } finally {
       await rm(root, { recursive: true, force: true });
     }
@@ -281,6 +335,7 @@ describe("executeThread", () => {
       const dataPath = join(root, "logs", hash, `${threadId}.data.jsonl`);
       const infoPath = join(root, "logs", hash, `${threadId}.info.jsonl`);
       await mkdir(join(root, "logs", hash), { recursive: true });
+      const cas = createCasStore(join(root, "cas"));
 
       const logger = createLogger({ sink: { kind: "file", path: infoPath } });
       const ac = new AbortController();
@@ -291,16 +346,23 @@ describe("executeThread", () => {
         { prompt: "hello", steps: [] },
         {
           maxRounds: 0,
+          depth: 0,
           signal: ac.signal,
           awaitAfterEachYield: async () => {},
           forkSourceThreadId: null,
           prefilledDiskSteps: null,
         },
-        { threadId, hash, dataJsonlPath: dataPath, infoJsonlPath: infoPath },
+        { threadId, hash, dataJsonlPath: dataPath, infoJsonlPath: infoPath, cas },
         logger,
       );
 
       expect(result.returnCode).toBe(0);
+      expect(typeof result.rootHash).toBe("string");
+
+      const rootYaml = await cas.get(result.rootHash);
+      const rootNode = parseMerkleNode(rootYaml ?? "");
+      expect(rootNode.type).toBe("thread");
+      expect(rootNode.children.length).toBe(0);
 
       const dataText = await readFile(dataPath, "utf8");
       const lines = dataText
@@ -312,4 +374,75 @@ describe("executeThread", () => {
       await rm(root, { recursive: true, force: true });
     }
   });
+
+  test("Merkle DAG: root → step nodes → content for full thread traversal", async () => {
+    restoreFetch = installMockChatCompletions([
+      { plan: "do-it", files: ["a.ts"] },
+      { diff: "+ok" },
+    ]);
+
+    const root = await mkdtemp(join(tmpdir(), "wf-engine-dag-"));
+    try {
+      const threadId = "01KQXKW18CT8G75T53R8F4G7YG";
+      const hash = "C9NMV6V2TQT81";
+      const dataPath = join(root, "logs", hash, `${threadId}.data.jsonl`);
+      const infoPath = join(root, "logs", hash, `${threadId}.info.jsonl`);
+      await mkdir(join(root, "logs", hash), { recursive: true });
+      const cas = createCasStore(join(root, "cas"));
+
+      const logger = createLogger({ sink: { kind: "file", path: infoPath } });
+      const ac = new AbortController();
+
+      const result = await executeThread(
+        demoWorkflow,
+        "demo-flow",
+        { prompt: "DAG test", steps: [] },
+        {
+          maxRounds: 5,
+          depth: 0,
+          signal: ac.signal,
+          awaitAfterEachYield: async () => {},
+          forkSourceThreadId: null,
+          prefilledDiskSteps: null,
+        },
+        { threadId, hash, dataJsonlPath: dataPath, infoJsonlPath: infoPath, cas },
+        logger,
+      );
+
+      const dataText = await readFile(dataPath, "utf8");
+      const lines = dataText
+        .trim()
+        .split("\n")
+        .filter((l) => l !== "");
+      expect(lines.length).toBe(3);
+
+      const rolePlanner = JSON.parse(lines[1] ?? "{}") as Record<string, unknown>;
+      const roleCoder = JSON.parse(lines[2] ?? "{}") as Record<string, unknown>;
+
+      const threadYaml = await cas.get(result.rootHash);
+      expect(threadYaml).not.toBeNull();
+      const threadNode = parseMerkleNode(threadYaml ?? "");
+      expect(threadNode.type).toBe("thread");
+
+      const bodies: string[] = [];
+      for (const stepHash of threadNode.children) {
+        const stepYaml = await cas.get(stepHash);
+        expect(stepYaml).not.toBeNull();
+        const stepNode = parseMerkleNode(stepYaml ?? "");
+        expect(stepNode.type).toBe("step");
+        expect(stepNode.children.length).toBe(1);
+        const contentHash = stepNode.children[0];
+        expect(contentHash).toBeDefined();
+        const body = await getContentMerklePayload(cas, contentHash ?? "");
+        expect(body).not.toBeNull();
+        bodies.push(body ?? "");
+      }
+
+      expect(bodies.sort()).toEqual(["code-body", "plan-body"].sort());
+      expect(rolePlanner.role).toBe("planner");
+      expect(roleCoder.role).toBe("coder");
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
 });

packages/workflow/__tests__/fork-thread.test.ts

@@ -7,9 +7,9 @@ import {
 } from "../src/fork-thread.js";
 
 const sampleDataJsonl = `{"name":"demo","hash":"C9NMV6V2TQT81","threadId":"01AAA1111111111111111111","parameters":{"prompt":"hi","options":{"maxRounds":5}},"timestamp":100}
-{"role":"planner","content":"p","meta":{},"timestamp":101}
-{"role":"coder","content":"c","meta":{},"timestamp":102}
-{"role":"reviewer","content":"r","meta":{},"timestamp":103}
+{"role":"planner","contentHash":"HP0000000000000000000001","meta":{},"refs":[],"timestamp":101}
+{"role":"coder","contentHash":"HP0000000000000000000002","meta":{},"refs":[],"timestamp":102}
+{"role":"reviewer","contentHash":"HP0000000000000000000003","meta":{},"refs":[],"timestamp":103}
 `;
 
 describe("fork-thread", () => {
@@ -24,6 +24,7 @@ describe("fork-thread", () => {
     expect(r.value.start.threadId).toBe("01AAA1111111111111111111");
     expect(r.value.start.prompt).toBe("hi");
     expect(r.value.start.maxRounds).toBe(5);
+    expect(r.value.start.depth).toBe(0);
     expect(r.value.roleSteps.length).toBe(3);
     expect(r.value.roleSteps[0]?.role).toBe("planner");
   });
@@ -83,6 +84,24 @@ describe("fork-thread", () => {
     expect(r.value.workflowName).toBe("demo");
     expect(r.value.historicalSteps.length).toBe(1);
     expect(r.value.historicalSteps[0]?.timestamp).toBe(101);
-    expect(r.value.runOptions).toEqual({ maxRounds: 5 });
+    expect(r.value.runOptions).toEqual({ maxRounds: 5, depth: 0 });
+  });
+
+  test("parseThreadDataJsonl reads explicit depth from start record", () => {
+    const text = `{"name":"demo","hash":"H","threadId":"01ZZZZZZZZZZZZZZZZZZZZZZ","parameters":{"prompt":"p","options":{"maxRounds":3,"depth":2}},"timestamp":1}
+{"role":"planner","contentHash":"HP0000000000000000000099","meta":{},"refs":[],"timestamp":2}
+`;
+    const r = parseThreadDataJsonl(text);
+    expect(r.ok).toBe(true);
+    if (!r.ok) {
+      return;
+    }
+    expect(r.value.start.depth).toBe(2);
+    const plan = buildForkPlan(text, null);
+    expect(plan.ok).toBe(true);
+    if (!plan.ok) {
+      return;
+    }
+    expect(plan.value.runOptions).toEqual({ maxRounds: 3, depth: 2 });
   });
 });

packages/workflow/__tests__/merkle.test.ts

@@ -0,0 +1,29 @@
+import { describe, expect, test } from "bun:test";
+
+import { createContentMerkleNode, parseMerkleNode, serializeMerkleNode } from "../src/merkle.js";
+
+describe("merkle", () => {
+  test("content node roundtrips through YAML", () => {
+    const node = createContentMerkleNode("hello\nworld");
+    const yaml = serializeMerkleNode(node);
+    const back = parseMerkleNode(yaml);
+    expect(back).toEqual(node);
+  });
+
+  test("step node with object payload roundtrips", () => {
+    const node = {
+      type: "step" as const,
+      payload: { role: "planner", foo: 1 },
+      children: ["ABC123", "DEF456"],
+    };
+    const yaml = serializeMerkleNode(node);
+    const back = parseMerkleNode(yaml);
+    expect(back.type).toBe("step");
+    expect(back.payload).toEqual({ role: "planner", foo: 1 });
+    expect(back.children).toEqual(["ABC123", "DEF456"]);
+  });
+
+  test("parse rejects invalid YAML root", () => {
+    expect(() => parseMerkleNode("[]")).toThrow();
+  });
+});

packages/workflow/__tests__/refs-tracking.test.ts

@@ -0,0 +1,201 @@
+import { afterEach, describe, expect, test } from "bun:test";
+import { mkdir, mkdtemp, readFile, rm } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import * as z from "zod/v4";
+
+import { createCasStore } from "../src/cas.js";
+import { createWorkflow } from "../src/create-workflow.js";
+import { executeThread } from "../src/engine.js";
+import { createExtract } from "../src/extract-fn.js";
+import { buildForkPlan, parseThreadDataJsonl } from "../src/fork-thread.js";
+import { createLogger } from "../src/logger.js";
+import { END } from "../src/types.js";
+
+const phaseSchema = z.object({
+  hash: z.string(),
+  title: z.string(),
+});
+
+const plannerMetaSchema = z.object({
+  phases: z.array(phaseSchema),
+});
+
+type RefsDemoMeta = {
+  planner: z.infer<typeof plannerMetaSchema>;
+};
+
+function installMockChatCompletions(sequence: ReadonlyArray<Record<string, unknown>>): () => void {
+  const origFetch = globalThis.fetch;
+  let i = 0;
+  const mockFetch = async (
+    input: Parameters<typeof fetch>[0],
+    init?: RequestInit,
+  ): Promise<Response> => {
+    const args = sequence[i] ?? sequence[sequence.length - 1];
+    if (args === undefined) {
+      throw new Error("installMockChatCompletions: empty sequence");
+    }
+    i += 1;
+    void input;
+    const body = init?.body ? (JSON.parse(String(init.body)) as Record<string, unknown>) : {};
+    const tools = body.tools;
+    const firstTool =
+      Array.isArray(tools) && tools.length > 0 && tools[0] !== null && typeof tools[0] === "object"
+        ? (tools[0] as Record<string, unknown>)
+        : null;
+    const fn =
+      firstTool !== null ? (firstTool.function as Record<string, unknown> | undefined) : undefined;
+    const toolName = typeof fn?.name === "string" ? fn.name : "extract";
+    return new Response(
+      JSON.stringify({
+        choices: [
+          {
+            message: {
+              tool_calls: [
+                {
+                  type: "function",
+                  function: {
+                    name: toolName,
+                    arguments: JSON.stringify(args),
+                  },
+                },
+              ],
+            },
+          },
+        ],
+      }),
+      { status: 200, headers: { "Content-Type": "application/json" } },
+    );
+  };
+  globalThis.fetch = Object.assign(mockFetch, {
+    preconnect: origFetch.preconnect.bind(origFetch),
+  }) as typeof fetch;
+  return () => {
+    globalThis.fetch = origFetch;
+  };
+}
+
+const refsDemoExtract = createExtract({
+  baseUrl: "http://127.0.0.1:9",
+  apiKey: "test",
+  model: "test",
+});
+
+const refsDemoWorkflow = createWorkflow<RefsDemoMeta>(
+  {
+    roles: {
+      planner: {
+        description: "Planner with phase hashes",
+        systemPrompt: "Plan.",
+        extractPrompt: "Extract phases with CAS hashes.",
+        schema: plannerMetaSchema,
+        extractRefs: (meta) => meta.phases.map((p) => p.hash),
+      },
+    },
+    moderator: (ctx) => (ctx.steps.length === 0 ? "planner" : END),
+  },
+  {
+    agent: async () => "plan-output",
+  },
+  refsDemoExtract,
+);
+
+describe("RoleStep refs tracking", () => {
+  let restoreFetch: (() => void) | null = null;
+
+  afterEach(() => {
+    restoreFetch?.();
+    restoreFetch = null;
+  });
+
+  test("parseThreadDataJsonl reads refs and defaults missing refs to []", () => {
+    const text = `{"name":"demo","hash":"C9NMV6V2TQT81","threadId":"01AAA1111111111111111111","parameters":{"prompt":"hi","options":{"maxRounds":5}},"timestamp":100}
+{"role":"planner","contentHash":"HPAYLOAD111111","meta":{},"refs":["H111AAAAAAAAA","H222AAAAAAAAA"],"timestamp":101}
+{"role":"coder","contentHash":"HPAYLOAD222222","meta":{},"timestamp":102}
+`;
+    const r = parseThreadDataJsonl(text);
+    expect(r.ok).toBe(true);
+    if (!r.ok) {
+      return;
+    }
+    expect(r.value.roleSteps[0]?.refs).toEqual(["H111AAAAAAAAA", "H222AAAAAAAAA"]);
+    expect(r.value.roleSteps[1]?.refs).toEqual([]);
+  });
+
+  test("executeThread persists refs from extractRefs on role yields", async () => {
+    restoreFetch = installMockChatCompletions([
+      {
+        phases: [
+          { hash: "C9NMV6V2TQT81", title: "phase-a" },
+          { hash: "C9NMV6V2TQT82", title: "phase-b" },
+        ],
+      },
+    ]);
+
+    const root = await mkdtemp(join(tmpdir(), "wf-refs-"));
+    try {
+      const threadId = "01KQXKW18CT8G75T53R8F4G7YG";
+      const hash = "C9NMV6V2TQT81";
+      const dataPath = join(root, "logs", hash, `${threadId}.data.jsonl`);
+      const infoPath = join(root, "logs", hash, `${threadId}.info.jsonl`);
+      await mkdir(join(root, "logs", hash), { recursive: true });
+      const cas = createCasStore(join(root, "cas"));
+
+      const logger = createLogger({ sink: { kind: "file", path: infoPath } });
+      const ac = new AbortController();
+
+      const result = await executeThread(
+        refsDemoWorkflow,
+        "refs-demo",
+        { prompt: "task", steps: [] },
+        {
+          maxRounds: 5,
+          depth: 0,
+          signal: ac.signal,
+          awaitAfterEachYield: async () => {},
+          forkSourceThreadId: null,
+          prefilledDiskSteps: null,
+        },
+        { threadId, hash, dataJsonlPath: dataPath, infoJsonlPath: infoPath, cas },
+        logger,
+      );
+
+      expect(result.returnCode).toBe(0);
+      expect(typeof result.rootHash).toBe("string");
+      expect(result.rootHash.length).toBeGreaterThan(0);
+
+      const dataText = await readFile(dataPath, "utf8");
+      const lines = dataText
+        .trim()
+        .split("\n")
+        .filter((l) => l !== "");
+      expect(lines.length).toBe(2);
+
+      const role1 = JSON.parse(lines[1] ?? "{}") as Record<string, unknown>;
+      expect(role1.role).toBe("planner");
+      const refs = role1.refs as string[];
+      expect(refs).toContain("C9NMV6V2TQT81");
+      expect(refs).toContain("C9NMV6V2TQT82");
+      expect(typeof role1.contentHash).toBe("string");
+      expect(refs).toContain(String(role1.contentHash));
+      expect(refs.length).toBe(3);
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  test("buildForkPlan carries refs on historical steps", () => {
+    const text = `{"name":"demo","hash":"C9NMV6V2TQT81","threadId":"01AAA1111111111111111111","parameters":{"prompt":"hi","options":{"maxRounds":5}},"timestamp":100}
+{"role":"planner","contentHash":"HP111111111111","meta":{},"refs":["KEEPREFAAAAAA"],"timestamp":101}
+{"role":"coder","contentHash":"HP222222222222","meta":{},"refs":["CODERHASHAAAA"],"timestamp":102}
+`;
+    const plan = buildForkPlan(text, null);
+    expect(plan.ok).toBe(true);
+    if (!plan.ok) {
+      return;
+    }
+    expect(plan.value.historicalSteps.length).toBe(1);
+    expect(plan.value.historicalSteps[0]?.refs).toEqual(["KEEPREFAAAAAA"]);
+  });
+});

packages/workflow/__tests__/storage-root.test.ts

@@ -0,0 +1,14 @@
+import { describe, expect, test } from "bun:test";
+import { join } from "node:path";
+
+import { getDefaultWorkflowStorageRoot, getGlobalCasDir } from "../src/storage-root.js";
+
+describe("getGlobalCasDir", () => {
+  test("joins cas segment under explicit storage root", () => {
+    expect(getGlobalCasDir("/tmp/wf-root")).toBe(join("/tmp/wf-root", "cas"));
+  });
+
+  test("defaults to default workflow root when storage root is undefined", () => {
+    expect(getGlobalCasDir(undefined)).toBe(join(getDefaultWorkflowStorageRoot(), "cas"));
+  });
+});

packages/workflow/__tests__/thread-jsonl-format.test.ts

@@ -10,6 +10,7 @@ describe("RFC-001 thread JSONL shapes", () => {
         prompt: "Fix the login redirect bug in #3",
         options: {
           maxRounds: 5,
+          depth: 0,
         },
       },
       timestamp: 1714963200000,
@@ -17,15 +18,18 @@ describe("RFC-001 thread JSONL shapes", () => {
 
     const roleRecord = {
       role: "planner",
-      content: "Plan: modify auth middleware...",
+      contentHash: "CPHASH000000000000000001",
       meta: { plan: "...", files: ["src/auth.ts"] },
+      refs: [] as string[],
       timestamp: 1714963201000,
     };
 
     expect(Object.keys(startRecord).sort()).toEqual(
       ["hash", "name", "parameters", "threadId", "timestamp"].sort(),
     );
-    expect(Object.keys(roleRecord).sort()).toEqual(["content", "meta", "role", "timestamp"].sort());
+    expect(Object.keys(roleRecord).sort()).toEqual(
+      ["contentHash", "meta", "refs", "role", "timestamp"].sort(),
+    );
   });
 
   test("documents the `.info.jsonl` debug record keys", () => {

packages/workflow/__tests__/worker.test.ts

@@ -5,22 +5,29 @@ import { createConnection } from "node:net";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 
+import { createCasStore } from "../src/cas.js";
+import { createContentMerkleNode, serializeMerkleNode } from "../src/merkle.js";
 import { getWorkerHostScriptPath } from "../src/worker-entry-path.js";
 
-const bundleSource = `export const descriptor = {
+const bundleSource = `import { putContentMerkleNode } from "@uncaged/workflow";
+
+export const descriptor = {
   description: "worker-test",
   roles: {
     planner: { description: "planner", schema: {} },
     coder: { description: "coder", schema: {} },
   },
 };
-export const run = async function* (input) {
+export const run = async function* (input, options) {
+  const cas = options.cas;
   const has = (r) => input.steps.some((s) => s.role === r);
   if (!has("planner")) {
-    yield { role: "planner", content: "p", meta: { plan: input.prompt } };
+    const h = await putContentMerkleNode(cas, "p");
+    yield { role: "planner", contentHash: h, meta: { plan: input.prompt }, refs: [h] };
   }
   if (!has("coder")) {
-    yield { role: "coder", content: "c", meta: { diff: "y" } };
+    const h = await putContentMerkleNode(cas, "c");
+    yield { role: "coder", contentHash: h, meta: { diff: "y" }, refs: [h] };
   }
   return { returnCode: 0, summary: "completed: moderator returned END" };
 };
@@ -102,7 +109,7 @@ describe("worker process", () => {
         threadId,
         workflowName: "demo-flow",
         prompt: "hello",
-        options: { maxRounds: 5 },
+        options: { maxRounds: 5, depth: 0 },
       });
 
       const exitCode: number = await new Promise((resolve) => {
@@ -143,6 +150,11 @@ describe("worker process", () => {
 
       const port = await readReadyPort(child);
 
+      const cas = createCasStore(join(root, "cas"));
+      const plannerReplayHash = await cas.put(
+        serializeMerkleNode(createContentMerkleNode("p-old")),
+      );
+
       const threadId = "01KQXKW18CT8G75T53R8F4G7YG";
       const srcId = "01SRCMMMMMMMMMMMMMMMMMMMM";
       await sendJson(port, {
@@ -150,12 +162,13 @@ describe("worker process", () => {
         threadId,
         workflowName: "demo-flow",
         prompt: "hello",
-        options: { maxRounds: 5 },
+        options: { maxRounds: 5, depth: 0 },
         steps: [
           {
             role: "planner",
-            content: "p-old",
+            contentHash: plannerReplayHash,
             meta: { plan: "z" },
+            refs: [plannerReplayHash],
             timestamp: 555,
           },
         ],

packages/workflow/__tests__/workflow-as-agent-integration.test.ts

@@ -0,0 +1,223 @@
+import { afterEach, describe, expect, test } from "bun:test";
+import { mkdir, mkdtemp, readdir, readFile, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import * as z from "zod/v4";
+
+import { createCasStore } from "../src/cas.js";
+import { createWorkflow } from "../src/create-workflow.js";
+import { executeThread } from "../src/engine.js";
+import { createExtract } from "../src/extract-fn.js";
+import { hashWorkflowBundleBytes } from "../src/hash.js";
+import { createLogger } from "../src/logger.js";
+import { getContentMerklePayload, parseMerkleNode } from "../src/merkle.js";
+import {
+  readWorkflowRegistry,
+  registerWorkflowVersion,
+  writeWorkflowRegistry,
+} from "../src/registry.js";
+import { END } from "../src/types.js";
+import { workflowAsAgent } from "../src/workflow-as-agent.js";
+
+const callerMetaSchema = z.object({ done: z.literal(true) });
+
+type ParentMeta = {
+  caller: z.infer<typeof callerMetaSchema>;
+};
+
+function installMockChatCompletions(sequence: ReadonlyArray<Record<string, unknown>>): () => void {
+  const origFetch = globalThis.fetch;
+  let i = 0;
+  const mockFetch = async (
+    input: Parameters<typeof fetch>[0],
+    init?: RequestInit,
+  ): Promise<Response> => {
+    const args = sequence[i] ?? sequence[sequence.length - 1];
+    if (args === undefined) {
+      throw new Error("installMockChatCompletions: empty sequence");
+    }
+    i += 1;
+    void input;
+    const body = init?.body ? (JSON.parse(String(init.body)) as Record<string, unknown>) : {};
+    const tools = body.tools;
+    const firstTool =
+      Array.isArray(tools) && tools.length > 0 && tools[0] !== null && typeof tools[0] === "object"
+        ? (tools[0] as Record<string, unknown>)
+        : null;
+    const fn =
+      firstTool !== null ? (firstTool.function as Record<string, unknown> | undefined) : undefined;
+    const toolName = typeof fn?.name === "string" ? fn.name : "extract";
+    return new Response(
+      JSON.stringify({
+        choices: [
+          {
+            message: {
+              tool_calls: [
+                {
+                  type: "function",
+                  function: {
+                    name: toolName,
+                    arguments: JSON.stringify(args),
+                  },
+                },
+              ],
+            },
+          },
+        ],
+      }),
+      { status: 200, headers: { "Content-Type": "application/json" } },
+    );
+  };
+  globalThis.fetch = Object.assign(mockFetch, {
+    preconnect: origFetch.preconnect.bind(origFetch),
+  }) as typeof fetch;
+  return () => {
+    globalThis.fetch = origFetch;
+  };
+}
+
+const parentExtract = createExtract({
+  baseUrl: "http://127.0.0.1:9",
+  apiKey: "test",
+  model: "test",
+});
+
+const childBundleSource = `import { putContentMerkleNode } from "@uncaged/workflow";
+
+export const descriptor = {
+  description: "child-integration",
+  roles: {
+    agent: {
+      description: "agent",
+      schema: { type: "object", properties: {}, additionalProperties: true },
+    },
+  },
+};
+export async function* run(input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "child-body");
+  yield { role: "agent", contentHash: h, meta: {}, refs: [h] };
+  return { returnCode: 0, summary: "child-done:" + input.prompt };
+}
+`;
+
+async function installChildWorkflow(storageRoot: string): Promise<{ hash: string }> {
+  const bytes = new TextEncoder().encode(childBundleSource);
+  const hash = hashWorkflowBundleBytes(bytes);
+  await mkdir(join(storageRoot, "bundles"), { recursive: true });
+  await writeFile(join(storageRoot, "bundles", `${hash}.esm.js`), childBundleSource, "utf8");
+  const reg = await readWorkflowRegistry(storageRoot);
+  if (!reg.ok) {
+    throw reg.error;
+  }
+  const next = registerWorkflowVersion(reg.value, "child-wf", hash, Date.now());
+  const wr = await writeWorkflowRegistry(storageRoot, next);
+  if (!wr.ok) {
+    throw wr.error;
+  }
+  return { hash };
+}
+
+describe("workflowAsAgent integration", () => {
+  let restoreFetch: (() => void) | null = null;
+
+  afterEach(() => {
+    restoreFetch?.();
+    restoreFetch = null;
+  });
+
+  test("createWorkflow parent invokes nested workflow via workflowAsAgent", async () => {
+    restoreFetch = installMockChatCompletions([{ done: true }]);
+
+    const root = await mkdtemp(join(tmpdir(), "wf-waa-int-"));
+    try {
+      const { hash: childHash } = await installChildWorkflow(root);
+
+      const parentWorkflow = createWorkflow<ParentMeta>(
+        {
+          roles: {
+            caller: {
+              description: "delegates to child workflow",
+              systemPrompt: "system",
+              extractPrompt: "extract done flag",
+              schema: callerMetaSchema,
+              extractRefs: null,
+            },
+          },
+          moderator: (ctx) => (ctx.steps.length === 0 ? "caller" : END),
+        },
+        { agent: workflowAsAgent("child-wf", { storageRoot: root }) },
+        parentExtract,
+      );
+
+      const threadId = "01KQXKW18CT8G75T53R8F4G7YG";
+      const parentHash = "C9NMV6V2TQT81";
+      const dataPath = join(root, "logs", parentHash, `${threadId}.data.jsonl`);
+      const infoPath = join(root, "logs", parentHash, `${threadId}.info.jsonl`);
+      await mkdir(join(root, "logs", parentHash), { recursive: true });
+      const cas = createCasStore(join(root, "cas"));
+
+      const logger = createLogger({ sink: { kind: "file", path: infoPath } });
+      const ac = new AbortController();
+
+      const result = await executeThread(
+        parentWorkflow,
+        "parent-wf",
+        { prompt: "from-parent", steps: [] },
+        {
+          maxRounds: 5,
+          depth: 0,
+          signal: ac.signal,
+          awaitAfterEachYield: async () => {},
+          forkSourceThreadId: null,
+          prefilledDiskSteps: null,
+        },
+        { threadId, hash: parentHash, dataJsonlPath: dataPath, infoJsonlPath: infoPath, cas },
+        logger,
+      );
+
+      expect(result.returnCode).toBe(0);
+      expect(typeof result.rootHash).toBe("string");
+
+      const parentText = await readFile(dataPath, "utf8");
+      const parentLines = parentText
+        .trim()
+        .split("\n")
+        .filter((l) => l !== "");
+      expect(parentLines.length).toBe(2);
+      const callerLine = JSON.parse(parentLines[1] ?? "{}") as Record<string, unknown>;
+      expect(callerLine.role).toBe("caller");
+      const childRootHash = await getContentMerklePayload(cas, String(callerLine.contentHash));
+      expect(childRootHash).not.toBeNull();
+      const childThreadYaml = await cas.get(childRootHash ?? "");
+      expect(childThreadYaml).not.toBeNull();
+      const childThreadNode = parseMerkleNode(childThreadYaml ?? "");
+      expect(childThreadNode.type).toBe("thread");
+      const childPayload = childThreadNode.payload as Record<string, unknown>;
+      expect(childPayload.workflow).toBe("child-wf");
+      const childResult = childPayload.result as Record<string, unknown>;
+      expect(childResult.summary).toBe("child-done:from-parent");
+
+      const childDir = join(root, "logs", childHash);
+      const childFiles = await readdir(childDir);
+      const childDataName = childFiles.find((n) => n.endsWith(".data.jsonl"));
+      expect(childDataName).toBeDefined();
+
+      const childText = await readFile(join(childDir, childDataName ?? ""), "utf8");
+      const childStart = JSON.parse(
+        childText
+          .trim()
+          .split("\n")
+          .filter((l) => l !== "")[0] ?? "{}",
+      ) as Record<string, unknown>;
+      expect(childStart.forkFrom).toEqual({ threadId });
+      const childOpts = (childStart.parameters as Record<string, unknown>).options as Record<
+        string,
+        unknown
+      >;
+      expect(childOpts.depth).toBe(1);
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+});

packages/workflow/__tests__/workflow-as-agent.test.ts

@@ -0,0 +1,128 @@
+import { describe, expect, test } from "bun:test";
+import { mkdir, mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { createCasStore } from "../src/cas.js";
+import { hashWorkflowBundleBytes } from "../src/hash.js";
+import { parseMerkleNode } from "../src/merkle.js";
+import {
+  readWorkflowRegistry,
+  registerWorkflowVersion,
+  writeWorkflowRegistry,
+} from "../src/registry.js";
+import { type AgentContext, START } from "../src/types.js";
+import { workflowAsAgent } from "../src/workflow-as-agent.js";
+
+function makeAgentCtx(params: {
+  storageRoot: string;
+  depth: number;
+  prompt: string;
+  maxRounds: number;
+}): AgentContext {
+  const ts = Date.now();
+  return {
+    threadId: "01PARENT000000000000000001AA",
+    depth: params.depth,
+    start: {
+      role: START,
+      content: params.prompt,
+      meta: { maxRounds: params.maxRounds },
+      timestamp: ts,
+    },
+    steps: [],
+    currentRole: {
+      name: "caller",
+      systemPrompt: "caller",
+    },
+    cas: createCasStore(join(params.storageRoot, "agent-ctx-cas")),
+  };
+}
+
+const childBundleSource = `import { putContentMerkleNode } from "@uncaged/workflow";
+
+export const descriptor = {
+  description: "child-test",
+  roles: {
+    agent: {
+      description: "agent",
+      schema: { type: "object", properties: {}, additionalProperties: true },
+    },
+  },
+};
+export async function* run(input, options) {
+  const cas = options.cas;
+  const h = await putContentMerkleNode(cas, "child-body");
+  yield { role: "agent", contentHash: h, meta: {}, refs: [h] };
+  return { returnCode: 0, summary: "child-done:" + input.prompt };
+}
+`;
+
+async function installChildWorkflow(storageRoot: string): Promise<{ hash: string }> {
+  const bytes = new TextEncoder().encode(childBundleSource);
+  const hash = hashWorkflowBundleBytes(bytes);
+  await mkdir(join(storageRoot, "bundles"), { recursive: true });
+  await writeFile(join(storageRoot, "bundles", `${hash}.esm.js`), childBundleSource, "utf8");
+  const reg = await readWorkflowRegistry(storageRoot);
+  if (!reg.ok) {
+    throw reg.error;
+  }
+  const next = registerWorkflowVersion(reg.value, "child-wf", hash, Date.now());
+  const wr = await writeWorkflowRegistry(storageRoot, next);
+  if (!wr.ok) {
+    throw wr.error;
+  }
+  return { hash };
+}
+
+describe("workflowAsAgent", () => {
+  test("returns error when workflow name is not registered", async () => {
+    const root = await mkdtemp(join(tmpdir(), "wf-waa-missing-"));
+    try {
+      const agent = workflowAsAgent("missing-wf", { storageRoot: root });
+      const out = await agent(
+        makeAgentCtx({ storageRoot: root, depth: 0, prompt: "x", maxRounds: 5 }),
+      );
+      expect(out).toContain("not found in registry");
+      expect(out).toContain("missing-wf");
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  test("runs registered workflow and returns child thread root CAS hash", async () => {
+    const root = await mkdtemp(join(tmpdir(), "wf-waa-ok-"));
+    try {
+      await installChildWorkflow(root);
+      const agent = workflowAsAgent("child-wf", { storageRoot: root });
+      const out = await agent(
+        makeAgentCtx({ storageRoot: root, depth: 0, prompt: "hello-parent", maxRounds: 5 }),
+      );
+      const cas = createCasStore(join(root, "cas"));
+      const threadYaml = await cas.get(out);
+      expect(threadYaml).not.toBeNull();
+      const node = parseMerkleNode(threadYaml ?? "");
+      expect(node.type).toBe("thread");
+      const payload = node.payload as Record<string, unknown>;
+      expect(payload.workflow).toBe("child-wf");
+      const resultObj = payload.result as Record<string, unknown>;
+      expect(resultObj.summary).toBe("child-done:hello-parent");
+      expect(node.children.length).toBe(1);
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  test("enforces depth limit (returns error string, does not throw)", async () => {
+    const root = await mkdtemp(join(tmpdir(), "wf-waa-depth-"));
+    try {
+      const agent = workflowAsAgent("child-wf", { storageRoot: root });
+      const out = await agent(
+        makeAgentCtx({ storageRoot: root, depth: 3, prompt: "x", maxRounds: 5 }),
+      );
+      expect(out).toContain("depth limit");
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+});

packages/workflow/src/bundle-import-env.ts

@@ -0,0 +1,8 @@
+import { pathToFileURL } from "node:url";
+
+/**
+ * Dynamic-import a workflow bundle path (see {@link extractBundleExports} — symlink must exist first).
+ */
+export async function importWorkflowBundleModule(bundlePath: string): Promise<unknown> {
+  return import(pathToFileURL(bundlePath).href);
+}

packages/workflow/src/bundle-validator.ts

@@ -41,9 +41,12 @@ function isAllowedImportSpecifier(spec: string): boolean {
   if (spec.length === 0) {
     return false;
   }
-  if (spec.startsWith(".") || spec.startsWith("/")) {
+  if (spec.startsWith(".") || spec.startsWith("/") || spec.startsWith("file:")) {
     return false;
   }
+  if (spec === "@uncaged/workflow") {
+    return true;
+  }
   return isBuiltin(spec);
 }
 
@@ -297,7 +300,7 @@ function validateImportDeclaration(node: ImportDeclaration): string | null {
     return "only static string import specifiers are allowed";
   }
   if (!isAllowedImportSpecifier(spec)) {
-    return `disallowed import specifier "${spec}" (only Node built-ins are allowed)`;
+    return `disallowed import specifier "${spec}" (only Node built-ins and "@uncaged/workflow" are allowed)`;
   }
   return null;
 }
@@ -312,7 +315,7 @@ function validateExportSource(
     return staticMessage;
   }
   if (!isAllowedImportSpecifier(spec)) {
-    return `${disallowedPrefix} "${spec}" (only Node built-ins are allowed)`;
+    return `${disallowedPrefix} "${spec}" (only Node built-ins and "@uncaged/workflow" are allowed)`;
   }
   return null;
 }
@@ -365,7 +368,7 @@ function bundleConstraintViolationForNode(node: Node): string | null {
 
 /**
  * Validate RFC-001 bundle rules: single-file ESM shape, named exports `run` + `descriptor`,
- * no default export, no dynamic `import()`, static imports restricted to Node builtins.
+ * no default export, no dynamic `import()`, static imports restricted to Node builtins plus `@uncaged/workflow`.
  */
 export function validateWorkflowBundle(input: WorkflowBundleValidationInput): Result<void, string> {
   if (!endsWithEsmJs(input.filePath)) {

packages/workflow/src/cas.ts

@@ -10,7 +10,7 @@ export type CasStore = {
   list(): Promise<string[]>;
 };
 
-export function createThreadCas(casDir: string): CasStore {
+export function createCasStore(casDir: string): CasStore {
   async function ensureDir(): Promise<void> {
     await mkdir(casDir, { recursive: true });
   }
@@ -68,3 +68,6 @@ export function createThreadCas(casDir: string): CasStore {
     },
   };
 }
+
+/** @deprecated Use {@link createCasStore} — CAS is global, not per-thread. */
+export const createThreadCas = createCasStore;

packages/workflow/src/create-workflow.ts

@@ -1,19 +1,22 @@
 import type { ExtractFn } from "./extract-fn.js";
+import { putContentMerkleNode } from "./merkle.js";
+import { mergeRefsWithContentHash } from "./refs-field.js";
 import {
   type AgentBinding,
   type AgentContext,
   END,
   type ExtractContext,
   type ModeratorContext,
+  type RoleDefinition,
   type RoleMeta,
   type RoleOutput,
   type RoleStep,
   START,
   type ThreadInput,
+  type WorkflowCompletion,
   type WorkflowDefinition,
   type WorkflowFn,
   type WorkflowFnOptions,
-  type WorkflowResult,
 } from "./types.js";
 
 function isRoleNext<M extends RoleMeta>(
@@ -22,6 +25,17 @@ function isRoleNext<M extends RoleMeta>(
   return next !== END;
 }
 
+function resolveExtractedRefs(
+  roleDef: RoleDefinition<Record<string, unknown>>,
+  meta: unknown,
+): string[] {
+  const extractRefsFn = roleDef.extractRefs;
+  if (extractRefsFn === null || typeof extractRefsFn !== "function") {
+    return [];
+  }
+  return extractRefsFn(meta as Record<string, unknown>);
+}
+
 /**
  * Binds pure role definitions + moderator to runtime agents and structured extraction.
  * Assign with `export const run = createWorkflow(def, binding, extract)`.
@@ -34,7 +48,7 @@ export function createWorkflow<M extends RoleMeta>(
   return async function* workflowLoop(
     input: ThreadInput,
     options: WorkflowFnOptions,
-  ): AsyncGenerator<RoleOutput, WorkflowResult> {
+  ): AsyncGenerator<RoleOutput, WorkflowCompletion> {
     const nowMs = Date.now();
     const start: ModeratorContext<M>["start"] = {
       role: START,
@@ -46,8 +60,9 @@ export function createWorkflow<M extends RoleMeta>(
     const baseTs = Date.now();
     let steps: RoleStep<M>[] = input.steps.map((out, i) => ({
       role: out.role,
-      content: out.content,
+      contentHash: out.contentHash,
       meta: out.meta,
+      refs: out.refs,
       timestamp: baseTs + i,
     })) as RoleStep<M>[];
 
@@ -61,6 +76,7 @@ export function createWorkflow<M extends RoleMeta>(
 
       const modCtx: ModeratorContext<M> = {
         threadId: options.threadId,
+        depth: options.depth,
         start,
         steps,
       };
@@ -79,6 +95,7 @@ export function createWorkflow<M extends RoleMeta>(
       const agentCtx: AgentContext<M> = {
         ...modCtx,
         currentRole: { name: next, systemPrompt: roleDef.systemPrompt },
+        cas: options.cas,
       };
 
       const agent = binding.overrides?.[next] ?? binding.agent;
@@ -96,15 +113,28 @@ export function createWorkflow<M extends RoleMeta>(
         extractCtx as unknown as ExtractContext,
       );
 
+      const contentHash = await putContentMerkleNode(options.cas, raw);
+
+      const refs = mergeRefsWithContentHash(
+        resolveExtractedRefs(roleDef as unknown as RoleDefinition<Record<string, unknown>>, meta),
+        contentHash,
+      );
+
       const ts = Date.now();
       const step = {
         role: next,
-        content: raw,
+        contentHash,
         meta,
+        refs,
         timestamp: ts,
       } as RoleStep<M>;
 
-      yield { role: step.role, content: step.content, meta: step.meta };
+      yield {
+        role: step.role,
+        contentHash: step.contentHash,
+        meta: step.meta,
+        refs: step.refs,
+      };
 
       steps = [...steps, step];
     }

packages/workflow/src/engine.ts

@@ -1,26 +1,39 @@
 import { appendFile, mkdir } from "node:fs/promises";
 import { dirname } from "node:path";
 
+import type { CasStore } from "./cas.js";
 import type { LogFn } from "./logger.js";
-import type { ThreadInput, WorkflowFn, WorkflowFnOptions, WorkflowResult } from "./types.js";
+import { getContentMerklePayload, putStepMerkleNode, putThreadMerkleNode } from "./merkle.js";
+import { normalizeRefsField } from "./refs-field.js";
+import type {
+  ThreadInput,
+  WorkflowCompletion,
+  WorkflowFn,
+  WorkflowFnOptions,
+  WorkflowResult,
+} from "./types.js";
 
 export type ExecuteThreadIo = {
   threadId: string;
   hash: string;
   dataJsonlPath: string;
   infoJsonlPath: string;
+  cas: CasStore;
 };
 
 /** One persisted role line in `.data.jsonl` (engine adds these for fork replay before running the generator). */
 export type PrefilledDiskStep = {
   role: string;
-  content: string;
+  contentHash: string;
   meta: Record<string, unknown>;
+  refs: string[];
   timestamp: number;
 };
 
 export type ExecuteThreadOptions = {
   maxRounds: number;
+  /** Passed to the bundle as `WorkflowFnOptions.depth`. */
+  depth: number;
   signal: AbortSignal;
   /** Invoked after each successful yield (and outer-loop checks); used for pause/resume. */
   awaitAfterEachYield: () => Promise<void>;
@@ -38,50 +51,123 @@ async function appendDataLine(path: string, record: unknown): Promise<void> {
   await appendFile(path, line, "utf8");
 }
 
+async function finalizeThreadResult(params: {
+  cas: CasStore;
+  workflowName: string;
+  threadId: string;
+  stepMerkleHashes: readonly string[];
+  completion: WorkflowCompletion;
+}): Promise<WorkflowResult> {
+  const rootHash = await putThreadMerkleNode(
+    params.cas,
+    {
+      workflow: params.workflowName,
+      threadId: params.threadId,
+      result: {
+        returnCode: params.completion.returnCode,
+        summary: params.completion.summary,
+      },
+    },
+    params.stepMerkleHashes,
+  );
+  return {
+    returnCode: params.completion.returnCode,
+    summary: params.completion.summary,
+    rootHash,
+  };
+}
+
 async function driveWorkflowGenerator(params: {
   fn: WorkflowFn;
+  workflowName: string;
   input: ThreadInput;
   bundleOptions: WorkflowFnOptions;
   executeOptions: ExecuteThreadOptions;
   dataJsonlPath: string;
   threadId: string;
   logger: LogFn;
+  cas: CasStore;
+  stepMerkleHashes: string[];
 }): Promise<WorkflowResult> {
-  const { fn, input, bundleOptions, executeOptions, dataJsonlPath, threadId, logger } = params;
+  const {
+    fn,
+    workflowName,
+    input,
+    bundleOptions,
+    executeOptions,
+    dataJsonlPath,
+    threadId,
+    logger,
+    cas,
+    stepMerkleHashes,
+  } = params;
   const gen = fn(input, bundleOptions);
   let written = 0;
 
   while (true) {
     if (executeOptions.signal.aborted) {
       logger("V8JX4NP2", `thread ${threadId} aborted`);
-      return { returnCode: 130, summary: "thread aborted" };
+      return await finalizeThreadResult({
+        cas,
+        workflowName,
+        threadId,
+        stepMerkleHashes,
+        completion: { returnCode: 130, summary: "thread aborted" },
+      });
     }
 
     if (written >= executeOptions.maxRounds) {
       logger("R3CW7YBQ", `thread ${threadId} stopped at maxRounds=${executeOptions.maxRounds}`);
-      return {
-        returnCode: 0,
-        summary: `completed: reached maxRounds (${executeOptions.maxRounds})`,
-      };
+      return await finalizeThreadResult({
+        cas,
+        workflowName,
+        threadId,
+        stepMerkleHashes,
+        completion: {
+          returnCode: 0,
+          summary: `completed: reached maxRounds (${executeOptions.maxRounds})`,
+        },
+      });
     }
 
     const iterResult = await gen.next();
 
     if (iterResult.done) {
       logger("F3HN8QKP", `thread ${threadId} generator finished`);
-      return iterResult.value;
+      const completion = iterResult.value;
+      return await finalizeThreadResult({
+        cas,
+        workflowName,
+        threadId,
+        stepMerkleHashes,
+        completion,
+      });
     }
 
     written++;
     const step = iterResult.value;
+    const resolved = await getContentMerklePayload(cas, step.contentHash);
+    if (resolved === null) {
+      throw new Error(
+        `role step ${step.role}: CAS blob missing for contentHash ${step.contentHash}`,
+      );
+    }
     const ts = Date.now();
     await appendDataLine(dataJsonlPath, {
       role: step.role,
-      content: step.content,
+      contentHash: step.contentHash,
       meta: step.meta,
+      refs: normalizeRefsField(step.refs),
       timestamp: ts,
     });
 
+    const stepNodeHash = await putStepMerkleNode(
+      cas,
+      { role: step.role, meta: step.meta },
+      step.contentHash,
+    );
+    stepMerkleHashes.push(stepNodeHash);
+
     logger("N7BW4YHQ", `thread ${threadId} wrote role ${step.role}`);
 
     await Promise.race([
@@ -97,7 +183,13 @@ async function driveWorkflowGenerator(params: {
 
     if (executeOptions.signal.aborted) {
       logger("V8JX4NP4", `thread ${threadId} aborted`);
-      return { returnCode: 130, summary: "thread aborted" };
+      return await finalizeThreadResult({
+        cas,
+        workflowName,
+        threadId,
+        stepMerkleHashes,
+        completion: { returnCode: 130, summary: "thread aborted" },
+      });
     }
   }
 }
@@ -133,6 +225,7 @@ export async function executeThread(
       prompt: input.prompt,
       options: {
         maxRounds: options.maxRounds,
+        depth: options.depth,
       },
     },
     timestamp: nowMs,
@@ -145,37 +238,63 @@ export async function executeThread(
 
   logger("T9HQ2KHM", `thread ${io.threadId} started for workflow ${workflowName}`);
 
+  const stepMerkleHashes: string[] = [];
+
   if (prefilled !== null) {
     for (const row of prefilled) {
+      const prefilledPayload = await getContentMerklePayload(io.cas, row.contentHash);
+      if (prefilledPayload === null) {
+        throw new Error(
+          `prefilled step ${row.role}: CAS blob missing for contentHash ${row.contentHash}`,
+        );
+      }
       await appendDataLine(io.dataJsonlPath, {
         role: row.role,
-        content: row.content,
+        contentHash: row.contentHash,
         meta: row.meta,
+        refs: normalizeRefsField(row.refs),
         timestamp: row.timestamp,
       });
+      const stepNodeHash = await putStepMerkleNode(
+        io.cas,
+        { role: row.role, meta: row.meta },
+        row.contentHash,
+      );
+      stepMerkleHashes.push(stepNodeHash);
     }
   }
 
   if (options.maxRounds <= 0) {
     logger("R3CW7YBQ", `thread ${io.threadId} stopped at maxRounds=${options.maxRounds}`);
-    return {
-      returnCode: 0,
-      summary: `completed: reached maxRounds (${options.maxRounds})`,
-    };
+    return await finalizeThreadResult({
+      cas: io.cas,
+      workflowName,
+      threadId: io.threadId,
+      stepMerkleHashes,
+      completion: {
+        returnCode: 0,
+        summary: `completed: reached maxRounds (${options.maxRounds})`,
+      },
+    });
   }
 
   const bundleOptions: WorkflowFnOptions = {
     threadId: io.threadId,
     maxRounds: options.maxRounds,
+    depth: options.depth,
+    cas: io.cas,
   };
 
   return await driveWorkflowGenerator({
     fn,
+    workflowName,
     input,
     bundleOptions,
     executeOptions: options,
     dataJsonlPath: io.dataJsonlPath,
     threadId: io.threadId,
     logger,
+    cas: io.cas,
+    stepMerkleHashes,
   });
 }

packages/workflow/src/ensure-uncaged-workflow-symlink.ts

@@ -0,0 +1,36 @@
+import { mkdir, readlink, symlink, unlink } from "node:fs/promises";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+
+/** This module lives in `@uncaged/workflow/src`; parent dir is the package root. */
+function installedWorkflowPackageDir(): string {
+  return fileURLToPath(new URL("..", import.meta.url));
+}
+
+/**
+ * Ensures `<storageRoot>/node_modules/@uncaged/workflow` points at the installed `@uncaged/workflow`
+ * package so workflow bundles loaded from `<storageRoot>/bundles/*.esm.js` can resolve `import "@uncaged/workflow"`.
+ */
+export async function ensureUncagedWorkflowSymlink(storageRoot: string): Promise<void> {
+  const target = installedWorkflowPackageDir();
+  const linkDir = path.join(storageRoot, "node_modules", "@uncaged");
+  const linkPath = path.join(linkDir, "workflow");
+  await mkdir(linkDir, { recursive: true });
+
+  try {
+    const existing = await readlink(linkPath);
+    const normalizedExisting = path.resolve(linkDir, existing);
+    if (normalizedExisting === target) {
+      return;
+    }
+    await unlink(linkPath);
+  } catch (e) {
+    const errObj = e as NodeJS.ErrnoException;
+    if (errObj.code !== "ENOENT" && errObj.code !== "EINVAL") {
+      throw e;
+    }
+  }
+
+  const linkType = process.platform === "win32" ? "junction" : "dir";
+  await symlink(target, linkPath, linkType);
+}

packages/workflow/src/extract-bundle-exports.ts

@@ -1,5 +1,5 @@
-import { pathToFileURL } from "node:url";
-
+import { importWorkflowBundleModule } from "./bundle-import-env.js";
+import { ensureUncagedWorkflowSymlink } from "./ensure-uncaged-workflow-symlink.js";
 import { err, ok, type Result } from "./result.js";
 import type { WorkflowFn } from "./types.js";
 import type { WorkflowDescriptor } from "./workflow-descriptor.js";
@@ -10,14 +10,23 @@ export type ExtractedBundleExports = {
   descriptor: WorkflowDescriptor;
 };
 
+export type ExtractBundleExportsOptions = {
+  /** When set, ensures `node_modules/@uncaged/workflow` exists under this root before import. */
+  storageRoot: string | null;
+};
+
 /** Load a workflow `.esm.js` bundle and read its named exports (`run`, `descriptor`). */
 export async function extractBundleExports(
   bundlePath: string,
+  options: ExtractBundleExportsOptions = { storageRoot: null },
 ): Promise<Result<ExtractedBundleExports, string>> {
   let modUnknown: unknown;
   try {
+    if (options.storageRoot !== null) {
+      await ensureUncagedWorkflowSymlink(options.storageRoot);
+    }
     // Dynamic import required: user bundle path resolved at runtime
-    modUnknown = await import(pathToFileURL(bundlePath).href);
+    modUnknown = await importWorkflowBundleModule(bundlePath);
   } catch (e) {
     const message = e instanceof Error ? e.message : String(e);
     return err(`failed to import bundle: ${message}`);

packages/workflow/src/extract-fn.ts

@@ -1,6 +1,7 @@
 import type * as z from "zod/v4";
 
 import { llmExtractWithRetry } from "./llm-extract.js";
+import { getContentMerklePayload } from "./merkle.js";
 import type { ExtractContext, LlmProvider } from "./types.js";
 
 export type ExtractFn = <T extends Record<string, unknown>>(
@@ -29,8 +30,12 @@ export function createExtract(provider: LlmProvider): ExtractFn {
     if (ctx.steps.length > 0) {
       lines.push("## Thread History");
       for (const step of ctx.steps) {
+        const body = await getContentMerklePayload(ctx.cas, step.contentHash);
+        if (body === null) {
+          throw new Error(`extract: missing CAS blob for step ${step.role}: ${step.contentHash}`);
+        }
         lines.push(`### ${step.role}`);
-        lines.push(step.content);
+        lines.push(body);
         lines.push(`Meta: ${JSON.stringify(step.meta)}`);
         lines.push("");
       }

packages/workflow/src/fork-thread.ts

@@ -1,3 +1,4 @@
+import { normalizeRefsField } from "./refs-field.js";
 import { err, ok, type Result } from "./result.js";
 import type { RoleOutput } from "./types.js";
 
@@ -10,6 +11,7 @@ export type ParsedThreadStartRecord = {
   threadId: string;
   prompt: string;
   maxRounds: number;
+  depth: number;
 };
 
 function parseRoleLine(
@@ -17,14 +19,14 @@ function parseRoleLine(
   lineIndex: number,
 ): Result<ForkHistoricalStep, string> {
   const role = obj.role;
-  const content = obj.content;
+  const contentHash = obj.contentHash;
   const meta = obj.meta;
   const timestamp = obj.timestamp;
   if (typeof role !== "string") {
     return err(`invalid role record at line ${lineIndex}: missing role`);
   }
-  if (typeof content !== "string") {
-    return err(`invalid role record at line ${lineIndex}: missing content`);
+  if (typeof contentHash !== "string") {
+    return err(`invalid role record at line ${lineIndex}: missing contentHash`);
   }
   if (meta === null || typeof meta !== "object") {
     return err(`invalid role record at line ${lineIndex}: missing meta`);
@@ -34,8 +36,9 @@ function parseRoleLine(
   }
   return ok({
     role,
-    content,
+    contentHash,
     meta: meta as Record<string, unknown>,
+    refs: normalizeRefsField(obj.refs),
     timestamp,
   });
 }
@@ -76,12 +79,17 @@ function parseStartRecordLine(firstLine: string): Result<ParsedThreadStartRecord
     return err("start record missing parameters.options.maxRounds");
   }
 
+  const depthRaw = optRec.depth;
+  const depth =
+    typeof depthRaw === "number" && Number.isFinite(depthRaw) ? Math.trunc(depthRaw) : 0;
+
   return ok({
     workflowName: name,
     hash,
     threadId,
     prompt,
     maxRounds,
+    depth,
   });
 }
 
@@ -194,7 +202,7 @@ export type ForkPlan = {
   hash: string;
   sourceThreadId: string;
   prompt: string;
-  runOptions: { maxRounds: number };
+  runOptions: { maxRounds: number; depth: number };
   historicalSteps: ForkHistoricalStep[];
 };
 
@@ -219,7 +227,7 @@ export function buildForkPlan(
     hash: start.hash,
     sourceThreadId: start.threadId,
     prompt: start.prompt,
-    runOptions: { maxRounds: start.maxRounds },
+    runOptions: { maxRounds: start.maxRounds, depth: start.depth },
     historicalSteps: selected.value,
   });
 }

packages/workflow/src/gc.ts

@@ -0,0 +1,131 @@
+import { readdir, readFile } from "node:fs/promises";
+import { join } from "node:path";
+
+import { type CasStore, createCasStore } from "./cas.js";
+import { parseThreadDataJsonl } from "./fork-thread.js";
+import { err, ok, type Result } from "./result.js";
+import { getGlobalCasDir } from "./storage-root.js";
+
+export type GcResult = {
+  scannedThreads: number;
+  activeRefs: number;
+  deletedEntries: number;
+  deletedHashes: string[];
+};
+
+async function listThreadDataJsonlPaths(storageRoot: string): Promise<Result<string[], string>> {
+  const logsRoot = join(storageRoot, "logs");
+  const paths: string[] = [];
+  let hashes: string[];
+  try {
+    hashes = await readdir(logsRoot);
+  } catch (e) {
+    const errObj = e as NodeJS.ErrnoException;
+    if (errObj.code === "ENOENT") {
+      return ok([]);
+    }
+    return err(`failed to read logs directory: ${String(e)}`);
+  }
+
+  for (const hash of hashes) {
+    const dir = join(logsRoot, hash);
+    let entries: string[];
+    try {
+      entries = await readdir(dir);
+    } catch {
+      continue;
+    }
+    for (const fileName of entries) {
+      if (fileName.endsWith(".data.jsonl")) {
+        paths.push(join(dir, fileName));
+      }
+    }
+  }
+
+  paths.sort();
+  return ok(paths);
+}
+
+async function collectActiveRefsFromDataPaths(
+  dataPaths: string[],
+): Promise<Result<Set<string>, string>> {
+  const activeRefs = new Set<string>();
+  for (const dataPath of dataPaths) {
+    let text: string;
+    try {
+      text = await readFile(dataPath, "utf8");
+    } catch (e) {
+      return err(`failed to read ${dataPath}: ${String(e)}`);
+    }
+    const parsed = parseThreadDataJsonl(text);
+    if (!parsed.ok) {
+      return err(`${dataPath}: ${parsed.error}`);
+    }
+    for (const step of parsed.value.roleSteps) {
+      for (const ref of step.refs) {
+        activeRefs.add(ref);
+      }
+    }
+  }
+  return ok(activeRefs);
+}
+
+async function deleteCasNotInSet(
+  cas: CasStore,
+  activeRefs: Set<string>,
+): Promise<Result<string[], string>> {
+  let listed: string[];
+  try {
+    listed = await cas.list();
+  } catch (e) {
+    return err(`failed to list cas entries: ${String(e)}`);
+  }
+
+  const deletedHashes: string[] = [];
+  for (const hash of listed) {
+    if (activeRefs.has(hash)) {
+      continue;
+    }
+    try {
+      await cas.delete(hash);
+    } catch (e) {
+      return err(`failed to delete cas ${hash}: ${String(e)}`);
+    }
+    deletedHashes.push(hash);
+  }
+
+  deletedHashes.sort();
+  return ok(deletedHashes);
+}
+
+/**
+ * Mark-and-sweep CAS GC: collect `refs` from all thread `.data.jsonl` files under `storageRoot`,
+ * then delete CAS blobs not referenced by any surviving thread data.
+ */
+export async function garbageCollectCas(storageRoot: string): Promise<Result<GcResult, string>> {
+  const pathsResult = await listThreadDataJsonlPaths(storageRoot);
+  if (!pathsResult.ok) {
+    return pathsResult;
+  }
+  const paths = pathsResult.value;
+
+  const refsResult = await collectActiveRefsFromDataPaths(paths);
+  if (!refsResult.ok) {
+    return refsResult;
+  }
+  const activeRefs = refsResult.value;
+
+  const cas = createCasStore(getGlobalCasDir(storageRoot));
+  const deletedResult = await deleteCasNotInSet(cas, activeRefs);
+  if (!deletedResult.ok) {
+    return deletedResult;
+  }
+  const deletedHashes = deletedResult.value;
+
+  return ok({
+    scannedThreads: paths.length,
+    activeRefs: activeRefs.size,
+    deletedEntries: deletedHashes.length,
+    deletedHashes,
+  });
+}

packages/workflow/src/index.ts

@@ -7,7 +7,7 @@ export {
 } from "./base32.js";
 export { buildDescriptor } from "./build-descriptor.js";
 export { validateWorkflowBundle, type WorkflowBundleValidationInput } from "./bundle-validator.js";
-export { type CasStore, createThreadCas } from "./cas.js";
+export { type CasStore, createCasStore, createThreadCas } from "./cas.js";
 export { createWorkflow } from "./create-workflow.js";
 export {
   type ExecuteThreadIo,
@@ -25,6 +25,7 @@ export {
   parseThreadDataJsonl,
   selectForkHistoricalSteps,
 } from "./fork-thread.js";
+export { type GcResult, garbageCollectCas } from "./gc.js";
 export { stringifyWorkflowDescriptor } from "./generate-descriptor.js";
 export { hashString, hashWorkflowBundleBytes } from "./hash.js";
 export {
@@ -39,6 +40,19 @@ export {
   type LogFn,
   type LoggerSink,
 } from "./logger.js";
+export {
+  createContentMerkleNode,
+  getContentMerklePayload,
+  type MerkleNode,
+  type MerkleNodeType,
+  parseMerkleNode,
+  putContentMerkleNode,
+  putStepMerkleNode,
+  putThreadMerkleNode,
+  type StepMerklePayload,
+  serializeMerkleNode,
+  type ThreadMerklePayload,
+} from "./merkle.js";
 export {
   getRegisteredWorkflow,
   listRegisteredWorkflowNames,
@@ -55,7 +69,7 @@ export {
   writeWorkflowRegistry,
 } from "./registry.js";
 export { err, ok, type Result } from "./result.js";
-export { getDefaultWorkflowStorageRoot } from "./storage-root.js";
+export { getDefaultWorkflowStorageRoot, getGlobalCasDir } from "./storage-root.js";
 export { createThreadPauseGate, type ThreadPauseGate } from "./thread-pause-gate.js";
 export {
   type AgentBinding,
@@ -74,6 +88,7 @@ export {
   type StartStep,
   type ThreadContext,
   type ThreadInput,
+  type WorkflowCompletion,
   type WorkflowDefinition,
   type WorkflowFn,
   type WorkflowFnOptions,
@@ -81,6 +96,7 @@ export {
 } from "./types.js";
 export { generateUlid } from "./ulid.js";
 export { getWorkerHostScriptPath } from "./worker-entry-path.js";
+export { type WorkflowAsAgentOptions, workflowAsAgent } from "./workflow-as-agent.js";
 export {
   validateWorkflowDescriptor,
   type WorkflowDescriptor,

packages/workflow/src/merkle.ts

@@ -0,0 +1,122 @@
+import { parse, stringify } from "yaml";
+
+import type { CasStore } from "./cas.js";
+
+export type MerkleNodeType = "content" | "step" | "thread";
+
+export type MerkleNode = {
+  type: MerkleNodeType;
+  payload: string | Record<string, unknown>;
+  children: string[];
+};
+
+export function serializeMerkleNode(node: MerkleNode): string {
+  return stringify(
+    { type: node.type, payload: node.payload, children: node.children },
+    { indent: 2 },
+  );
+}
+
+export function parseMerkleNode(yamlText: string): MerkleNode {
+  const raw = parse(yamlText) as unknown;
+  if (raw === null || typeof raw !== "object") {
+    throw new Error("merkle: YAML root must be an object");
+  }
+  const rec = raw as Record<string, unknown>;
+  const type = rec.type;
+  const payload = rec.payload;
+  const children = rec.children;
+  if (type !== "content" && type !== "step" && type !== "thread") {
+    throw new Error("merkle: invalid or missing type");
+  }
+  if (typeof payload !== "string" && (payload === null || typeof payload !== "object")) {
+    throw new Error("merkle: payload must be a string or object");
+  }
+  if (!Array.isArray(children)) {
+    throw new Error("merkle: children must be an array");
+  }
+  const childHashes: string[] = [];
+  for (const c of children) {
+    if (typeof c !== "string") {
+      throw new Error("merkle: child hash must be a string");
+    }
+    childHashes.push(c);
+  }
+  return {
+    type,
+    payload: typeof payload === "string" ? payload : (payload as Record<string, unknown>),
+    children: childHashes,
+  };
+}
+
+export function createContentMerkleNode(payload: string): MerkleNode {
+  return { type: "content", payload, children: [] };
+}
+
+export type StepMerklePayload = {
+  role: string;
+  meta: Record<string, unknown>;
+};
+
+export type ThreadMerklePayload = {
+  workflow: string;
+  threadId: string;
+  result: {
+    returnCode: number;
+    summary: string;
+  };
+};
+
+/** Serializes a step Merkle node (role + meta + content child) and stores it in CAS. */
+export async function putStepMerkleNode(
+  store: CasStore,
+  payload: StepMerklePayload,
+  contentHash: string,
+): Promise<string> {
+  const node: MerkleNode = {
+    type: "step",
+    payload: { role: payload.role, meta: payload.meta },
+    children: [contentHash],
+  };
+  return store.put(serializeMerkleNode(node));
+}
+
+/** Serializes the thread root Merkle node and stores it in CAS. */
+export async function putThreadMerkleNode(
+  store: CasStore,
+  payload: ThreadMerklePayload,
+  stepHashes: readonly string[],
+): Promise<string> {
+  const node: MerkleNode = {
+    type: "thread",
+    payload: {
+      workflow: payload.workflow,
+      threadId: payload.threadId,
+      result: payload.result,
+    },
+    children: [...stepHashes],
+  };
+  return store.put(serializeMerkleNode(node));
+}
+
+/** Serializes a content Merkle node and stores it in CAS; returns its hash. */
+export async function putContentMerkleNode(store: CasStore, content: string): Promise<string> {
+  const yamlText = serializeMerkleNode(createContentMerkleNode(content));
+  return store.put(yamlText);
+}
+
+/** Loads a CAS blob and returns the payload string for a `content` Merkle node. */
+export async function getContentMerklePayload(
+  store: CasStore,
+  hash: string,
+): Promise<string | null> {
+  const yamlText = await store.get(hash);
+  if (yamlText === null) {
+    return null;
+  }
+  const node = parseMerkleNode(yamlText);
+  if (node.type !== "content" || typeof node.payload !== "string") {
+    return null;
+  }
+  return node.payload;
+}

packages/workflow/src/refs-field.ts

@@ -0,0 +1,22 @@
+/** Append `contentHash` to `refs` when not already present (dedupe by first occurrence order). */
+export function mergeRefsWithContentHash(refs: string[], contentHash: string): string[] {
+  const out = [...refs];
+  if (!out.includes(contentHash)) {
+    out.push(contentHash);
+  }
+  return out;
+}
+
+/** Normalize `refs` from persisted JSONL or IPC payloads (missing or invalid → []). */
+export function normalizeRefsField(value: unknown): string[] {
+  if (!Array.isArray(value)) {
+    return [];
+  }
+  const out: string[] = [];
+  for (const x of value) {
+    if (typeof x === "string") {
+      out.push(x);
+    }
+  }
+  return out;
+}

packages/workflow/src/storage-root.ts

@@ -5,3 +5,9 @@ import { join } from "node:path";
 export function getDefaultWorkflowStorageRoot(): string {
   return join(homedir(), ".uncaged", "workflow");
 }
+
+/** Global content-addressed store directory under the workflow storage root (`<root>/cas`). */
+export function getGlobalCasDir(storageRoot: string | undefined): string {
+  const root = storageRoot ?? getDefaultWorkflowStorageRoot();
+  return join(root, "cas");
+}

packages/workflow/src/types.ts

@@ -1,5 +1,7 @@
 import type * as z from "zod/v4";
 
+import type { CasStore } from "./cas.js";
+
 /** Sentinel values for automaton control flow. */
 export const START = "__start__" as const;
 export const END = "__end__" as const;
@@ -17,16 +19,24 @@ export type LlmProvider = {
 /** What each generator yield produces — one role's output (engine adds `timestamp` when persisting). */
 export type RoleOutput = {
   role: string;
-  content: string;
+  /** CAS hash of the serialized Merkle content node for this step's body text. */
+  contentHash: string;
   meta: Record<string, unknown>;
+  /** CAS hashes produced or consumed by this step (for GC traceability). */
+  refs: string[];
 };
 
-/** What the workflow AsyncGenerator returns when done. */
-export type WorkflowResult = {
+/** Generator completion value from a workflow bundle (`run` export). Root hash is added by the engine. */
+export type WorkflowCompletion = {
   returnCode: number;
   summary: string;
 };
 
+/** Final thread outcome from {@link executeThread}, including Merkle thread root CAS hash. */
+export type WorkflowResult = WorkflowCompletion & {
+  rootHash: string;
+};
+
 /** Input to a workflow — prompt plus optional historical steps for fork/resume. */
 export type ThreadInput = {
   prompt: string;
@@ -37,13 +47,17 @@ export type ThreadInput = {
 export type WorkflowFnOptions = {
   threadId: string;
   maxRounds: number;
+  /** Nesting depth for workflow-as-agent chains; root threads use `0`. */
+  depth: number;
+  /** Global CAS store for Merkle content blobs (role step bodies). */
+  cas: CasStore;
 };
 
 /** Bundle contract — named export `run` is a function returning an AsyncGenerator. */
 export type WorkflowFn = (
   input: ThreadInput,
   options: WorkflowFnOptions,
-) => AsyncGenerator<RoleOutput, WorkflowResult>;
+) => AsyncGenerator<RoleOutput, WorkflowCompletion>;
 
 /** Engine start frame: initial prompt + thread identity. */
 export type StartStep = {
@@ -55,12 +69,20 @@ export type StartStep = {
 
 /** A completed role step in the thread. */
 export type RoleStep<M extends RoleMeta> = {
-  [K in keyof M & string]: { role: K; meta: M[K]; content: string; timestamp: number };
+  [K in keyof M & string]: {
+    role: K;
+    meta: M[K];
+    contentHash: string;
+    refs: string[];
+    timestamp: number;
+  };
 }[keyof M & string];
 
 /** Phase 1: Moderator decides next role. */
 export type ModeratorContext<M extends RoleMeta = RoleMeta> = {
   threadId: string;
+  /** Same as `WorkflowFnOptions.depth` for the active thread. */
+  depth: number;
   start: StartStep;
   steps: RoleStep<M>[];
 };
@@ -71,6 +93,7 @@ export type AgentContext<M extends RoleMeta = RoleMeta> = ModeratorContext<M> &
     name: string;
     systemPrompt: string;
   };
+  cas: CasStore;
 };
 
 /** Phase 3: Extractor runs — has agent output; the extraction instruction is a separate argument to the extract function. */
@@ -96,6 +119,8 @@ export type RoleDefinition<Meta extends Record<string, unknown>> = {
   systemPrompt: string;
   extractPrompt: string;
   schema: z.ZodType<Meta>;
+  /** When non-null, produces CAS hashes to persist on this role's steps (see `RoleOutput.refs`). */
+  extractRefs: ((meta: Meta) => string[]) | null;
 };
 
 /**

packages/workflow/src/worker.ts

@@ -1,11 +1,15 @@
 import { mkdir, unlink, writeFile } from "node:fs/promises";
 import { createServer, type Socket } from "node:net";
 import { dirname, join } from "node:path";
-import { pathToFileURL } from "node:url";
+import { importWorkflowBundleModule } from "./bundle-import-env.js";
+import { createCasStore } from "./cas.js";
 import type { PrefilledDiskStep } from "./engine.js";
 import { type ExecuteThreadIo, executeThread } from "./engine.js";
+import { ensureUncagedWorkflowSymlink } from "./ensure-uncaged-workflow-symlink.js";
 import { createLogger } from "./logger.js";
+import { normalizeRefsField } from "./refs-field.js";
 import { err, ok, type Result } from "./result.js";
+import { getGlobalCasDir } from "./storage-root.js";
 import { createThreadPauseGate, type ThreadPauseGate } from "./thread-pause-gate.js";
 import type { RoleOutput, WorkflowFn } from "./types.js";
 
@@ -16,7 +20,7 @@ type RunCommand = {
   threadId: string;
   workflowName: string;
   prompt: string;
-  options: { maxRounds: number };
+  options: { maxRounds: number; depth: number };
   steps: RoleOutput[];
   /** Timestamps aligned with `steps` for `.data.jsonl` replay; length must match `steps` when non-null. */
   stepTimestamps: number[] | null;
@@ -47,15 +51,20 @@ type ThreadHandle = {
 
 function parseRoleOutputRecord(obj: Record<string, unknown>): RoleOutput | null {
   const role = obj.role;
-  const content = obj.content;
+  const contentHash = obj.contentHash;
   const meta = obj.meta;
-  if (typeof role !== "string" || typeof content !== "string") {
+  if (typeof role !== "string" || typeof contentHash !== "string") {
     return null;
   }
   if (meta === null || typeof meta !== "object") {
     return null;
   }
-  return { role, content, meta: meta as Record<string, unknown> };
+  return {
+    role,
+    contentHash,
+    meta: meta as Record<string, unknown>,
+    refs: normalizeRefsField(obj.refs),
+  };
 }
 
 function parseRunStepsPayload(rec: Record<string, unknown>): {
@@ -118,6 +127,9 @@ function parseRunControlPayload(rec: Record<string, unknown>): RunCommand | null
   if (typeof maxRounds !== "number") {
     return null;
   }
+  const depthRaw = optRec.depth;
+  const depth =
+    typeof depthRaw === "number" && Number.isFinite(depthRaw) ? Math.trunc(depthRaw) : 0;
   const parsedSteps = parseRunStepsPayload(rec);
   if (parsedSteps === null) {
     return null;
@@ -135,7 +147,7 @@ function parseRunControlPayload(rec: Record<string, unknown>): RunCommand | null
     threadId,
     workflowName,
     prompt,
-    options: { maxRounds },
+    options: { maxRounds, depth },
     steps: parsedSteps.steps,
     stepTimestamps: parsedSteps.stepTimestamps,
     forkSourceThreadId,
@@ -291,8 +303,9 @@ async function main(): Promise<void> {
     return;
   }
 
+  await ensureUncagedWorkflowSymlink(storageRoot);
   // Dynamic import required: user bundle path resolved at runtime
-  const modUnknown: unknown = await import(pathToFileURL(bundlePath).href);
+  const modUnknown: unknown = await importWorkflowBundleModule(bundlePath);
   const modRec = modUnknown as Record<string, unknown>;
   const runExport = modRec.run;
   if (!isWorkflowFnLike(runExport)) {
@@ -306,6 +319,8 @@ async function main(): Promise<void> {
   let activeThreads = 0;
   let shutdownTimer: ReturnType<typeof setTimeout> | null = null;
 
+  const cas = createCasStore(getGlobalCasDir(storageRoot));
+
   const workerCtlPath = join(storageRoot, "workers", `${hash}.json`);
 
   function cancelShutdownTimer(): void {
@@ -354,6 +369,7 @@ async function main(): Promise<void> {
       hash,
       dataJsonlPath,
       infoJsonlPath,
+      cas,
     };
 
     const existing = threads.get(threadId);
@@ -380,8 +396,9 @@ async function main(): Promise<void> {
           const ts = cmd.stepTimestamps?.[i];
           return {
             role: step.role,
-            content: step.content,
+            contentHash: step.contentHash,
             meta: step.meta,
+            refs: normalizeRefsField(step.refs),
             timestamp: typeof ts === "number" && ts > 0 ? ts : baseTs + i,
           };
         });

packages/workflow/src/workflow-as-agent.ts

@@ -0,0 +1,101 @@
+import { join } from "node:path";
+
+import { createCasStore } from "./cas.js";
+import { type ExecuteThreadIo, executeThread } from "./engine.js";
+import { extractBundleExports } from "./extract-bundle-exports.js";
+import { createLogger } from "./logger.js";
+import { getRegisteredWorkflow, readWorkflowRegistry } from "./registry.js";
+import { getDefaultWorkflowStorageRoot, getGlobalCasDir } from "./storage-root.js";
+import type { AgentContext, AgentFn, ThreadInput } from "./types.js";
+import { generateUlid } from "./ulid.js";
+
+/** Maximum `WorkflowFnOptions.depth` allowed for a child spawned via `workflowAsAgent`. */
+const WORKFLOW_AS_AGENT_MAX_DEPTH = 3;
+
+export type WorkflowAsAgentOptions = {
+  /** When `null`, uses `getDefaultWorkflowStorageRoot()`. */
+  storageRoot: string | null;
+};
+
+function resolveWorkflowAsAgentStorageRoot(options: WorkflowAsAgentOptions | null): string {
+  if (options !== null && options.storageRoot !== null) {
+    return options.storageRoot;
+  }
+  return getDefaultWorkflowStorageRoot();
+}
+
+/**
+ * Returns an {@link AgentFn} that runs another registered workflow in a new thread,
+ * using the parent thread's initial prompt (`ctx.start.content`) as the child {@link ThreadInput.prompt}.
+ */
+export function workflowAsAgent(
+  workflowName: string,
+  options: WorkflowAsAgentOptions | null = null,
+): AgentFn {
+  return async (ctx: AgentContext): Promise<string> => {
+    const nextDepth = ctx.depth + 1;
+    if (nextDepth > WORKFLOW_AS_AGENT_MAX_DEPTH) {
+      return `ERROR: workflow-as-agent depth limit exceeded (max ${WORKFLOW_AS_AGENT_MAX_DEPTH})`;
+    }
+
+    const storageRoot = resolveWorkflowAsAgentStorageRoot(options);
+
+    const registryResult = await readWorkflowRegistry(storageRoot);
+    if (!registryResult.ok) {
+      return `ERROR: failed to read workflow registry: ${registryResult.error.message}`;
+    }
+
+    const entry = getRegisteredWorkflow(registryResult.value, workflowName);
+    if (entry === null) {
+      return `ERROR: workflow "${workflowName}" not found in registry`;
+    }
+
+    const bundlePath = join(storageRoot, "bundles", `${entry.hash}.esm.js`);
+    const bundleExportsResult = await extractBundleExports(bundlePath, { storageRoot });
+    if (!bundleExportsResult.ok) {
+      return `ERROR: ${bundleExportsResult.error}`;
+    }
+
+    const input: ThreadInput = {
+      prompt: ctx.start.content,
+      steps: [],
+    };
+
+    const childThreadId = generateUlid(Date.now());
+    const dataJsonlPath = join(storageRoot, "logs", entry.hash, `${childThreadId}.data.jsonl`);
+    const infoJsonlPath = join(storageRoot, "logs", entry.hash, `${childThreadId}.info.jsonl`);
+
+    const io: ExecuteThreadIo = {
+      threadId: childThreadId,
+      hash: entry.hash,
+      dataJsonlPath,
+      infoJsonlPath,
+      cas: createCasStore(getGlobalCasDir(storageRoot)),
+    };
+
+    const logger = createLogger({ sink: { kind: "file", path: infoJsonlPath } });
+    const signalNever = new AbortController();
+
+    try {
+      const result = await executeThread(
+        bundleExportsResult.value.run,
+        workflowName,
+        input,
+        {
+          maxRounds: ctx.start.meta.maxRounds,
+          depth: nextDepth,
+          signal: signalNever.signal,
+          awaitAfterEachYield: async () => {},
+          forkSourceThreadId: ctx.threadId,
+          prefilledDiskSteps: null,
+        },
+        io,
+        logger,
+      );
+      return result.rootHash;
+    } catch (e) {
+      const message = e instanceof Error ? e.message : String(e);
+      return `ERROR: ${message}`;
+    }
+  };
+}