diff --git a/packages/cli-workflow/src/__tests__/include-tag.test.ts b/packages/cli-workflow/src/__tests__/include-tag.test.ts
new file mode 100644
index 0000000..8c738ed
--- /dev/null
+++ b/packages/cli-workflow/src/__tests__/include-tag.test.ts
@@ -0,0 +1,60 @@
+import { mkdir, mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { afterEach, beforeEach, describe, expect, test } from "vitest";
+import { parse } from "yaml";
+import { createIncludeTag } from "../include.js";
+
+let tmpDir: string;
+
+beforeEach(async () => {
+  tmpDir = await mkdtemp(join(tmpdir(), "include-tag-test-"));
+});
+
+afterEach(async () => {
+  await rm(tmpDir, { recursive: true, force: true });
+});
+
+describe("!include tag", () => {
+  test("includes .md file as string", async () => {
+    await writeFile(join(tmpDir, "prompt.md"), "You are an analyst.");
+    const yaml = "system: !include prompt.md";
+    const result = parse(yaml, { customTags: [createIncludeTag(tmpDir)] });
+    expect(result.system).toBe("You are an analyst.");
+  });
+
+  test("includes .json file as parsed object", async () => {
+    await writeFile(join(tmpDir, "schema.json"), '{"type":"object","properties":{}}');
+    const yaml = "outputSchema: !include schema.json";
+    const result = parse(yaml, { customTags: [createIncludeTag(tmpDir)] });
+    expect(result.outputSchema).toEqual({ type: "object", properties: {} });
+  });
+
+  test("includes .yaml file as parsed object", async () => {
+    await writeFile(join(tmpDir, "config.yaml"), "key: value\nlist:\n  - a\n  - b");
+    const yaml = "config: !include config.yaml";
+    const result = parse(yaml, { customTags: [createIncludeTag(tmpDir)] });
+    expect(result.config).toEqual({ key: "value", list: ["a", "b"] });
+  });
+
+  test("resolves relative subdirectory paths", async () => {
+    const subdir = join(tmpDir, "roles");
+    await mkdir(subdir, { recursive: true });
+    await writeFile(join(subdir, "analyst.md"), "Analyze data.");
+    const yaml = "system: !include roles/analyst.md";
+    const result = parse(yaml, { customTags: [createIncludeTag(tmpDir)] });
+    expect(result.system).toBe("Analyze data.");
+  });
+
+  test("throws on missing file", () => {
+    const yaml = "system: !include nonexistent.md";
+    expect(() => parse(yaml, { customTags: [createIncludeTag(tmpDir)] })).toThrow();
+  });
+
+  test("includes .txt file as string", async () => {
+    await writeFile(join(tmpDir, "note.txt"), "Hello world");
+    const yaml = "note: !include note.txt";
+    const result = parse(yaml, { customTags: [createIncludeTag(tmpDir)] });
+    expect(result.note).toBe("Hello world");
+  });
+});
diff --git a/packages/cli-workflow/src/__tests__/workflow-resolution.test.ts b/packages/cli-workflow/src/__tests__/workflow-resolution.test.ts
index 9c38ae0..d8d8106 100644
--- a/packages/cli-workflow/src/__tests__/workflow-resolution.test.ts
+++ b/packages/cli-workflow/src/__tests__/workflow-resolution.test.ts
@@ -257,6 +257,43 @@ describe("Strategy 3: Local Discovery", () => {
 
     expect(result.workflow).toMatch(/^[0-9A-HJKMNP-TV-Z]{13}$/);
   });
+
+  test("should find workflow in folder-based layout (name/index.yaml)", async () => {
+    await makeUwfStore(storageRoot);
+    const workflowDir = join(projectRoot, ".workflow", "solve-issue");
+    await mkdir(workflowDir, { recursive: true });
+    await writeFile(join(workflowDir, "index.yaml"), await createWorkflowYaml("solve-issue"));
+
+    const result = await cmdThreadStart(storageRoot, "solve-issue", "prompt", projectRoot);
+
+    expect(result.workflow).toMatch(/^[0-9A-HJKMNP-TV-Z]{13}$/);
+    const uwf = await makeUwfStore(storageRoot);
+    const node = uwf.store.get(result.workflow);
+    expect(node).not.toBeNull();
+    if (node !== null) {
+      expect((node.payload as WorkflowPayload).name).toBe("solve-issue");
+    }
+  });
+
+  test("should prefer flat file over folder-based layout", async () => {
+    await makeUwfStore(storageRoot);
+    const workflowDir = join(projectRoot, ".workflow");
+    await mkdir(workflowDir, { recursive: true });
+    await writeFile(join(workflowDir, "solve-issue.yaml"), await createWorkflowYaml("solve-issue", "flat"));
+
+    const folderDir = join(workflowDir, "solve-issue");
+    await mkdir(folderDir, { recursive: true });
+    await writeFile(join(folderDir, "index.yaml"), await createWorkflowYaml("solve-issue", "folder"));
+
+    const result = await cmdThreadStart(storageRoot, "solve-issue", "prompt", projectRoot);
+
+    const uwf = await makeUwfStore(storageRoot);
+    const node = uwf.store.get(result.workflow);
+    expect(node).not.toBeNull();
+    if (node !== null) {
+      expect((node.payload as WorkflowPayload).description).toBe("Test workflow (flat)");
+    }
+  });
 });
 
 // ── Strategy 4: Global Registry Fallback ──────────────────────────────────────
diff --git a/packages/cli-workflow/src/commands/thread.ts b/packages/cli-workflow/src/commands/thread.ts
index 67dc39e..16a4c8c 100644
--- a/packages/cli-workflow/src/commands/thread.ts
+++ b/packages/cli-workflow/src/commands/thread.ts
@@ -27,6 +27,7 @@ import type { AdapterOutput } from "@uncaged/workflow-util-agent";
 import { getEnvPath, loadWorkflowConfig } from "@uncaged/workflow-util-agent";
 import { config as loadDotenv } from "dotenv";
 import { parse } from "yaml";
+import { createIncludeTag } from "../include.js";
 import { createMarker, deleteMarker, isThreadRunning } from "../background/index.js";
 import { evaluate } from "../moderator/index.js";
 import {
@@ -118,6 +119,10 @@ async function findWorkflowInDir(dir: string, name: string): Promise<string | nu
       return result;
     }
   }
+  for (const indexName of ["index.yaml", "index.yml"]) {
+    const candidate = resolvePath(dir, ".workflow", name, indexName);
+    try { await access(candidate); return candidate; } catch { /* not found */ }
+  }
 
   // Check .workflows/ directory as fallback (legacy)
   for (const ext of [".yaml", ".yml"]) {
@@ -126,6 +131,10 @@ async function findWorkflowInDir(dir: string, name: string): Promise<string | nu
       return result;
     }
   }
+  for (const indexName of ["index.yaml", "index.yml"]) {
+    const candidate = resolvePath(dir, ".workflows", name, indexName);
+    try { await access(candidate); return candidate; } catch { /* not found */ }
+  }
 
   return null;
 }
@@ -172,7 +181,7 @@ async function materializeLocalWorkflow(uwf: UwfStore, filePath: string): Promis
 
   let raw: unknown;
   try {
-    raw = parse(text) as unknown;
+    raw = parse(text, { customTags: [createIncludeTag(dirname(filePath))] }) as unknown;
   } catch (e) {
     fail(`invalid YAML in ${filePath}: ${e instanceof Error ? e.message : String(e)}`);
   }
diff --git a/packages/cli-workflow/src/commands/workflow.ts b/packages/cli-workflow/src/commands/workflow.ts
index 791fd09..45be273 100644
--- a/packages/cli-workflow/src/commands/workflow.ts
+++ b/packages/cli-workflow/src/commands/workflow.ts
@@ -1,9 +1,11 @@
 import { readFile } from "node:fs/promises";
+import { dirname, resolve as resolvePath } from "node:path";
 
 import type { JSONSchema } from "@uncaged/json-cas";
 import { putSchema, validate } from "@uncaged/json-cas";
 import type { CasRef, RoleDefinition, Target, WorkflowPayload } from "@uncaged/workflow-protocol";
 import { parse } from "yaml";
+import { createIncludeTag } from "../include.js";
 
 import {
   createUwfStore,
@@ -123,7 +125,7 @@ export async function cmdWorkflowAdd(
 
   let raw: unknown;
   try {
-    raw = parse(text) as unknown;
+    raw = parse(text, { customTags: [createIncludeTag(dirname(resolvePath(filePath)))] }) as unknown;
   } catch (e) {
     fail(`invalid YAML: ${e instanceof Error ? e.message : String(e)}`);
   }
diff --git a/packages/cli-workflow/src/include.ts b/packages/cli-workflow/src/include.ts
new file mode 100644
index 0000000..4e4014f
--- /dev/null
+++ b/packages/cli-workflow/src/include.ts
@@ -0,0 +1,25 @@
+import { readFileSync } from "node:fs";
+import { extname, resolve } from "node:path";
+import { parse as parseYaml } from "yaml";
+
+/**
+ * Create a YAML customTags entry for !include that resolves file paths
+ * relative to the given base directory.
+ */
+export function createIncludeTag(baseDir: string) {
+  return {
+    tag: "!include",
+    resolve(str: string) {
+      const filePath = resolve(baseDir, str);
+      const content = readFileSync(filePath, "utf8");
+      const ext = extname(filePath).toLowerCase();
+      if (ext === ".json") {
+        return JSON.parse(content);
+      }
+      if (ext === ".yaml" || ext === ".yml") {
+        return parseYaml(content);
+      }
+      return content;
+    },
+  };
+}
diff --git a/packages/cli-workflow/src/store.ts b/packages/cli-workflow/src/store.ts
index be4dec2..4abb41b 100644
--- a/packages/cli-workflow/src/store.ts
+++ b/packages/cli-workflow/src/store.ts
@@ -1,4 +1,5 @@
-import { appendFile, mkdir, readdir, readFile, writeFile } from "node:fs/promises";
+import { access, appendFile, mkdir, readdir, readFile, writeFile } from "node:fs/promises";
+import type { Dirent } from "node:fs";
 import { homedir } from "node:os";
 import { join } from "node:path";
 
@@ -27,9 +28,9 @@ export async function discoverProjectWorkflows(
   projectRoot: string,
 ): Promise<ProjectWorkflowEntry[]> {
   const dir = join(projectRoot, ".workflows");
-  let entries: string[];
+  let dirents: Dirent[];
   try {
-    entries = await readdir(dir);
+    dirents = await readdir(dir, { withFileTypes: true });
   } catch (e) {
     const err = e as NodeJS.ErrnoException;
     if (err.code === "ENOENT" || err.code === "ENOTDIR") {
@@ -39,12 +40,22 @@ export async function discoverProjectWorkflows(
   }
 
   const result: ProjectWorkflowEntry[] = [];
-  for (const entry of entries) {
-    if (!entry.endsWith(".yaml") && !entry.endsWith(".yml")) {
-      continue;
+  for (const entry of dirents) {
+    if (entry.isFile() && (entry.name.endsWith(".yaml") || entry.name.endsWith(".yml"))) {
+      const stem = entry.name.endsWith(".yaml") ? entry.name.slice(0, -5) : entry.name.slice(0, -4);
+      result.push({ name: stem, filePath: join(dir, entry.name) });
+    } else if (entry.isDirectory()) {
+      for (const indexName of ["index.yaml", "index.yml"]) {
+        const indexPath = join(dir, entry.name, indexName);
+        try {
+          await access(indexPath);
+          result.push({ name: entry.name, filePath: indexPath });
+          break;
+        } catch {
+          // not found, try next
+        }
+      }
     }
-    const stem = entry.endsWith(".yaml") ? entry.slice(0, -5) : entry.slice(0, -4);
-    result.push({ name: stem, filePath: join(dir, entry) });
   }
   return result;
 }
diff --git a/packages/cli-workflow/src/validate.ts b/packages/cli-workflow/src/validate.ts
index bf94022..76683c6 100644
--- a/packages/cli-workflow/src/validate.ts
+++ b/packages/cli-workflow/src/validate.ts
@@ -1,4 +1,4 @@
-import { basename } from "node:path";
+import { basename, dirname } from "node:path";
 import type { CasRef, WorkflowPayload } from "@uncaged/workflow-protocol";
 
 const CAS_REF_PATTERN = /^[0-9A-HJKMNP-TV-Z]{13}$/;
@@ -68,9 +68,11 @@ function isGraph(value: unknown): boolean {
  */
 export function workflowNameFromPath(filePath: string): string {
   const base = basename(filePath);
-  if (base.endsWith(".yaml")) return base.slice(0, -5);
-  if (base.endsWith(".yml")) return base.slice(0, -4);
-  return base;
+  const stem = base.endsWith(".yaml") ? base.slice(0, -5) : base.endsWith(".yml") ? base.slice(0, -4) : base;
+  if (stem === "index") {
+    return basename(dirname(filePath));
+  }
+  return stem;
 }
 
 /**