diff --git a/packages/markdown-reader/README.md b/packages/markdown-reader/README.md
index eacd7d0e..d81bc357 100644
--- a/packages/markdown-reader/README.md
+++ b/packages/markdown-reader/README.md
@@ -17,8 +17,8 @@ const { markdown, section } = await readSection({ file, section: "2.1" });
 
 ## MCP tool names
 
-- `markdown_reader__read`
-- `markdown_reader__read_section`
+- `read`
+- `read_section`
 
 ## Standalone server invocation
 
diff --git a/packages/markdown-reader/scripts/smoke-test.ts b/packages/markdown-reader/scripts/smoke-test.ts
index 87edc103..876dcae1 100644
--- a/packages/markdown-reader/scripts/smoke-test.ts
+++ b/packages/markdown-reader/scripts/smoke-test.ts
@@ -21,7 +21,7 @@ async function run(): Promise<void> {
     const { tools } = await client.listTools();
     const names = tools.map((t) => t.name).sort();
 
-    const expected = ["markdown_reader__read", "markdown_reader__read_section"];
+    const expected = ["read", "read_section"];
     const namesMatch =
       names.length === expected.length && expected.every((n, i) => names[i] === n);
 
@@ -31,7 +31,7 @@ async function run(): Promise<void> {
     console.log(`✓ tools/list — ${names.join(", ")}`);
 
     const result = await client.callTool({
-      name: "markdown_reader__read",
+      name: "read",
       arguments: { file: "docs/plans/markdown-reader.md" },
     });
 
@@ -39,7 +39,7 @@ async function run(): Promise<void> {
     if (text?.type !== "text" || !text.text.includes("2.1")) {
       throw new Error(`tools/call response missing TOC: ${JSON.stringify(result)}`);
     }
-    console.log("✓ tools/call markdown_reader__read — TOC contains 2.1");
+    console.log("✓ tools/call read — TOC contains 2.1");
   } finally {
     await client.close();
   }
diff --git a/packages/markdown-reader/src/mcp/run.test.ts b/packages/markdown-reader/src/mcp/run.test.ts
index 8c569dea..c6ed4ae9 100644
--- a/packages/markdown-reader/src/mcp/run.test.ts
+++ b/packages/markdown-reader/src/mcp/run.test.ts
@@ -28,7 +28,8 @@ describe("runMarkdownReaderMcp", () => {
     expect(runMCPMock).toHaveBeenCalledTimes(1);
     expect(runMCPMock).toHaveBeenCalledWith(markdownGroupMock, {
       name: "markdown-reader",
-      version: "0.0.1"
+      version: "0.0.1",
+      omitRootToolNamePrefix: true
     });
   });
 
diff --git a/packages/markdown-reader/src/mcp/run.ts b/packages/markdown-reader/src/mcp/run.ts
index a3af0592..7bc81886 100644
--- a/packages/markdown-reader/src/mcp/run.ts
+++ b/packages/markdown-reader/src/mcp/run.ts
@@ -5,6 +5,7 @@ import { markdownGroup } from "./group.js";
 export async function runMarkdownReaderMcp(): Promise<void> {
   await runMCP(markdownGroup, {
     name: "markdown-reader",
-    version: packageJson.version
+    version: packageJson.version,
+    omitRootToolNamePrefix: true
   });
 }
diff --git a/packages/markdown-reader/src/mcp/tools.test.ts b/packages/markdown-reader/src/mcp/tools.test.ts
index acfc50db..e0bd88e7 100644
--- a/packages/markdown-reader/src/mcp/tools.test.ts
+++ b/packages/markdown-reader/src/mcp/tools.test.ts
@@ -4,17 +4,18 @@ import { McpClient, createSdkTestPair } from "tiny-mcp-client";
 import { markdownGroup } from "./group.js";
 
 const EXPECTED_TOOL_NAMES = [
-  "markdown_reader__read",
-  "markdown_reader__read_section",
-  "markdown_reader__approvals__list",
-  "markdown_reader__approvals__show"
+  "read",
+  "read_section",
+  "approvals__list",
+  "approvals__show"
 ];
 const FIXTURE_PATH = "packages/markdown-reader/src/testing/fixtures/with-frontmatter.md";
 
 async function createClientPair() {
   const server = createMCPServer(markdownGroup, {
     name: "markdown-reader",
-    version: "0.0.1"
+    version: "0.0.1",
+    omitRootToolNamePrefix: true
   });
 
   return createSdkTestPair(server, () =>
@@ -37,7 +38,7 @@ describe("markdown-reader MCP tools", () => {
       expect(tools.tools.map((tool) => tool.name)).toEqual(EXPECTED_TOOL_NAMES);
 
       const result = await client.callTool({
-        name: "markdown_reader__read",
+        name: "read",
         arguments: {
           file: FIXTURE_PATH
         }
diff --git a/packages/markdown-reader/src/testing/fixtures/markdown-reader-plan.md b/packages/markdown-reader/src/testing/fixtures/markdown-reader-plan.md
index f27422d6..4da52840 100644
--- a/packages/markdown-reader/src/testing/fixtures/markdown-reader-plan.md
+++ b/packages/markdown-reader/src/testing/fixtures/markdown-reader-plan.md
@@ -152,10 +152,10 @@ Agent-side configuration example (Claude Code `~/.claude.json` or `.mcp.json`):
 }
 ```
 
-MCP tool names exposed by this server (derived by toolcraft from `group.name + command.name`):
+MCP tool names exposed by this server (derived by toolcraft from command names with the root prefix omitted):
 
-- `markdown_reader__read` — params `{ file, depth? }`.
-- `markdown_reader__read_section` — params `{ file, section, includeChildren? }`.
+- `read` — params `{ file, depth? }`.
+- `read_section` — params `{ file, section, includeChildren? }`.
 
 ### Error cases users see
 
@@ -184,7 +184,7 @@ const { markdown, section } = await readSection({ file, section: "2.1" });
   - `src/core/read-markdown.ts`, `src/core/read-section.ts` — orchestrators used by both the SDK and MCP tool handlers. File I/O goes through an injectable `fs` so tests use `memfs`.
   - `src/mcp/tools.ts` — two `defineCommand` entries (`scope: ["mcp"]`) that wrap the orchestrators as MCP tools.
   - `src/mcp/group.ts` — `markdownGroup = defineGroup({ name: "markdown-reader", scope: ["mcp"], children: [readTool, readSectionTool] })`.
-  - `src/mcp/run.ts` — `runMarkdownReaderMcp()` → `runMCP(markdownGroup, { name: "markdown-reader", version })` from `toolcraft/mcp`. Mirrors [packages/terminal-pilot-mcp/src/index.ts](packages/terminal-pilot-mcp/src/index.ts).
+  - `src/mcp/run.ts` — `runMarkdownReaderMcp()` → `runMCP(markdownGroup, { name: "markdown-reader", version, omitRootToolNamePrefix: true })` from `toolcraft/mcp`. Mirrors [packages/terminal-pilot-mcp/src/index.ts](packages/terminal-pilot-mcp/src/index.ts).
   - `src/testing/fixtures/*.md` — static sample docs used by unit tests.
 - CLI wiring lives in [src/cli/commands/plan.ts](src/cli/commands/plan.ts). Three new commander subcommands under the existing `plan` group:
   - `plan markdown-read` — imports `readMarkdown` from `@poe-code/markdown-reader`, prints via the existing `writeOutput` + `resolveOutputOption` helpers in that file (`terminal` / `md` / `json`).
@@ -334,7 +334,7 @@ export const markdownGroup = defineGroup({
 
 // src/mcp/run.ts
 export async function runMarkdownReaderMcp(): Promise<void> {
-  await runMCP(markdownGroup, { name: "markdown-reader", version: packageJson.version });
+  await runMCP(markdownGroup, { name: "markdown-reader", version: packageJson.version, omitRootToolNamePrefix: true });
 }
 ```
 
@@ -384,7 +384,7 @@ All tests are vitest, colocated, run under the package's `npm test` script that
   - `npm run dev -- plan markdown-read-section docs/plans/markdown-reader.md "Command: plan markdown-read"` returns the same body.
   - `npm run dev -- plan markdown-read missing.md` exits non-zero with a `UserError`-style message, not a stack trace.
   - `npm run dev -- plan --help` shows the three new subcommands.
-  - `npm run dev -- plan markdown-reader-mcp` passes an MCP handshake smoke test: an `initialize` request over stdio returns a capabilities payload, a `tools/list` request returns exactly `markdown_reader__read` and `markdown_reader__read_section`, and a `tools/call` on `markdown_reader__read` with `{ file: "docs/plans/markdown-reader.md" }` returns a TOC. Pattern to copy: [packages/terminal-pilot-mcp/scripts/smoke-test.ts](packages/terminal-pilot-mcp/scripts/smoke-test.ts).
+  - `npm run dev -- plan markdown-reader-mcp` passes an MCP handshake smoke test: an `initialize` request over stdio returns a capabilities payload, a `tools/list` request returns exactly `read` and `read_section`, and a `tools/call` on `read` with `{ file: "docs/plans/markdown-reader.md" }` returns a TOC. Pattern to copy: [packages/terminal-pilot-mcp/scripts/smoke-test.ts](packages/terminal-pilot-mcp/scripts/smoke-test.ts).
   - `npm run screenshot-poe-code -- plan markdown-read docs/plans/markdown-reader.md` — visually validate the terminal renderer once, attach to PR.
 - **Verification commands** (exact): `npm run build`, `npm test`, `npm run lint`, `npm run dev -- plan markdown-read docs/plans/markdown-reader.md`, `npm run dev -- plan markdown-read-section docs/plans/markdown-reader.md 2.1`, `npm run dev -- plan markdown-read-section docs/plans/markdown-reader.md 2.1 --no-include-children`, MCP smoke script against `npm run dev -- plan markdown-reader-mcp`.
 - **Fixtures / setup**: none external. All fixtures are in-repo markdown strings under `src/testing/fixtures/`.
diff --git a/packages/terminal-pilot-mcp/src/index.ts b/packages/terminal-pilot-mcp/src/index.ts
index a9fabe96..afa39e88 100644
--- a/packages/terminal-pilot-mcp/src/index.ts
+++ b/packages/terminal-pilot-mcp/src/index.ts
@@ -4,6 +4,7 @@ import { terminalPilotGroup } from "terminal-pilot/commands";
 export async function main(): Promise<void> {
   await runMCP(terminalPilotGroup, {
     name: "terminal-pilot",
-    version: "0.0.1"
+    version: "0.0.1",
+    omitRootToolNamePrefix: true
   });
 }
diff --git a/packages/terminal-pilot-mcp/src/mcp-server.test.ts b/packages/terminal-pilot-mcp/src/mcp-server.test.ts
index 850d0bd3..8fc9ea32 100644
--- a/packages/terminal-pilot-mcp/src/mcp-server.test.ts
+++ b/packages/terminal-pilot-mcp/src/mcp-server.test.ts
@@ -28,7 +28,8 @@ describe("terminal-pilot-mcp entry point", () => {
     expect(runMCPMock).toHaveBeenCalledTimes(1);
     expect(runMCPMock).toHaveBeenCalledWith(terminalPilotGroupMock, {
       name: "terminal-pilot",
-      version: "0.0.1"
+      version: "0.0.1",
+      omitRootToolNamePrefix: true
     });
   });
 
diff --git a/packages/terminal-pilot-mcp/src/mcp-tools.test.ts b/packages/terminal-pilot-mcp/src/mcp-tools.test.ts
index 5a6d9ffd..15e2a1b4 100644
--- a/packages/terminal-pilot-mcp/src/mcp-tools.test.ts
+++ b/packages/terminal-pilot-mcp/src/mcp-tools.test.ts
@@ -5,21 +5,21 @@ import { terminalPilotGroup } from "terminal-pilot/commands";
 import type { TerminalPilotRuntime } from "terminal-pilot/commands";
 
 const EXPECTED_TOOL_NAMES = [
-  "terminal_pilot__create_session",
-  "terminal_pilot__fill",
-  "terminal_pilot__type",
-  "terminal_pilot__press_key",
-  "terminal_pilot__send_signal",
-  "terminal_pilot__wait_for",
-  "terminal_pilot__wait_for_exit",
-  "terminal_pilot__read_screen",
-  "terminal_pilot__read_history",
-  "terminal_pilot__resize",
-  "terminal_pilot__close_session",
-  "terminal_pilot__get_session",
-  "terminal_pilot__list_sessions",
-  "terminal_pilot__approvals__list",
-  "terminal_pilot__approvals__show"
+  "create_session",
+  "fill",
+  "type",
+  "press_key",
+  "send_signal",
+  "wait_for",
+  "wait_for_exit",
+  "read_screen",
+  "read_history",
+  "resize",
+  "close_session",
+  "get_session",
+  "list_sessions",
+  "approvals__list",
+  "approvals__show"
 ];
 
 const runtime: TerminalPilotRuntime = {
@@ -102,6 +102,7 @@ describe("terminal-pilot-mcp tool surface", () => {
     const server = createMCPServer(terminalPilotGroup, {
       name: "terminal-pilot",
       version: "0.0.1",
+      omitRootToolNamePrefix: true,
       services: {
         terminalPilotRuntime: runtime
       }
diff --git a/packages/toolcraft-openapi/src/define-client.test.ts b/packages/toolcraft-openapi/src/define-client.test.ts
index 67e2ad4d..993a8367 100644
--- a/packages/toolcraft-openapi/src/define-client.test.ts
+++ b/packages/toolcraft-openapi/src/define-client.test.ts
@@ -123,6 +123,7 @@ describe("defineClient", () => {
     const server = createMCPServer(client.root, {
       name: client.name,
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client: mcpClient, cleanup } = await createClientPair(server);
 
@@ -130,9 +131,9 @@ describe("defineClient", () => {
       const result = await mcpClient.listTools();
 
       expect(result.tools.map((tool) => tool.name)).toEqual([
-        "internal_agent__bots__list",
-        "internal_agent__approvals__list",
-        "internal_agent__approvals__show",
+        "bots__list",
+        "approvals__list",
+        "approvals__show",
       ]);
     } finally {
       await cleanup();
@@ -178,13 +179,14 @@ describe("defineClient", () => {
     const server = createMCPServer(client.root, {
       name: client.name,
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
       services: client.services,
     });
     const { client: mcpClient, cleanup } = await createClientPair(server);
 
     try {
       const tools = await mcpClient.listTools();
-      const tool = tools.tools.find((candidate) => candidate.name === "internal_agent__bots__view");
+      const tool = tools.tools.find((candidate) => candidate.name === "bots__view");
 
       expect(tool).toMatchObject({
         inputSchema: {
@@ -202,7 +204,7 @@ describe("defineClient", () => {
       });
 
       const result = await mcpClient.callTool({
-        name: "internal_agent__bots__view",
+        name: "bots__view",
         arguments: {
           bot_handle: "my-bot",
           limit: 2,
diff --git a/packages/toolcraft-openapi/src/runtime.test.ts b/packages/toolcraft-openapi/src/runtime.test.ts
index 59b0ae37..a0d4d2c7 100644
--- a/packages/toolcraft-openapi/src/runtime.test.ts
+++ b/packages/toolcraft-openapi/src/runtime.test.ts
@@ -447,7 +447,8 @@ describe("commandsFromSpec", () => {
     });
     const server = createMCPServer(client.root, {
       name: client.name,
-      version: "1.0.0"
+      version: "1.0.0",
+      omitRootToolNamePrefix: true
     });
     const { client: mcpClient, cleanup } = await createClientPair(server);
 
@@ -470,7 +471,7 @@ describe("commandsFromSpec", () => {
 
       expect(tools.tools).toContainEqual(
         expect.objectContaining({
-          name: "internal_agent__bots__set_official_bot",
+          name: "bots__set_official_bot",
           inputSchema: expect.objectContaining({
             required: ["bot_handle", "official"],
             properties: expect.objectContaining({
@@ -495,7 +496,8 @@ describe("commandsFromSpec", () => {
     });
     const server = createMCPServer(client.root, {
       name: client.name,
-      version: "1.0.0"
+      version: "1.0.0",
+      omitRootToolNamePrefix: true
     });
     const { client: mcpClient, cleanup } = await createClientPair(server);
 
@@ -504,7 +506,7 @@ describe("commandsFromSpec", () => {
 
       expect(tools.tools).toContainEqual(
         expect.objectContaining({
-          name: "internal_agent__campaigns__update_campaign",
+          name: "campaigns__update_campaign",
           inputSchema: expect.objectContaining({
             additionalProperties: false,
             required: ["campaign_id", "name"]
diff --git a/packages/toolcraft/README.md b/packages/toolcraft/README.md
index cac98876..94a0b525 100644
--- a/packages/toolcraft/README.md
+++ b/packages/toolcraft/README.md
@@ -459,6 +459,7 @@ If you have an existing MCP server you want to keep running, use the MCP proxy:
 - `services?` / `humanInLoop?` / `apiVersion?`
 - `projectRoot?: string` — root used for MCP proxy cache files (`.toolcraft/mcp/*.json`).
 - `tools?: string[]` — allowlist of MCP tool names or group prefixes. Tool names are `__`-joined snake_case path segments (`root__bot__create`); a prefix like `root__bot` includes every descendant tool.
+- `omitRootToolNamePrefix?: boolean` — defaults to `false`. Set to `true` to omit the root group name from single-root MCP tool names (`bot__create`).
 - `casing?: "snake" | "camel"` — affects MCP **input-schema property names** only. Tool names always stay `__`-joined snake_case.
 
 ### `HumanInLoopRuntimeOptions`
diff --git a/packages/toolcraft/src/entrypoints-mcp-proxy.test.ts b/packages/toolcraft/src/entrypoints-mcp-proxy.test.ts
index 673f08de..5eee02cb 100644
--- a/packages/toolcraft/src/entrypoints-mcp-proxy.test.ts
+++ b/packages/toolcraft/src/entrypoints-mcp-proxy.test.ts
@@ -267,13 +267,14 @@ describe("MCP proxy entrypoints", () => {
     await createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
 
     expect(serverState.created).toHaveLength(1);
     expect(serverState.created[0]?.tools).toEqual([
-      "root__github__create_issue",
-      "root__approvals__list",
-      "root__approvals__show",
+      "github__create_issue",
+      "approvals__list",
+      "approvals__show",
     ]);
   });
 
diff --git a/packages/toolcraft/src/human-in-loop/approvals-commands.test.ts b/packages/toolcraft/src/human-in-loop/approvals-commands.test.ts
index e54cec28..4f2a7226 100644
--- a/packages/toolcraft/src/human-in-loop/approvals-commands.test.ts
+++ b/packages/toolcraft/src/human-in-loop/approvals-commands.test.ts
@@ -303,6 +303,7 @@ describe("approvals built-in commands", () => {
       {
         name: "toolcraft-test",
         version: "1.0.0",
+        omitRootToolNamePrefix: true,
         humanInLoop: {
           taskList,
         },
@@ -321,9 +322,9 @@ describe("approvals built-in commands", () => {
       const { tools } = await client.listTools();
       const toolNames = tools.map((tool) => tool.name);
 
-      expect(toolNames).toContain("root__approvals__list");
-      expect(toolNames).toContain("root__approvals__show");
-      expect(toolNames).not.toContain("root__approvals__run");
+      expect(toolNames).toContain("approvals__list");
+      expect(toolNames).toContain("approvals__show");
+      expect(toolNames).not.toContain("approvals__run");
     } finally {
       await cleanup();
     }
diff --git a/packages/toolcraft/src/human-in-loop/mcp-runtime.integration.test.ts b/packages/toolcraft/src/human-in-loop/mcp-runtime.integration.test.ts
index a0a3c64e..65e2644a 100644
--- a/packages/toolcraft/src/human-in-loop/mcp-runtime.integration.test.ts
+++ b/packages/toolcraft/src/human-in-loop/mcp-runtime.integration.test.ts
@@ -97,6 +97,7 @@ describe("human-in-loop MCP runtime", () => {
     const server = createMCPServer(createRoot("sync", handler), {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
       humanInLoop: {
         provider,
       },
@@ -105,7 +106,7 @@ describe("human-in-loop MCP runtime", () => {
 
     try {
       const result = await client.callTool({
-        name: "root__deploy__prod",
+        name: "deploy__prod",
         arguments: {
           target: "prod",
         },
@@ -137,6 +138,7 @@ describe("human-in-loop MCP runtime", () => {
     const server = createMCPServer(createRoot("sync", handler), {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
       humanInLoop: {
         provider,
       },
@@ -145,7 +147,7 @@ describe("human-in-loop MCP runtime", () => {
 
     try {
       const result = await client.callTool({
-        name: "root__deploy__prod",
+        name: "deploy__prod",
         arguments: {
           target: "prod",
         },
@@ -185,6 +187,7 @@ describe("human-in-loop MCP runtime", () => {
     const server = createMCPServer(createRoot("async", handler), {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
       humanInLoop: {
         provider,
         taskList,
@@ -198,7 +201,7 @@ describe("human-in-loop MCP runtime", () => {
 
     try {
       const result = await client.callTool({
-        name: "root__deploy__prod",
+        name: "deploy__prod",
         arguments: {
           target: "prod",
         },
@@ -228,7 +231,7 @@ describe("human-in-loop MCP runtime", () => {
       });
 
       const approvalResult = await client.callTool({
-        name: "root__approvals__show",
+        name: "approvals__show",
         arguments: {
           approval_id: pending.approvalId,
         },
diff --git a/packages/toolcraft/src/mcp-proxy-integration.test.ts b/packages/toolcraft/src/mcp-proxy-integration.test.ts
index 3e17082c..f891201a 100644
--- a/packages/toolcraft/src/mcp-proxy-integration.test.ts
+++ b/packages/toolcraft/src/mcp-proxy-integration.test.ts
@@ -903,6 +903,7 @@ describe("mcp proxy integration", () => {
     const server = createMCPServer(createProxyRoot(harness, { rename }).root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createSdkTestPair(server, () =>
       new McpClient({
@@ -916,9 +917,9 @@ describe("mcp proxy integration", () => {
     try {
       const { tools } = await client.listTools();
 
-      expect(tools.map((tool) => tool.name)).toContain("root__github__sub__renamed");
+      expect(tools.map((tool) => tool.name)).toContain("github__sub__renamed");
       const result = await client.callTool({
-        name: "root__github__sub__renamed",
+        name: "github__sub__renamed",
         arguments: { text: "xyz" },
       });
 
diff --git a/packages/toolcraft/src/mcp-runtime-options.test.ts b/packages/toolcraft/src/mcp-runtime-options.test.ts
index 74b6b33c..32a82096 100644
--- a/packages/toolcraft/src/mcp-runtime-options.test.ts
+++ b/packages/toolcraft/src/mcp-runtime-options.test.ts
@@ -63,6 +63,7 @@ describe("createMCPServer human-in-loop runtime options plumbing", () => {
       {
         name: "toolcraft-test",
         version: "1.0.0",
+        omitRootToolNamePrefix: true,
       }
     );
     const { client, cleanup } = await createClient(server);
@@ -70,7 +71,7 @@ describe("createMCPServer human-in-loop runtime options plumbing", () => {
     try {
       await expect(
         client.callTool({
-          name: "root__deploy",
+          name: "deploy",
           arguments: {
             target: "prod",
           },
diff --git a/packages/toolcraft/src/mcp.ts b/packages/toolcraft/src/mcp.ts
index 15994695..b4f92770 100644
--- a/packages/toolcraft/src/mcp.ts
+++ b/packages/toolcraft/src/mcp.ts
@@ -62,6 +62,12 @@ export interface RunMCPOptions<TServices extends object = Record<string, unknown
    * that subtree.
    */
   tools?: string[];
+  /**
+   * Omit the root group name from MCP tool names for a single root group.
+   *
+   * Defaults to false, so existing MCP tool names keep the root group prefix.
+   */
+  omitRootToolNamePrefix?: boolean;
   services?: TServices;
   /**
    * Controls MCP input-schema key casing and accepted argument-key casing.
@@ -281,7 +287,8 @@ function formatToolName(path: string[]): string {
 function enumerateTools<TServices extends object>(
   root: Group<TServices>,
   casing: Casing,
-  allowlist: string[] | undefined
+  allowlist: string[] | undefined,
+  omitRootToolNamePrefix: boolean
 ): ToolDefinition<TServices>[] {
   const tools: ToolDefinition<TServices>[] = [];
 
@@ -323,7 +330,7 @@ function enumerateTools<TServices extends object>(
     }
   }
 
-  const rootPath = root.name.length === 0 ? [] : [root.name];
+  const rootPath = omitRootToolNamePrefix || root.name.length === 0 ? [] : [root.name];
 
   for (const child of root.children) {
     visit(child, rootPath, []);
@@ -571,7 +578,7 @@ function createResolvedMCPServer<TServices extends object = Record<string, unkno
   } as TServices;
   validateServices(services as Record<string, unknown>);
 
-  const tools = enumerateTools(root, casing, options.tools);
+  const tools = enumerateTools(root, casing, options.tools, options.omitRootToolNamePrefix ?? false);
   const version = resolveMCPVersion(options.version);
   const server = createServer({ name: options.name, version });
 
diff --git a/packages/toolcraft/src/toolcraft.test.ts b/packages/toolcraft/src/toolcraft.test.ts
index b601b918..9540e42d 100644
--- a/packages/toolcraft/src/toolcraft.test.ts
+++ b/packages/toolcraft/src/toolcraft.test.ts
@@ -784,6 +784,34 @@ describe("createMCPServer", () => {
     );
   }
 
+  it("keeps the root group name in MCP tool names by default", async () => {
+    const root = defineGroup({
+      name: "root",
+      children: [
+        defineCommand({
+          name: "deploy",
+          scope: ["mcp"],
+          params: S.Object({}),
+          handler: async () => "ok",
+        }),
+      ],
+    });
+
+    const server = createMCPServer(root, {
+      name: "toolcraft-test",
+      version: "1.0.0",
+    });
+    const { client, cleanup } = await createClient(server);
+
+    try {
+      const result = await client.listTools();
+
+      expect(result.tools.map((tool) => tool.name)).toContain("root__deploy");
+    } finally {
+      await cleanup();
+    }
+  });
+
   it("lists only mcp-scoped commands that match the allowlist and applies schema casing", async () => {
     const usage = defineCommand({
       name: "usage",
@@ -839,14 +867,15 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
-      tools: ["root__usage", "root__bot"],
+      omitRootToolNamePrefix: true,
+      tools: ["usage", "bot"],
     });
     const { client, cleanup } = await createClient(server);
 
     try {
       const result = await client.listTools();
 
-      expect(result.tools.map((tool) => tool.name)).toEqual(["root__usage", "root__bot__create"]);
+      expect(result.tools.map((tool) => tool.name)).toEqual(["usage", "bot__create"]);
       expect(result.tools[0]?.inputSchema).toEqual({
         type: "object",
         properties: {
@@ -911,6 +940,7 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
@@ -954,6 +984,7 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
@@ -961,7 +992,7 @@ describe("createMCPServer", () => {
       const result = await client.listTools();
 
       expect(result.tools).toHaveLength(3);
-      expect(result.tools[0]?.name).toBe("root__run");
+      expect(result.tools[0]?.name).toBe("run");
       expect(result.tools[0]?.inputSchema).toEqual({
         type: "object",
         properties: {
@@ -999,6 +1030,7 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
@@ -1017,7 +1049,7 @@ describe("createMCPServer", () => {
       });
 
       const callResult = await client.callTool({
-        name: "root__run",
+        name: "run",
         arguments: {
           limit: null,
         },
@@ -1049,13 +1081,14 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
     try {
       await expect(
         client.callTool({
-          name: "root__run",
+          name: "run",
           arguments: {
             count: 1.5,
           },
@@ -1092,6 +1125,7 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
@@ -1155,7 +1189,8 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
-      tools: ["root__bot_admin__bot"],
+      omitRootToolNamePrefix: true,
+      tools: ["bot_admin__bot"],
       casing: "camel",
     });
     const { client, cleanup } = await createClient(server);
@@ -1164,8 +1199,8 @@ describe("createMCPServer", () => {
       const result = await client.listTools();
 
       expect(result.tools.map((tool) => tool.name)).toEqual([
-        "root__bot_admin__bot__create_bot",
-        "root__bot_admin__bot__remove_bot",
+        "bot_admin__bot__create_bot",
+        "bot_admin__bot__remove_bot",
       ]);
       expect(result.tools[0]).toMatchObject({
         description: "Create a bot Parameters: botName (required), botConfig.apiKey (required).",
@@ -1300,12 +1335,13 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
     try {
       const callPromise = client.callTool({
-        name: "root__deploy",
+        name: "deploy",
         arguments: {},
       });
 
@@ -1343,11 +1379,12 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
     try {
-      await expect(client.callTool({ name: "root__deploy", arguments: {} })).rejects.toSatisfy((error: unknown) => {
+      await expect(client.callTool({ name: "deploy", arguments: {} })).rejects.toSatisfy((error: unknown) => {
         expect(error).toBeInstanceOf(McpError);
         expect(error).toMatchObject({
           code: ERROR_INVALID_PARAMS,
@@ -1378,12 +1415,13 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
     try {
       const callPromise = client.callTool({
-        name: "root__deploy",
+        name: "deploy",
         arguments: {},
       });
 
@@ -1409,6 +1447,7 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
@@ -1466,13 +1505,14 @@ describe("createMCPServer", () => {
       services: {
         region: "us",
       },
+      omitRootToolNamePrefix: true,
       casing: "camel",
     });
     const { client, cleanup } = await createClient(server);
 
     try {
       const result = await client.callTool({
-        name: "root__deploy",
+        name: "deploy",
         arguments: {
           botName: "demo",
         },
@@ -1515,12 +1555,13 @@ describe("createMCPServer", () => {
     const server = createMCPServer(root, {
       name: "toolcraft-test",
       version: "1.0.0",
+      omitRootToolNamePrefix: true,
     });
     const { client, cleanup } = await createClient(server);
 
     try {
       const callPromise = client.callTool({
-        name: "root__explode",
+        name: "explode",
         arguments: {},
       });