fix(cli): replace markdown headings with XML tags in thread read output

Changed uwf thread read to wrap role prompts and agent outputs in XML tags
(<prompt> and <output>) instead of markdown headings (### Prompt, ### Content).
This prevents Claude Code from treating step outputs as structural headings.

- Updated formatStepPrompt to use <prompt>...</prompt> tags
- Updated formatStepContent to use <output>...</output> tags
- Added comprehensive test suite in thread-read-xml-tags.test.ts
- Updated existing tests to verify XML tag behavior

Fixes #459

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

packages/cli-workflow/src/__tests__/thread-read-xml-tags.test.ts

@@ -0,0 +1,683 @@
+import { mkdir, mkdtemp, rm } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { bootstrap, putSchema } from "@uncaged/json-cas";
+import { createFsStore } from "@uncaged/json-cas-fs";
+import type { CasRef, ThreadId } from "@uncaged/workflow-protocol";
+import { afterEach, beforeEach, describe, expect, test } from "vitest";
+import { cmdThreadRead, THREAD_READ_DEFAULT_QUOTA } from "../commands/thread.js";
+import { registerUwfSchemas } from "../schemas.js";
+import type { UwfStore } from "../store.js";
+import { saveThreadsIndex } from "../store.js";
+
+// ── schemas used in tests ────────────────────────────────────────────────────
+
+const TURN_SCHEMA = {
+  title: "hermes-turn",
+  type: "object" as const,
+  required: ["index", "role", "content"],
+  properties: {
+    index: { type: "integer" as const },
+    role: { type: "string" as const },
+    content: { type: "string" as const },
+    toolCalls: {
+      anyOf: [
+        { type: "array" as const, items: { type: "object" as const } },
+        { type: "null" as const },
+      ],
+    },
+    reasoning: { anyOf: [{ type: "string" as const }, { type: "null" as const }] },
+  },
+  additionalProperties: false,
+};
+
+const DETAIL_SCHEMA = {
+  title: "hermes-detail",
+  type: "object" as const,
+  required: ["sessionId", "model", "duration", "turnCount", "turns"],
+  properties: {
+    sessionId: { type: "string" as const },
+    model: { type: "string" as const },
+    duration: { type: "integer" as const },
+    turnCount: { type: "integer" as const },
+    turns: {
+      type: "array" as const,
+      items: { type: "string" as const, format: "cas_ref" },
+    },
+  },
+  additionalProperties: false,
+};
+
+// ── helpers ───────────────────────────────────────────────────────────────────
+
+async function makeUwfStore(storageRoot: string): Promise<UwfStore> {
+  const casDir = join(storageRoot, "cas");
+  await mkdir(casDir, { recursive: true });
+  const store = createFsStore(casDir);
+  const schemas = await registerUwfSchemas(store);
+  return { storageRoot, store, schemas };
+}
+
+async function registerDetailSchemas(store: ReturnType<typeof createFsStore>) {
+  await bootstrap(store);
+  const [turn, detail] = await Promise.all([
+    putSchema(store, TURN_SCHEMA),
+    putSchema(store, DETAIL_SCHEMA),
+  ]);
+  return { turn, detail };
+}
+
+// ── fixture ───────────────────────────────────────────────────────────────────
+
+let tmpDir: string;
+
+beforeEach(async () => {
+  tmpDir = await mkdtemp(join(tmpdir(), "cli-uwf-test-"));
+});
+
+afterEach(async () => {
+  await rm(tmpDir, { recursive: true, force: true });
+});
+
+// ── thread read XML tag isolation ─────────────────────────────────────────────
+
+describe("thread read XML tag isolation", () => {
+  test("scenario 1: wraps output in XML tags instead of heading", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+    const detailSchemas = await registerDetailSchemas(uwf.store);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {
+        planner: {
+          description: "Planner",
+          goal: "You are a planning agent. Your task is to...",
+          capabilities: [],
+          procedure: "Plan the work.",
+          output: "Summarize the plan.",
+          meta: "placeholder00" as CasRef,
+        },
+      },
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Fix issue #459",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const turnHash = await uwf.store.put(detailSchemas.turn, {
+      index: 0,
+      role: "assistant",
+      content:
+        "---\nstatus: ready\nplan: CMWGHQKT58RY4\n---\n\n# Analysis Complete\n## Issue Summary\nThe issue requires XML tag isolation.",
+      toolCalls: null,
+      reasoning: null,
+    });
+    const detailHash = await uwf.store.put(detailSchemas.detail, {
+      sessionId: "sx",
+      model: "mx",
+      duration: 500,
+      turnCount: 1,
+      turns: [turnHash],
+    });
+
+    const stepHash = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: null,
+      role: "planner",
+      output: outputHash,
+      detail: detailHash,
+      agent: "uwf-claude-code",
+    });
+
+    const threadId = "01JTEST0000000000000001" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: stepHash });
+
+    const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
+
+    // Should wrap output in XML tags
+    expect(markdown).toContain("<output>");
+    expect(markdown).toContain("</output>");
+
+    // Should not have ### Content heading
+    expect(markdown).not.toContain("### Content");
+
+    // Should preserve markdown headings inside output tags
+    expect(markdown).toContain("# Analysis Complete");
+    expect(markdown).toContain("## Issue Summary");
+  });
+
+  test("scenario 2: wraps prompt in XML tags", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+    const detailSchemas = await registerDetailSchemas(uwf.store);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {
+        planner: {
+          description: "Planner",
+          goal: "You are a planning agent. Your task is to analyze and plan.",
+          capabilities: [],
+          procedure: "Plan the work.",
+          output: "Summarize the plan.",
+          meta: "placeholder00" as CasRef,
+        },
+      },
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Fix issue",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const turnHash = await uwf.store.put(detailSchemas.turn, {
+      index: 0,
+      role: "assistant",
+      content: "---\nstatus: ready\n---\n\nContent here...",
+      toolCalls: null,
+      reasoning: null,
+    });
+    const detailHash = await uwf.store.put(detailSchemas.detail, {
+      sessionId: "sx",
+      model: "mx",
+      duration: 500,
+      turnCount: 1,
+      turns: [turnHash],
+    });
+
+    const stepHash = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: null,
+      role: "planner",
+      output: outputHash,
+      detail: detailHash,
+      agent: "uwf-claude-code",
+    });
+
+    const threadId = "01JTEST0000000000000002" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: stepHash });
+
+    const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
+
+    // Should wrap prompt in XML tags
+    expect(markdown).toContain("<prompt>");
+    expect(markdown).toContain("</prompt>");
+    expect(markdown).toContain("You are a planning agent. Your task is to analyze and plan.");
+
+    // Should not have ### Prompt heading
+    expect(markdown).not.toContain("### Prompt");
+
+    // Should wrap output in XML tags
+    expect(markdown).toContain("<output>");
+    expect(markdown).toContain("</output>");
+  });
+
+  test("scenario 3: same role repeated does not show prompt twice", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {
+        writer: {
+          description: "Writer",
+          goal: "You are a writer agent.",
+          capabilities: [],
+          procedure: "Write content.",
+          output: "Summarize writing.",
+          meta: "placeholder00" as CasRef,
+        },
+      },
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Write something",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const step1 = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: null,
+      role: "writer",
+      output: outputHash,
+      detail: null,
+      agent: "uwf-test",
+    });
+
+    const step2 = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: step1 as CasRef,
+      role: "writer",
+      output: outputHash,
+      detail: null,
+      agent: "uwf-test",
+    });
+
+    const threadId = "01JTEST0000000000000003" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: step2 });
+
+    const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
+
+    // Should only show prompt tags once
+    const promptCount = (markdown.match(/<prompt>/g) ?? []).length;
+    expect(promptCount).toBe(1);
+  });
+
+  test("scenario 4: step with no detail shows no output tags", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {
+        worker: {
+          description: "Worker",
+          goal: "You are a worker agent.",
+          capabilities: [],
+          procedure: "Do work.",
+          output: "Summarize work.",
+          meta: "placeholder00" as CasRef,
+        },
+      },
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Do stuff",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const stepHash = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: null,
+      role: "worker",
+      output: outputHash,
+      detail: null,
+      agent: "uwf-test",
+    });
+
+    const threadId = "01JTEST0000000000000004" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: stepHash });
+
+    const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
+
+    // Should not have output tags
+    expect(markdown).not.toContain("<output>");
+    expect(markdown).not.toContain("</output>");
+
+    // Step header should still be displayed
+    expect(markdown).toContain("## Step 1: worker");
+
+    // Prompt should still be shown
+    expect(markdown).toContain("<prompt>");
+  });
+
+  test("scenario 5: empty content shows no output tags", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Do stuff",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    // A detail ref that doesn't exist → extractLastAssistantContent returns null
+    const missingDetailRef = "missingdetail0" as CasRef;
+
+    const stepHash = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: null,
+      role: "worker",
+      output: outputHash,
+      detail: missingDetailRef,
+      agent: "uwf-test",
+    });
+
+    const threadId = "01JTEST0000000000000005" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: stepHash });
+
+    const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
+
+    // Should not have output tags
+    expect(markdown).not.toContain("<output>");
+    expect(markdown).not.toContain("</output>");
+  });
+
+  test("scenario 6: thread read with --start flag shows task section", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {
+        roleA: {
+          description: "Role A",
+          goal: "Goal for roleA",
+          capabilities: [],
+          procedure: "Do stuff.",
+          output: "Output.",
+          meta: "placeholder00" as CasRef,
+        },
+      },
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Initial prompt",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const stepHash = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: null,
+      role: "roleA",
+      output: outputHash,
+      detail: null,
+      agent: "uwf-test",
+    });
+
+    const threadId = "01JTEST0000000000000006" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: stepHash });
+
+    const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, true);
+
+    // Should include task section
+    expect(markdown).toContain("# Thread");
+    expect(markdown).toContain("## Task");
+    expect(markdown).toContain("Initial prompt");
+
+    // Prompts should use XML tags
+    expect(markdown).toContain("<prompt>");
+  });
+
+  test("scenario 7: thread read with --before parameter", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {
+        roleA: {
+          description: "Role A",
+          goal: "Goal for roleA",
+          capabilities: [],
+          procedure: "Do stuff.",
+          output: "Output.",
+          meta: "placeholder00" as CasRef,
+        },
+        roleB: {
+          description: "Role B",
+          goal: "Goal for roleB",
+          capabilities: [],
+          procedure: "Do stuff.",
+          output: "Output.",
+          meta: "placeholder00" as CasRef,
+        },
+        roleC: {
+          description: "Role C",
+          goal: "Goal for roleC",
+          capabilities: [],
+          procedure: "Do stuff.",
+          output: "Output.",
+          meta: "placeholder00" as CasRef,
+        },
+      },
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Initial prompt",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const step1 = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: null,
+      role: "roleA",
+      output: outputHash,
+      detail: null,
+      agent: "uwf-test",
+    });
+
+    const step2 = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: step1 as CasRef,
+      role: "roleB",
+      output: outputHash,
+      detail: null,
+      agent: "uwf-test",
+    });
+
+    const step3 = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: step2 as CasRef,
+      role: "roleC",
+      output: outputHash,
+      detail: null,
+      agent: "uwf-test",
+    });
+
+    const threadId = "01JTEST0000000000000007" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: step3 });
+
+    const markdown = await cmdThreadRead(
+      tmpDir,
+      threadId,
+      THREAD_READ_DEFAULT_QUOTA,
+      step2 as CasRef,
+      false,
+    );
+
+    // Should only show roleA
+    expect(markdown).toContain("roleA");
+    expect(markdown).not.toContain("roleB");
+    expect(markdown).not.toContain("roleC");
+
+    // Should use XML tags
+    expect(markdown).toContain("<prompt>");
+  });
+
+  test("scenario 9: special characters in content are preserved", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+    const detailSchemas = await registerDetailSchemas(uwf.store);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {
+        writer: {
+          description: "Writer",
+          goal: "You are a writer.",
+          capabilities: [],
+          procedure: "Write content.",
+          output: "Summarize.",
+          meta: "placeholder00" as CasRef,
+        },
+      },
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Write something",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const turnHash = await uwf.store.put(detailSchemas.turn, {
+      index: 0,
+      role: "assistant",
+      content: "Content with <special> & characters > like <this>",
+      toolCalls: null,
+      reasoning: null,
+    });
+    const detailHash = await uwf.store.put(detailSchemas.detail, {
+      sessionId: "sx",
+      model: "mx",
+      duration: 500,
+      turnCount: 1,
+      turns: [turnHash],
+    });
+
+    const stepHash = await uwf.store.put(uwf.schemas.stepNode, {
+      start: startHash,
+      prev: null,
+      role: "writer",
+      output: outputHash,
+      detail: detailHash,
+      agent: "uwf-test",
+    });
+
+    const threadId = "01JTEST0000000000000008" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: stepHash });
+
+    const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
+
+    // Special characters should be preserved as-is
+    expect(markdown).toContain("Content with <special> & characters > like <this>");
+  });
+
+  test("scenario 10: quota limit with XML tags", async () => {
+    const uwf = await makeUwfStore(tmpDir);
+
+    const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "test-wf",
+      description: "desc",
+      roles: {
+        roleA: {
+          description: "Role A",
+          goal: "Goal for roleA",
+          capabilities: [],
+          procedure: "Do stuff.",
+          output: "Output.",
+          meta: "placeholder00" as CasRef,
+        },
+      },
+      conditions: {},
+      graph: {},
+    });
+
+    const startHash = await uwf.store.put(uwf.schemas.startNode, {
+      workflow: workflowHash,
+      prompt: "Initial prompt",
+    });
+
+    const outputHash = await uwf.store.put(uwf.schemas.workflow, {
+      name: "out",
+      description: "",
+      roles: {},
+      conditions: {},
+      graph: {},
+    });
+
+    const steps: CasRef[] = [];
+    let prev: CasRef | null = null;
+    for (let i = 0; i < 5; i++) {
+      const step = (await uwf.store.put(uwf.schemas.stepNode, {
+        start: startHash,
+        prev,
+        role: "roleA",
+        output: outputHash,
+        detail: null,
+        agent: "uwf-test",
+      })) as CasRef;
+      steps.push(step);
+      prev = step;
+    }
+
+    const threadId = "01JTEST0000000000000009" as ThreadId;
+    await saveThreadsIndex(tmpDir, { [threadId]: steps[steps.length - 1]! });
+
+    // Use very small quota
+    const markdown = await cmdThreadRead(tmpDir, threadId, 1, null, false);
+
+    // Should have skip hint
+    expect(markdown).toContain("earlier step");
+
+    // Should have XML tags for displayed steps
+    if (markdown.includes("<prompt>")) {
+      expect(markdown).toContain("</prompt>");
+    }
+  });
+});

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

@@ -198,10 +198,10 @@ describe("extractLastAssistantContent", () => {
   });
 });
 
-// ── cmdThreadRead: ### Content section ───────────────────────────────────────
+// ── cmdThreadRead: <output> section ──────────────────────────────────────────
 
-describe("cmdThreadRead ### Content section", () => {
-  test("includes ### Content before ### Output when detail has assistant turns", async () => {
+describe("cmdThreadRead <output> section", () => {
+  test("includes <output> tags when detail has assistant turns", async () => {
     const uwf = await makeUwfStore(tmpDir);
     const detailSchemas = await registerDetailSchemas(uwf.store);
 
@@ -264,12 +264,13 @@ describe("cmdThreadRead ### Content section", () => {
 
     const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
 
-    expect(markdown).toContain("### Content");
+    expect(markdown).toContain("<output>");
+    expect(markdown).toContain("</output>");
     expect(markdown).toContain("The assistant response text");
-    expect(markdown).not.toContain("### Output");
+    expect(markdown).not.toContain("### Content");
   });
 
-  test("omits ### Content when detail has no matching assistant turns", async () => {
+  test("omits <output> tags when detail has no matching assistant turns", async () => {
     const uwf = await makeUwfStore(tmpDir);
 
     const workflowHash = await uwf.store.put(uwf.schemas.workflow, {
@@ -308,8 +309,9 @@ describe("cmdThreadRead ### Content section", () => {
 
     const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
 
+    expect(markdown).not.toContain("<output>");
+    expect(markdown).not.toContain("</output>");
     expect(markdown).not.toContain("### Content");
-    expect(markdown).not.toContain("### Output");
   });
 });
 
@@ -384,9 +386,9 @@ describe("cmdThreadStepDetails", () => {
   });
 });
 
-// ── cmdThreadRead: ### Prompt deduplication ───────────────────────────────────
+// ── cmdThreadRead: <prompt> deduplication ────────────────────────────────────
 
-describe("cmdThreadRead ### Prompt deduplication", () => {
+describe("cmdThreadRead <prompt> deduplication", () => {
   async function makeThreadWithRoles(uwf: UwfStore, roles: string[]): Promise<string> {
     const roleMap: Record<string, unknown> = {};
     for (const r of [...new Set(roles)]) {
@@ -434,36 +436,36 @@ describe("cmdThreadRead ### Prompt deduplication", () => {
     return stepHash;
   }
 
-  test("same consecutive role shows ### Prompt once", async () => {
+  test("same consecutive role shows <prompt> once", async () => {
     const uwf = await makeUwfStore(tmpDir);
     const headHash = await makeThreadWithRoles(uwf, ["writer", "writer"]);
     const threadId = "01JTEST0000000000000003" as ThreadId;
     await saveThreadsIndex(tmpDir, { [threadId]: headHash });
 
     const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
-    const count = (markdown.match(/### Prompt/g) ?? []).length;
+    const count = (markdown.match(/<prompt>/g) ?? []).length;
     expect(count).toBe(1);
   });
 
-  test("different consecutive roles each show ### Prompt", async () => {
+  test("different consecutive roles each show <prompt>", async () => {
     const uwf = await makeUwfStore(tmpDir);
     const headHash = await makeThreadWithRoles(uwf, ["planner", "coder"]);
     const threadId = "01JTEST0000000000000004" as ThreadId;
     await saveThreadsIndex(tmpDir, { [threadId]: headHash });
 
     const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
-    const count = (markdown.match(/### Prompt/g) ?? []).length;
+    const count = (markdown.match(/<prompt>/g) ?? []).length;
     expect(count).toBe(2);
   });
 
-  test("non-consecutive same role shows ### Prompt twice", async () => {
+  test("non-consecutive same role shows <prompt> twice", async () => {
     const uwf = await makeUwfStore(tmpDir);
     const headHash = await makeThreadWithRoles(uwf, ["roleA", "roleB", "roleA"]);
     const threadId = "01JTEST0000000000000005" as ThreadId;
     await saveThreadsIndex(tmpDir, { [threadId]: headHash });
 
     const markdown = await cmdThreadRead(tmpDir, threadId, THREAD_READ_DEFAULT_QUOTA, null, false);
-    const count = (markdown.match(/### Prompt/g) ?? []).length;
+    const count = (markdown.match(/<prompt>/g) ?? []).length;
     expect(count).toBe(2);
   });
 });

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

@@ -665,14 +665,14 @@ function formatStepPrompt(
 ): string {
   if (!roleDef || shownPromptRoles.has(role)) return "";
   shownPromptRoles.add(role);
-  return ["", "", "### Prompt", "", roleDef.goal].join("\n");
+  return ["", "", "<prompt>", roleDef.goal, "</prompt>"].join("\n");
 }
 
 function formatStepContent(uwf: UwfStore, item: OrderedStepItem): string {
   if (!item.payload.detail) return "";
   const content = extractLastAssistantContent(uwf, item.payload.detail);
   if (content === null) return "";
-  return ["", "", "### Content", "", content].join("\n");
+  return ["", "", "<output>", content, "</output>"].join("\n");
 }
 
 function formatStartSection(options: {

packages/workflow-agent-builtin/__tests__/loop.test.ts

@@ -19,7 +19,14 @@ mock.module("../src/tools/index.js", () => ({
   getBuiltinTools: () => [],
 }));
 
-import { executeTurnTools, runBuiltinLoop, shouldNudge } from "../src/loop.js";
+import {
+  executeTurnTools,
+  extractFinalText,
+  runBuiltinLoop,
+  shouldInjectDeadlineWarning,
+  shouldNudge,
+  shouldProcessToolCalls,
+} from "../src/loop.js";
 
 const fakeProvider = {} as any;
 const fakeToolCtx = {} as any;
@@ -154,3 +161,96 @@ describe("runBuiltinLoop integration", () => {
     expect(original.length).toBe(1);
   });
 });
+
+describe("shouldInjectDeadlineWarning", () => {
+  test("5.1 returns true when turn count reaches warning threshold and not yet warned", () => {
+    expect(shouldInjectDeadlineWarning(7, 10, false, false)).toBe(true);
+  });
+  test("5.2 returns false when already warned", () => {
+    expect(shouldInjectDeadlineWarning(7, 10, true, false)).toBe(false);
+  });
+  test("5.3 returns false when noTools is true", () => {
+    expect(shouldInjectDeadlineWarning(7, 10, false, true)).toBe(false);
+  });
+  test("5.4 returns false when turns remaining > DEADLINE_WARNING_TURNS", () => {
+    expect(shouldInjectDeadlineWarning(5, 10, false, false)).toBe(false);
+  });
+  test("5.5 returns true when exactly at warning threshold", () => {
+    expect(shouldInjectDeadlineWarning(7, 10, false, false)).toBe(true);
+  });
+  test("5.6 returns false when turns remaining is 0", () => {
+    expect(shouldInjectDeadlineWarning(10, 10, false, false)).toBe(false);
+  });
+});
+
+describe("shouldProcessToolCalls", () => {
+  test("6.1 returns true when toolCalls present and noTools=false", () => {
+    expect(shouldProcessToolCalls([{ id: "x", name: "read", arguments: "{}" }], false)).toBe(true);
+  });
+  test("6.2 returns false when toolCalls is null", () => {
+    expect(shouldProcessToolCalls(null, false)).toBe(false);
+  });
+  test("6.3 returns false when toolCalls is empty array", () => {
+    expect(shouldProcessToolCalls([], false)).toBe(false);
+  });
+  test("6.4 returns false when noTools=true", () => {
+    expect(shouldProcessToolCalls([{ id: "x", name: "read", arguments: "{}" }], true)).toBe(false);
+  });
+  test("6.5 returns true when multiple tool calls present", () => {
+    expect(
+      shouldProcessToolCalls(
+        [
+          { id: "x1", name: "read", arguments: "{}" },
+          { id: "x2", name: "write", arguments: "{}" },
+        ],
+        false,
+      ),
+    ).toBe(true);
+  });
+});
+
+describe("extractFinalText", () => {
+  test("7.1 returns last assistant message content", () => {
+    const messages = [
+      { role: "system" as const, content: "sys", tool_calls: null },
+      { role: "assistant" as const, content: "first", tool_calls: null },
+      { role: "assistant" as const, content: "last", tool_calls: null },
+    ];
+    expect(extractFinalText(messages)).toBe("last");
+  });
+  test("7.2 returns empty string when no assistant messages", () => {
+    expect(extractFinalText([{ role: "system" as const, content: "sys", tool_calls: null }])).toBe(
+      "",
+    );
+  });
+  test("7.3 skips assistant messages with null content", () => {
+    const messages = [
+      { role: "assistant" as const, content: "first", tool_calls: null },
+      {
+        role: "assistant" as const,
+        content: null,
+        tool_calls: [{ id: "x", name: "t", arguments: "{}" }],
+      },
+      { role: "assistant" as const, content: "second", tool_calls: null },
+    ];
+    expect(extractFinalText(messages)).toBe("second");
+  });
+  test("7.4 skips assistant messages with empty content", () => {
+    const messages = [
+      { role: "assistant" as const, content: "first", tool_calls: null },
+      { role: "assistant" as const, content: "", tool_calls: null },
+      { role: "user" as const, content: "nudge", tool_calls: null },
+    ];
+    expect(extractFinalText(messages)).toBe("first");
+  });
+  test("7.5 handles empty messages array", () => {
+    expect(extractFinalText([])).toBe("");
+  });
+  test("7.6 handles messages with only user and system roles", () => {
+    const messages = [
+      { role: "system" as const, content: "sys", tool_calls: null },
+      { role: "user" as const, content: "query", tool_calls: null },
+    ];
+    expect(extractFinalText(messages)).toBe("");
+  });
+});

packages/workflow-agent-builtin/src/loop.ts

@@ -1,7 +1,12 @@
 import type { ResolvedLlmProvider } from "@uncaged/workflow-agent-kit";
 import { createLogger } from "@uncaged/workflow-util";
 
-import { type ChatMessage, chatCompletionWithTools, type LlmToolCall } from "./llm/index.js";
+import {
+  type ChatMessage,
+  chatCompletionWithTools,
+  type LlmToolCall,
+  type OpenAiToolDefinition,
+} from "./llm/index.js";
 import { appendSessionTurn } from "./session.js";
 import {
   builtinToolsToOpenAi,
@@ -80,10 +85,184 @@ export type ShouldNudgeOptions = {
 const MAX_NUDGES = 3;
 const DEADLINE_WARNING_TURNS = 3;
 
+export function shouldInjectDeadlineWarning(
+  turn: number,
+  maxTurns: number,
+  alreadyWarned: boolean,
+  noTools: boolean,
+): boolean {
+  const turnsRemaining = maxTurns - turn;
+  return (
+    !noTools && !alreadyWarned && turnsRemaining > 0 && turnsRemaining <= DEADLINE_WARNING_TURNS
+  );
+}
+
+export function shouldProcessToolCalls(toolCalls: LlmToolCall[] | null, noTools: boolean): boolean {
+  return !noTools && toolCalls !== null && toolCalls.length > 0;
+}
+
+export function extractFinalText(messages: ChatMessage[]): string {
+  for (let i = messages.length - 1; i >= 0; i--) {
+    const msg = messages[i];
+    if (
+      msg !== undefined &&
+      msg.role === "assistant" &&
+      msg.content !== null &&
+      msg.content.trim() !== ""
+    ) {
+      return msg.content;
+    }
+  }
+  return "";
+}
+
+function injectDeadlineWarning(messages: ChatMessage[], turnsRemaining: number): void {
+  log("4NRXW6KT", `${turnsRemaining} turns remaining, injecting deadline warning`);
+  messages.push({
+    role: "user",
+    content:
+      `⚠️ You have ${turnsRemaining} turns remaining. ` +
+      "Wrap up your work and output the YAML frontmatter starting with `---`. " +
+      "If you cannot finish in time, output frontmatter with `status: failed` and describe what remains.",
+  });
+}
+
+type HandleTextOnlyTurnResult = {
+  shouldBreak: boolean;
+  finalText: string;
+  turnCount: number;
+  nudgeCount: number;
+  turnAdjustment: number;
+};
+
+async function handleTextOnlyTurn(
+  text: string,
+  messages: ChatMessage[],
+  storageRoot: string,
+  sessionId: string,
+  noTools: boolean,
+  turn: number,
+  maxTurns: number,
+  currentNudgeCount: number,
+): Promise<HandleTextOnlyTurnResult> {
+  await appendTurn(storageRoot, sessionId, {
+    role: "assistant",
+    content: text,
+    toolCalls: null,
+    reasoning: null,
+  });
+  const turnCount = 1;
+  let nudgeCount = currentNudgeCount;
+  let turnAdjustment = 0;
+
+  if (shouldNudge({ noTools, text, turn, maxTurns })) {
+    nudgeCount += 1;
+    log("7FXQM2KN", `text-only turn without frontmatter, nudge ${nudgeCount}/${MAX_NUDGES}`);
+    const nudge =
+      "You stopped calling tools but your response does not start with the required `---` YAML frontmatter. " +
+      "Either continue using tools to complete your work, or output your final response starting with `---`.";
+    messages.push({ role: "user", content: nudge });
+    // Nudge doesn't consume turn budget (up to MAX_NUDGES)
+    if (nudgeCount <= MAX_NUDGES) {
+      turnAdjustment = -1;
+    }
+    return { shouldBreak: false, finalText: "", turnCount, nudgeCount, turnAdjustment };
+  }
+
+  return { shouldBreak: true, finalText: text, turnCount, nudgeCount, turnAdjustment };
+}
+
+async function handleToolCallTurn(
+  content: string,
+  toolCalls: LlmToolCall[],
+  messages: ChatMessage[],
+  storageRoot: string,
+  sessionId: string,
+  toolCtx: ToolContext,
+): Promise<number> {
+  await appendTurn(storageRoot, sessionId, {
+    role: "assistant",
+    content,
+    toolCalls: mapToolCallsForPayload(toolCalls),
+    reasoning: null,
+  });
+  let turnCount = 1;
+
+  // Execute tools
+  turnCount += await executeTurnTools(toolCalls, toolCtx, messages, storageRoot, sessionId);
+
+  return turnCount;
+}
+
 export function shouldNudge({ noTools, text, turn, maxTurns }: ShouldNudgeOptions): boolean {
   return !noTools && !text.trimStart().startsWith("---") && turn < maxTurns - 1;
 }
 
+type ProcessLoopIterationResult = {
+  shouldBreak: boolean;
+  finalText: string;
+  turnCount: number;
+  nudgeCount: number;
+  turnAdjustment: number;
+};
+
+async function processLoopIteration(
+  options: RunBuiltinLoopOptions,
+  messages: ChatMessage[],
+  openAiTools: OpenAiToolDefinition[],
+  turn: number,
+  nudgeCount: number,
+): Promise<ProcessLoopIterationResult> {
+  const response = await chatCompletionWithTools(
+    options.provider,
+    messages,
+    openAiTools.length > 0 ? openAiTools : null,
+  );
+
+  // When noTools is set, ignore any tool_calls the LLM might still return
+  const effectiveToolCalls = options.noTools ? null : (response.toolCalls ?? null);
+
+  const assistantMessage: ChatMessage = {
+    role: "assistant",
+    content: response.content,
+    tool_calls: effectiveToolCalls,
+  };
+  messages.push(assistantMessage);
+
+  if (!shouldProcessToolCalls(effectiveToolCalls, options.noTools)) {
+    const text = response.content ?? "";
+    const result = await handleTextOnlyTurn(
+      text,
+      messages,
+      options.storageRoot,
+      options.sessionId,
+      options.noTools,
+      turn,
+      options.maxTurns,
+      nudgeCount,
+    );
+    return result;
+  }
+
+  // At this point, effectiveToolCalls is guaranteed to be non-null and non-empty
+  const turnCount = await handleToolCallTurn(
+    response.content ?? "",
+    effectiveToolCalls as LlmToolCall[],
+    messages,
+    options.storageRoot,
+    options.sessionId,
+    options.toolCtx,
+  );
+
+  return {
+    shouldBreak: false,
+    finalText: "",
+    turnCount,
+    nudgeCount,
+    turnAdjustment: 0,
+  };
+}
+
 /** Agent run loop: LLM ↔ tools until no tool_calls or maxTurns. */
 export async function runBuiltinLoop(
   options: RunBuiltinLoopOptions,
@@ -99,95 +278,25 @@ export async function runBuiltinLoop(
     log("8K2M4N7P", `builtin loop turn ${turn + 1}/${options.maxTurns}`);
 
     // Warn agent when approaching turn limit
-    const turnsRemaining = options.maxTurns - turn;
-    if (!options.noTools && !deadlineWarned && turnsRemaining <= DEADLINE_WARNING_TURNS) {
+    if (shouldInjectDeadlineWarning(turn, options.maxTurns, deadlineWarned, options.noTools)) {
       deadlineWarned = true;
-      log("4NRXW6KT", `${turnsRemaining} turns remaining, injecting deadline warning`);
-      messages.push({
-        role: "user",
-        content:
-          `⚠️ You have ${turnsRemaining} turns remaining. ` +
-          "Wrap up your work and output the YAML frontmatter starting with `---`. " +
-          "If you cannot finish in time, output frontmatter with `status: failed` and describe what remains.",
-      });
+      const turnsRemaining = options.maxTurns - turn;
+      injectDeadlineWarning(messages, turnsRemaining);
     }
 
-    const response = await chatCompletionWithTools(
-      options.provider,
-      messages,
-      openAiTools.length > 0 ? openAiTools : null,
-    );
+    const result = await processLoopIteration(options, messages, openAiTools, turn, nudgeCount);
+    turnCount += result.turnCount;
+    nudgeCount = result.nudgeCount;
+    turn += result.turnAdjustment;
 
-    // When noTools is set, ignore any tool_calls the LLM might still return
-    const effectiveToolCalls = options.noTools ? null : (response.toolCalls ?? null);
-
-    const assistantMessage: ChatMessage = {
-      role: "assistant",
-      content: response.content,
-      tool_calls: effectiveToolCalls,
-    };
-    messages.push(assistantMessage);
-
-    if (effectiveToolCalls === null || effectiveToolCalls.length === 0) {
-      const text = response.content ?? "";
-      await appendTurn(options.storageRoot, options.sessionId, {
-        role: "assistant",
-        content: text,
-        toolCalls: null,
-        reasoning: null,
-      });
-      turnCount += 1;
-
-      if (shouldNudge({ noTools: options.noTools, text, turn, maxTurns: options.maxTurns })) {
-        nudgeCount += 1;
-        log("7FXQM2KN", `text-only turn without frontmatter, nudge ${nudgeCount}/${MAX_NUDGES}`);
-        const nudge =
-          "You stopped calling tools but your response does not start with the required `---` YAML frontmatter. " +
-          "Either continue using tools to complete your work, or output your final response starting with `---`.";
-        messages.push({ role: "user", content: nudge });
-        // Nudge doesn't consume turn budget (up to MAX_NUDGES)
-        if (nudgeCount <= MAX_NUDGES) {
-          turn -= 1;
-        }
-        continue;
-      }
-
-      finalText = text;
+    if (result.shouldBreak) {
+      finalText = result.finalText;
       break;
     }
-
-    // Assistant turn with tool calls
-    await appendTurn(options.storageRoot, options.sessionId, {
-      role: "assistant",
-      content: response.content ?? "",
-      toolCalls: mapToolCallsForPayload(effectiveToolCalls),
-      reasoning: null,
-    });
-    turnCount += 1;
-
-    // Execute tools
-    turnCount += await executeTurnTools(
-      effectiveToolCalls,
-      options.toolCtx,
-      messages,
-      options.storageRoot,
-      options.sessionId,
-    );
   }
 
-  if (finalText === "" && messages.length > 0) {
-    for (let i = messages.length - 1; i >= 0; i--) {
-      const msg = messages[i];
-      if (
-        msg !== undefined &&
-        msg.role === "assistant" &&
-        msg.content !== null &&
-        msg.content.trim() !== ""
-      ) {
-        finalText = msg.content;
-        break;
-      }
-    }
+  if (finalText === "") {
+    finalText = extractFinalText(messages);
   }
 
   return { finalText, messages, turnCount };