9 files changed, 669 insertions, 82 deletions
diff --git a/packages/cli/src/config/config.test.ts b/packages/cli/src/config/config.test.ts
index 55780320..7f47660d 100644
--- a/packages/cli/src/config/config.test.ts
+++ b/packages/cli/src/config/config.test.ts
@@ -35,6 +35,11 @@ vi.mock('@google/gemini-cli-core', async () => {
   );
   return {
     ...actualServer,
+    IdeClient: vi.fn().mockImplementation(() => ({
+      getConnectionStatus: vi.fn(),
+      initialize: vi.fn(),
+      shutdown: vi.fn(),
+    })),
     loadEnvironment: vi.fn(),
     loadServerHierarchicalMemory: vi.fn(
       (cwd, debug, fileService, extensionPaths, _maxDirs) =>
diff --git a/packages/cli/src/config/extension.test.ts b/packages/cli/src/config/extension.test.ts
index 6b2a3f83..85852bd7 100644
--- a/packages/cli/src/config/extension.test.ts
+++ b/packages/cli/src/config/extension.test.ts
@@ -42,6 +42,31 @@ describe('loadExtensions', () => {
     fs.rmSync(tempHomeDir, { recursive: true, force: true });
   });
 
+  it('should include extension path in loaded extension', () => {
+    const workspaceExtensionsDir = path.join(
+      tempWorkspaceDir,
+      EXTENSIONS_DIRECTORY_NAME,
+    );
+    fs.mkdirSync(workspaceExtensionsDir, { recursive: true });
+
+    const extensionDir = path.join(workspaceExtensionsDir, 'test-extension');
+    fs.mkdirSync(extensionDir, { recursive: true });
+
+    const config = {
+      name: 'test-extension',
+      version: '1.0.0',
+    };
+    fs.writeFileSync(
+      path.join(extensionDir, EXTENSIONS_CONFIG_FILENAME),
+      JSON.stringify(config),
+    );
+
+    const extensions = loadExtensions(tempWorkspaceDir);
+    expect(extensions).toHaveLength(1);
+    expect(extensions[0].path).toBe(extensionDir);
+    expect(extensions[0].config.name).toBe('test-extension');
+  });
+
   it('should load context file path when GEMINI.md is present', () => {
     const workspaceExtensionsDir = path.join(
       tempWorkspaceDir,
diff --git a/packages/cli/src/config/extension.ts b/packages/cli/src/config/extension.ts
index adefec29..1922f55a 100644
--- a/packages/cli/src/config/extension.ts
+++ b/packages/cli/src/config/extension.ts
@@ -13,6 +13,7 @@ export const EXTENSIONS_DIRECTORY_NAME = path.join('.gemini', 'extensions');
 export const EXTENSIONS_CONFIG_FILENAME = 'gemini-extension.json';
 
 export interface Extension {
+  path: string;
   config: ExtensionConfig;
   contextFiles: string[];
 }
@@ -90,6 +91,7 @@ function loadExtension(extensionDir: string): Extension | null {
       .filter((contextFilePath) => fs.existsSync(contextFilePath));
 
     return {
+      path: extensionDir,
       config,
       contextFiles,
     };
@@ -121,6 +123,7 @@ export function annotateActiveExtensions(
       name: extension.config.name,
       version: extension.config.version,
       isActive: true,
+      path: extension.path,
     }));
   }
 
@@ -136,6 +139,7 @@ export function annotateActiveExtensions(
       name: extension.config.name,
       version: extension.config.version,
       isActive: false,
+      path: extension.path,
     }));
   }
 
@@ -153,6 +157,7 @@ export function annotateActiveExtensions(
       name: extension.config.name,
       version: extension.config.version,
       isActive,
+      path: extension.path,
     });
   }
 
diff --git a/packages/cli/src/services/CommandService.test.ts b/packages/cli/src/services/CommandService.test.ts
index 28731f81..e2d5b9f5 100644
--- a/packages/cli/src/services/CommandService.test.ts
+++ b/packages/cli/src/services/CommandService.test.ts
@@ -177,4 +177,176 @@ describe('CommandService', () => {
     expect(loader2.loadCommands).toHaveBeenCalledTimes(1);
     expect(loader2.loadCommands).toHaveBeenCalledWith(signal);
   });
+
+  it('should rename extension commands when they conflict', async () => {
+    const builtinCommand = createMockCommand('deploy', CommandKind.BUILT_IN);
+    const userCommand = createMockCommand('sync', CommandKind.FILE);
+    const extensionCommand1 = {
+      ...createMockCommand('deploy', CommandKind.FILE),
+      extensionName: 'firebase',
+      description: '[firebase] Deploy to Firebase',
+    };
+    const extensionCommand2 = {
+      ...createMockCommand('sync', CommandKind.FILE),
+      extensionName: 'git-helper',
+      description: '[git-helper] Sync with remote',
+    };
+
+    const mockLoader1 = new MockCommandLoader([builtinCommand]);
+    const mockLoader2 = new MockCommandLoader([
+      userCommand,
+      extensionCommand1,
+      extensionCommand2,
+    ]);
+
+    const service = await CommandService.create(
+      [mockLoader1, mockLoader2],
+      new AbortController().signal,
+    );
+
+    const commands = service.getCommands();
+    expect(commands).toHaveLength(4);
+
+    // Built-in command keeps original name
+    const deployBuiltin = commands.find(
+      (cmd) => cmd.name === 'deploy' && !cmd.extensionName,
+    );
+    expect(deployBuiltin).toBeDefined();
+    expect(deployBuiltin?.kind).toBe(CommandKind.BUILT_IN);
+
+    // Extension command conflicting with built-in gets renamed
+    const deployExtension = commands.find(
+      (cmd) => cmd.name === 'firebase.deploy',
+    );
+    expect(deployExtension).toBeDefined();
+    expect(deployExtension?.extensionName).toBe('firebase');
+
+    // User command keeps original name
+    const syncUser = commands.find(
+      (cmd) => cmd.name === 'sync' && !cmd.extensionName,
+    );
+    expect(syncUser).toBeDefined();
+    expect(syncUser?.kind).toBe(CommandKind.FILE);
+
+    // Extension command conflicting with user command gets renamed
+    const syncExtension = commands.find(
+      (cmd) => cmd.name === 'git-helper.sync',
+    );
+    expect(syncExtension).toBeDefined();
+    expect(syncExtension?.extensionName).toBe('git-helper');
+  });
+
+  it('should handle user/project command override correctly', async () => {
+    const builtinCommand = createMockCommand('help', CommandKind.BUILT_IN);
+    const userCommand = createMockCommand('help', CommandKind.FILE);
+    const projectCommand = createMockCommand('deploy', CommandKind.FILE);
+    const userDeployCommand = createMockCommand('deploy', CommandKind.FILE);
+
+    const mockLoader1 = new MockCommandLoader([builtinCommand]);
+    const mockLoader2 = new MockCommandLoader([
+      userCommand,
+      userDeployCommand,
+      projectCommand,
+    ]);
+
+    const service = await CommandService.create(
+      [mockLoader1, mockLoader2],
+      new AbortController().signal,
+    );
+
+    const commands = service.getCommands();
+    expect(commands).toHaveLength(2);
+
+    // User command overrides built-in
+    const helpCommand = commands.find((cmd) => cmd.name === 'help');
+    expect(helpCommand).toBeDefined();
+    expect(helpCommand?.kind).toBe(CommandKind.FILE);
+
+    // Project command overrides user command (last wins)
+    const deployCommand = commands.find((cmd) => cmd.name === 'deploy');
+    expect(deployCommand).toBeDefined();
+    expect(deployCommand?.kind).toBe(CommandKind.FILE);
+  });
+
+  it('should handle secondary conflicts when renaming extension commands', async () => {
+    // User has both /deploy and /gcp.deploy commands
+    const userCommand1 = createMockCommand('deploy', CommandKind.FILE);
+    const userCommand2 = createMockCommand('gcp.deploy', CommandKind.FILE);
+
+    // Extension also has a deploy command that will conflict with user's /deploy
+    const extensionCommand = {
+      ...createMockCommand('deploy', CommandKind.FILE),
+      extensionName: 'gcp',
+      description: '[gcp] Deploy to Google Cloud',
+    };
+
+    const mockLoader = new MockCommandLoader([
+      userCommand1,
+      userCommand2,
+      extensionCommand,
+    ]);
+
+    const service = await CommandService.create(
+      [mockLoader],
+      new AbortController().signal,
+    );
+
+    const commands = service.getCommands();
+    expect(commands).toHaveLength(3);
+
+    // Original user command keeps its name
+    const deployUser = commands.find(
+      (cmd) => cmd.name === 'deploy' && !cmd.extensionName,
+    );
+    expect(deployUser).toBeDefined();
+
+    // User's dot notation command keeps its name
+    const gcpDeployUser = commands.find(
+      (cmd) => cmd.name === 'gcp.deploy' && !cmd.extensionName,
+    );
+    expect(gcpDeployUser).toBeDefined();
+
+    // Extension command gets renamed with suffix due to secondary conflict
+    const deployExtension = commands.find(
+      (cmd) => cmd.name === 'gcp.deploy1' && cmd.extensionName === 'gcp',
+    );
+    expect(deployExtension).toBeDefined();
+    expect(deployExtension?.description).toBe('[gcp] Deploy to Google Cloud');
+  });
+
+  it('should handle multiple secondary conflicts with incrementing suffixes', async () => {
+    // User has /deploy, /gcp.deploy, and /gcp.deploy1
+    const userCommand1 = createMockCommand('deploy', CommandKind.FILE);
+    const userCommand2 = createMockCommand('gcp.deploy', CommandKind.FILE);
+    const userCommand3 = createMockCommand('gcp.deploy1', CommandKind.FILE);
+
+    // Extension has a deploy command
+    const extensionCommand = {
+      ...createMockCommand('deploy', CommandKind.FILE),
+      extensionName: 'gcp',
+      description: '[gcp] Deploy to Google Cloud',
+    };
+
+    const mockLoader = new MockCommandLoader([
+      userCommand1,
+      userCommand2,
+      userCommand3,
+      extensionCommand,
+    ]);
+
+    const service = await CommandService.create(
+      [mockLoader],
+      new AbortController().signal,
+    );
+
+    const commands = service.getCommands();
+    expect(commands).toHaveLength(4);
+
+    // Extension command gets renamed with suffix 2 due to multiple conflicts
+    const deployExtension = commands.find(
+      (cmd) => cmd.name === 'gcp.deploy2' && cmd.extensionName === 'gcp',
+    );
+    expect(deployExtension).toBeDefined();
+    expect(deployExtension?.description).toBe('[gcp] Deploy to Google Cloud');
+  });
 });
diff --git a/packages/cli/src/services/CommandService.ts b/packages/cli/src/services/CommandService.ts
index ef4f4d14..78e4817b 100644
--- a/packages/cli/src/services/CommandService.ts
+++ b/packages/cli/src/services/CommandService.ts
@@ -30,13 +30,17 @@ export class CommandService {
    *
    * This factory method orchestrates the entire command loading process. It
    * runs all provided loaders in parallel, aggregates their results, handles
-   * name conflicts by letting the last-loaded command win, and then returns a
+   * name conflicts for extension commands by renaming them, and then returns a
    * fully constructed `CommandService` instance.
    *
+   * Conflict resolution:
+   * - Extension commands that conflict with existing commands are renamed to
+   *   `extensionName.commandName`
+   * - Non-extension commands (built-in, user, project) override earlier commands
+   *   with the same name based on loader order
+   *
    * @param loaders An array of objects that conform to the `ICommandLoader`
-   *   interface. The order of loaders is significant: if multiple loaders
-   *   provide a command with the same name, the command from the loader that
-   *   appears later in the array will take precedence.
+   *   interface. Built-in commands should come first, followed by FileCommandLoader.
    * @param signal An AbortSignal to cancel the loading process.
    * @returns A promise that resolves to a new, fully initialized `CommandService` instance.
    */
@@ -57,12 +61,28 @@ export class CommandService {
       }
     }
 
-    // De-duplicate commands using a Map. The last one found with a given name wins.
-    // This creates a natural override system based on the order of the loaders
-    // passed to the constructor.
     const commandMap = new Map<string, SlashCommand>();
     for (const cmd of allCommands) {
-      commandMap.set(cmd.name, cmd);
+      let finalName = cmd.name;
+
+      // Extension commands get renamed if they conflict with existing commands
+      if (cmd.extensionName && commandMap.has(cmd.name)) {
+        let renamedName = `${cmd.extensionName}.${cmd.name}`;
+        let suffix = 1;
+
+        // Keep trying until we find a name that doesn't conflict
+        while (commandMap.has(renamedName)) {
+          renamedName = `${cmd.extensionName}.${cmd.name}${suffix}`;
+          suffix++;
+        }
+
+        finalName = renamedName;
+      }
+
+      commandMap.set(finalName, {
+        ...cmd,
+        name: finalName,
+      });
     }
 
     const finalCommands = Object.freeze(Array.from(commandMap.values()));
diff --git a/packages/cli/src/services/FileCommandLoader.test.ts b/packages/cli/src/services/FileCommandLoader.test.ts
index e3cbceb2..f4f8ac2c 100644
--- a/packages/cli/src/services/FileCommandLoader.test.ts
+++ b/packages/cli/src/services/FileCommandLoader.test.ts
@@ -4,13 +4,14 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-import { FileCommandLoader } from './FileCommandLoader.js';
+import * as path from 'node:path';
 import {
   Config,
   getProjectCommandsDir,
   getUserCommandsDir,
 } from '@google/gemini-cli-core';
 import mock from 'mock-fs';
+import { FileCommandLoader } from './FileCommandLoader.js';
 import { assert, vi } from 'vitest';
 import { createMockCommandContext } from '../test-utils/mockCommandContext.js';
 import {
@@ -85,7 +86,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
 
     expect(commands).toHaveLength(1);
@@ -176,7 +177,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
 
     expect(commands).toHaveLength(2);
@@ -194,9 +195,11 @@ describe('FileCommandLoader', () => {
         },
       },
     });
-    const loader = new FileCommandLoader({
-      getProjectRoot: () => '/path/to/project',
-    } as Config);
+    const mockConfig = {
+      getProjectRoot: vi.fn(() => '/path/to/project'),
+      getExtensions: vi.fn(() => []),
+    } as Config;
+    const loader = new FileCommandLoader(mockConfig);
     const commands = await loader.loadCommands(signal);
     expect(commands).toHaveLength(1);
     expect(commands[0]!.name).toBe('gcp:pipelines:run');
@@ -212,7 +215,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
 
     expect(commands).toHaveLength(1);
@@ -221,7 +224,7 @@ describe('FileCommandLoader', () => {
     expect(command.name).toBe('git:commit');
   });
 
-  it('overrides user commands with project commands', async () => {
+  it('returns both user and project commands in order', async () => {
     const userCommandsDir = getUserCommandsDir();
     const projectCommandsDir = getProjectCommandsDir(process.cwd());
     mock({
@@ -233,16 +236,15 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader({
-      getProjectRoot: () => process.cwd(),
-    } as Config);
+    const mockConfig = {
+      getProjectRoot: vi.fn(() => process.cwd()),
+      getExtensions: vi.fn(() => []),
+    } as Config;
+    const loader = new FileCommandLoader(mockConfig);
     const commands = await loader.loadCommands(signal);
 
-    expect(commands).toHaveLength(1);
-    const command = commands[0];
-    expect(command).toBeDefined();
-
-    const result = await command.action?.(
+    expect(commands).toHaveLength(2);
+    const userResult = await commands[0].action?.(
       createMockCommandContext({
         invocation: {
           raw: '/test',
@@ -252,10 +254,25 @@ describe('FileCommandLoader', () => {
       }),
       '',
     );
-    if (result?.type === 'submit_prompt') {
-      expect(result.content).toBe('Project prompt');
+    if (userResult?.type === 'submit_prompt') {
+      expect(userResult.content).toBe('User prompt');
     } else {
-      assert.fail('Incorrect action type');
+      assert.fail('Incorrect action type for user command');
+    }
+    const projectResult = await commands[1].action?.(
+      createMockCommandContext({
+        invocation: {
+          raw: '/test',
+          name: 'test',
+          args: '',
+        },
+      }),
+      '',
+    );
+    if (projectResult?.type === 'submit_prompt') {
+      expect(projectResult.content).toBe('Project prompt');
+    } else {
+      assert.fail('Incorrect action type for project command');
     }
   });
 
@@ -268,7 +285,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
 
     expect(commands).toHaveLength(1);
@@ -284,7 +301,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
 
     expect(commands).toHaveLength(1);
@@ -299,7 +316,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
     const command = commands[0];
     expect(command).toBeDefined();
@@ -308,7 +325,7 @@ describe('FileCommandLoader', () => {
 
   it('handles file system errors gracefully', async () => {
     mock({}); // Mock an empty file system
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
     expect(commands).toHaveLength(0);
   });
@@ -321,7 +338,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
     const command = commands[0];
     expect(command).toBeDefined();
@@ -336,7 +353,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
     const command = commands[0];
     expect(command).toBeDefined();
@@ -351,7 +368,7 @@ describe('FileCommandLoader', () => {
       },
     });
 
-    const loader = new FileCommandLoader(null as unknown as Config);
+    const loader = new FileCommandLoader(null);
     const commands = await loader.loadCommands(signal);
 
     expect(commands).toHaveLength(1);
@@ -362,6 +379,298 @@ describe('FileCommandLoader', () => {
     expect(command.name).toBe('legacy_command');
   });
 
+  describe('Extension Command Loading', () => {
+    it('loads commands from active extensions', async () => {
+      const userCommandsDir = getUserCommandsDir();
+      const projectCommandsDir = getProjectCommandsDir(process.cwd());
+      const extensionDir = path.join(
+        process.cwd(),
+        '.gemini/extensions/test-ext',
+      );
+
+      mock({
+        [userCommandsDir]: {
+          'user.toml': 'prompt = "User command"',
+        },
+        [projectCommandsDir]: {
+          'project.toml': 'prompt = "Project command"',
+        },
+        [extensionDir]: {
+          'gemini-extension.json': JSON.stringify({
+            name: 'test-ext',
+            version: '1.0.0',
+          }),
+          commands: {
+            'ext.toml': 'prompt = "Extension command"',
+          },
+        },
+      });
+
+      const mockConfig = {
+        getProjectRoot: vi.fn(() => process.cwd()),
+        getExtensions: vi.fn(() => [
+          {
+            name: 'test-ext',
+            version: '1.0.0',
+            isActive: true,
+            path: extensionDir,
+          },
+        ]),
+      } as Config;
+      const loader = new FileCommandLoader(mockConfig);
+      const commands = await loader.loadCommands(signal);
+
+      expect(commands).toHaveLength(3);
+      const commandNames = commands.map((cmd) => cmd.name);
+      expect(commandNames).toEqual(['user', 'project', 'ext']);
+
+      const extCommand = commands.find((cmd) => cmd.name === 'ext');
+      expect(extCommand?.extensionName).toBe('test-ext');
+      expect(extCommand?.description).toMatch(/^\[test-ext\]/);
+    });
+
+    it('extension commands have extensionName metadata for conflict resolution', async () => {
+      const userCommandsDir = getUserCommandsDir();
+      const projectCommandsDir = getProjectCommandsDir(process.cwd());
+      const extensionDir = path.join(
+        process.cwd(),
+        '.gemini/extensions/test-ext',
+      );
+
+      mock({
+        [extensionDir]: {
+          'gemini-extension.json': JSON.stringify({
+            name: 'test-ext',
+            version: '1.0.0',
+          }),
+          commands: {
+            'deploy.toml': 'prompt = "Extension deploy command"',
+          },
+        },
+        [userCommandsDir]: {
+          'deploy.toml': 'prompt = "User deploy command"',
+        },
+        [projectCommandsDir]: {
+          'deploy.toml': 'prompt = "Project deploy command"',
+        },
+      });
+
+      const mockConfig = {
+        getProjectRoot: vi.fn(() => process.cwd()),
+        getExtensions: vi.fn(() => [
+          {
+            name: 'test-ext',
+            version: '1.0.0',
+            isActive: true,
+            path: extensionDir,
+          },
+        ]),
+      } as Config;
+      const loader = new FileCommandLoader(mockConfig);
+      const commands = await loader.loadCommands(signal);
+
+      // Return all commands, even duplicates
+      expect(commands).toHaveLength(3);
+
+      expect(commands[0].name).toBe('deploy');
+      expect(commands[0].extensionName).toBeUndefined();
+      const result0 = await commands[0].action?.(
+        createMockCommandContext({
+          invocation: {
+            raw: '/deploy',
+            name: 'deploy',
+            args: '',
+          },
+        }),
+        '',
+      );
+      expect(result0?.type).toBe('submit_prompt');
+      if (result0?.type === 'submit_prompt') {
+        expect(result0.content).toBe('User deploy command');
+      }
+
+      expect(commands[1].name).toBe('deploy');
+      expect(commands[1].extensionName).toBeUndefined();
+      const result1 = await commands[1].action?.(
+        createMockCommandContext({
+          invocation: {
+            raw: '/deploy',
+            name: 'deploy',
+            args: '',
+          },
+        }),
+        '',
+      );
+      expect(result1?.type).toBe('submit_prompt');
+      if (result1?.type === 'submit_prompt') {
+        expect(result1.content).toBe('Project deploy command');
+      }
+
+      expect(commands[2].name).toBe('deploy');
+      expect(commands[2].extensionName).toBe('test-ext');
+      expect(commands[2].description).toMatch(/^\[test-ext\]/);
+      const result2 = await commands[2].action?.(
+        createMockCommandContext({
+          invocation: {
+            raw: '/deploy',
+            name: 'deploy',
+            args: '',
+          },
+        }),
+        '',
+      );
+      expect(result2?.type).toBe('submit_prompt');
+      if (result2?.type === 'submit_prompt') {
+        expect(result2.content).toBe('Extension deploy command');
+      }
+    });
+
+    it('only loads commands from active extensions', async () => {
+      const extensionDir1 = path.join(
+        process.cwd(),
+        '.gemini/extensions/active-ext',
+      );
+      const extensionDir2 = path.join(
+        process.cwd(),
+        '.gemini/extensions/inactive-ext',
+      );
+
+      mock({
+        [extensionDir1]: {
+          'gemini-extension.json': JSON.stringify({
+            name: 'active-ext',
+            version: '1.0.0',
+          }),
+          commands: {
+            'active.toml': 'prompt = "Active extension command"',
+          },
+        },
+        [extensionDir2]: {
+          'gemini-extension.json': JSON.stringify({
+            name: 'inactive-ext',
+            version: '1.0.0',
+          }),
+          commands: {
+            'inactive.toml': 'prompt = "Inactive extension command"',
+          },
+        },
+      });
+
+      const mockConfig = {
+        getProjectRoot: vi.fn(() => process.cwd()),
+        getExtensions: vi.fn(() => [
+          {
+            name: 'active-ext',
+            version: '1.0.0',
+            isActive: true,
+            path: extensionDir1,
+          },
+          {
+            name: 'inactive-ext',
+            version: '1.0.0',
+            isActive: false,
+            path: extensionDir2,
+          },
+        ]),
+      } as Config;
+      const loader = new FileCommandLoader(mockConfig);
+      const commands = await loader.loadCommands(signal);
+
+      expect(commands).toHaveLength(1);
+      expect(commands[0].name).toBe('active');
+      expect(commands[0].extensionName).toBe('active-ext');
+      expect(commands[0].description).toMatch(/^\[active-ext\]/);
+    });
+
+    it('handles missing extension commands directory gracefully', async () => {
+      const extensionDir = path.join(
+        process.cwd(),
+        '.gemini/extensions/no-commands',
+      );
+
+      mock({
+        [extensionDir]: {
+          'gemini-extension.json': JSON.stringify({
+            name: 'no-commands',
+            version: '1.0.0',
+          }),
+          // No commands directory
+        },
+      });
+
+      const mockConfig = {
+        getProjectRoot: vi.fn(() => process.cwd()),
+        getExtensions: vi.fn(() => [
+          {
+            name: 'no-commands',
+            version: '1.0.0',
+            isActive: true,
+            path: extensionDir,
+          },
+        ]),
+      } as Config;
+      const loader = new FileCommandLoader(mockConfig);
+      const commands = await loader.loadCommands(signal);
+      expect(commands).toHaveLength(0);
+    });
+
+    it('handles nested command structure in extensions', async () => {
+      const extensionDir = path.join(process.cwd(), '.gemini/extensions/a');
+
+      mock({
+        [extensionDir]: {
+          'gemini-extension.json': JSON.stringify({
+            name: 'a',
+            version: '1.0.0',
+          }),
+          commands: {
+            b: {
+              'c.toml': 'prompt = "Nested command from extension a"',
+              d: {
+                'e.toml': 'prompt = "Deeply nested command"',
+              },
+            },
+            'simple.toml': 'prompt = "Simple command"',
+          },
+        },
+      });
+
+      const mockConfig = {
+        getProjectRoot: vi.fn(() => process.cwd()),
+        getExtensions: vi.fn(() => [
+          { name: 'a', version: '1.0.0', isActive: true, path: extensionDir },
+        ]),
+      } as Config;
+      const loader = new FileCommandLoader(mockConfig);
+      const commands = await loader.loadCommands(signal);
+
+      expect(commands).toHaveLength(3);
+
+      const commandNames = commands.map((cmd) => cmd.name).sort();
+      expect(commandNames).toEqual(['b:c', 'b:d:e', 'simple']);
+
+      const nestedCmd = commands.find((cmd) => cmd.name === 'b:c');
+      expect(nestedCmd?.extensionName).toBe('a');
+      expect(nestedCmd?.description).toMatch(/^\[a\]/);
+      expect(nestedCmd).toBeDefined();
+      const result = await nestedCmd!.action?.(
+        createMockCommandContext({
+          invocation: {
+            raw: '/b:c',
+            name: 'b:c',
+            args: '',
+          },
+        }),
+        '',
+      );
+      if (result?.type === 'submit_prompt') {
+        expect(result.content).toBe('Nested command from extension a');
+      } else {
+        assert.fail('Incorrect action type');
+      }
+    });
+  });
+
   describe('Shorthand Argument Processor Integration', () => {
     it('correctly processes a command with {{args}}', async () => {
       const userCommandsDir = getUserCommandsDir();
diff --git a/packages/cli/src/services/FileCommandLoader.ts b/packages/cli/src/services/FileCommandLoader.ts
index c96acead..5b8d8c42 100644
--- a/packages/cli/src/services/FileCommandLoader.ts
+++ b/packages/cli/src/services/FileCommandLoader.ts
@@ -35,6 +35,11 @@ import {
   ShellProcessor,
 } from './prompt-processors/shellProcessor.js';
 
+interface CommandDirectory {
+  path: string;
+  extensionName?: string;
+}
+
 /**
  * Defines the Zod schema for a command definition file. This serves as the
  * single source of truth for both validation and type inference.
@@ -65,13 +70,18 @@ export class FileCommandLoader implements ICommandLoader {
   }
 
   /**
-   * Loads all commands, applying the precedence rule where project-level
-   * commands override user-level commands with the same name.
+   * Loads all commands from user, project, and extension directories.
+   * Returns commands in order: user → project → extensions (alphabetically).
+   *
+   * Order is important for conflict resolution in CommandService:
+   * - User/project commands (without extensionName) use "last wins" strategy
+   * - Extension commands (with extensionName) get renamed if conflicts exist
+   *
    * @param signal An AbortSignal to cancel the loading process.
-   * @returns A promise that resolves to an array of loaded SlashCommands.
+   * @returns A promise that resolves to an array of all loaded SlashCommands.
    */
   async loadCommands(signal: AbortSignal): Promise<SlashCommand[]> {
-    const commandMap = new Map<string, SlashCommand>();
+    const allCommands: SlashCommand[] = [];
     const globOptions = {
       nodir: true,
       dot: true,
@@ -79,54 +89,85 @@ export class FileCommandLoader implements ICommandLoader {
       follow: true,
     };
 
-    try {
-      // User Commands
-      const userDir = getUserCommandsDir();
-      const userFiles = await glob('**/*.toml', {
-        ...globOptions,
-        cwd: userDir,
-      });
-      const userCommandPromises = userFiles.map((file) =>
-        this.parseAndAdaptFile(path.join(userDir, file), userDir),
-      );
-      const userCommands = (await Promise.all(userCommandPromises)).filter(
-        (cmd): cmd is SlashCommand => cmd !== null,
-      );
-      for (const cmd of userCommands) {
-        commandMap.set(cmd.name, cmd);
-      }
+    // Load commands from each directory
+    const commandDirs = this.getCommandDirectories();
+    for (const dirInfo of commandDirs) {
+      try {
+        const files = await glob('**/*.toml', {
+          ...globOptions,
+          cwd: dirInfo.path,
+        });
 
-      // Project Commands (these intentionally override user commands)
-      const projectDir = getProjectCommandsDir(this.projectRoot);
-      const projectFiles = await glob('**/*.toml', {
-        ...globOptions,
-        cwd: projectDir,
-      });
-      const projectCommandPromises = projectFiles.map((file) =>
-        this.parseAndAdaptFile(path.join(projectDir, file), projectDir),
-      );
-      const projectCommands = (
-        await Promise.all(projectCommandPromises)
-      ).filter((cmd): cmd is SlashCommand => cmd !== null);
-      for (const cmd of projectCommands) {
-        commandMap.set(cmd.name, cmd);
+        const commandPromises = files.map((file) =>
+          this.parseAndAdaptFile(
+            path.join(dirInfo.path, file),
+            dirInfo.path,
+            dirInfo.extensionName,
+          ),
+        );
+
+        const commands = (await Promise.all(commandPromises)).filter(
+          (cmd): cmd is SlashCommand => cmd !== null,
+        );
+
+        // Add all commands without deduplication
+        allCommands.push(...commands);
+      } catch (error) {
+        if ((error as NodeJS.ErrnoException).code !== 'ENOENT') {
+          console.error(
+            `[FileCommandLoader] Error loading commands from ${dirInfo.path}:`,
+            error,
+          );
+        }
       }
-    } catch (error) {
-      console.error(`[FileCommandLoader] Error during file search:`, error);
     }
 
-    return Array.from(commandMap.values());
+    return allCommands;
+  }
+
+  /**
+   * Get all command directories in order for loading.
+   * User commands → Project commands → Extension commands
+   * This order ensures extension commands can detect all conflicts.
+   */
+  private getCommandDirectories(): CommandDirectory[] {
+    const dirs: CommandDirectory[] = [];
+
+    // 1. User commands
+    dirs.push({ path: getUserCommandsDir() });
+
+    // 2. Project commands (override user commands)
+    dirs.push({ path: getProjectCommandsDir(this.projectRoot) });
+
+    // 3. Extension commands (processed last to detect all conflicts)
+    if (this.config) {
+      const activeExtensions = this.config
+        .getExtensions()
+        .filter((ext) => ext.isActive)
+        .sort((a, b) => a.name.localeCompare(b.name)); // Sort alphabetically for deterministic loading
+
+      const extensionCommandDirs = activeExtensions.map((ext) => ({
+        path: path.join(ext.path, 'commands'),
+        extensionName: ext.name,
+      }));
+
+      dirs.push(...extensionCommandDirs);
+    }
+
+    return dirs;
   }
 
   /**
    * Parses a single .toml file and transforms it into a SlashCommand object.
    * @param filePath The absolute path to the .toml file.
    * @param baseDir The root command directory for name calculation.
+   * @param extensionName Optional extension name to prefix commands with.
    * @returns A promise resolving to a SlashCommand, or null if the file is invalid.
    */
   private async parseAndAdaptFile(
     filePath: string,
     baseDir: string,
+    extensionName?: string,
   ): Promise<SlashCommand | null> {
     let fileContent: string;
     try {
@@ -167,7 +208,7 @@ export class FileCommandLoader implements ICommandLoader {
       0,
       relativePathWithExt.length - 5, // length of '.toml'
     );
-    const commandName = relativePath
+    const baseCommandName = relativePath
       .split(path.sep)
       // Sanitize each path segment to prevent ambiguity. Since ':' is our
       // namespace separator, we replace any literal colons in filenames
@@ -175,11 +216,18 @@ export class FileCommandLoader implements ICommandLoader {
       .map((segment) => segment.replaceAll(':', '_'))
       .join(':');
 
+    // Add extension name tag for extension commands
+    const defaultDescription = `Custom command from ${path.basename(filePath)}`;
+    let description = validDef.description || defaultDescription;
+    if (extensionName) {
+      description = `[${extensionName}] ${description}`;
+    }
+
     const processors: IPromptProcessor[] = [];
 
     // Add the Shell Processor if needed.
     if (validDef.prompt.includes(SHELL_INJECTION_TRIGGER)) {
-      processors.push(new ShellProcessor(commandName));
+      processors.push(new ShellProcessor(baseCommandName));
     }
 
     // The presence of '{{args}}' is the switch that determines the behavior.
@@ -190,18 +238,17 @@ export class FileCommandLoader implements ICommandLoader {
     }
 
     return {
-      name: commandName,
-      description:
-        validDef.description ||
-        `Custom command from ${path.basename(filePath)}`,
+      name: baseCommandName,
+      description,
       kind: CommandKind.FILE,
+      extensionName,
       action: async (
         context: CommandContext,
         _args: string,
       ): Promise<SlashCommandActionReturn> => {
         if (!context.invocation) {
           console.error(
-            `[FileCommandLoader] Critical error: Command '${commandName}' was executed without invocation context.`,
+            `[FileCommandLoader] Critical error: Command '${baseCommandName}' was executed without invocation context.`,
           );
           return {
             type: 'submit_prompt',
diff --git a/packages/cli/src/ui/commands/types.ts b/packages/cli/src/ui/commands/types.ts
index 2844177f..900be866 100644
--- a/packages/cli/src/ui/commands/types.ts
+++ b/packages/cli/src/ui/commands/types.ts
@@ -157,6 +157,9 @@ export interface SlashCommand {
 
   kind: CommandKind;
 
+  // Optional metadata for extension commands
+  extensionName?: string;
+
   // The action to run. Optional for parent commands that only group sub-commands.
   action?: (
     context: CommandContext,
diff --git a/packages/cli/src/ui/hooks/slashCommandProcessor.test.ts b/packages/cli/src/ui/hooks/slashCommandProcessor.test.ts
index 5b367cd4..42c2e277 100644
--- a/packages/cli/src/ui/hooks/slashCommandProcessor.test.ts
+++ b/packages/cli/src/ui/hooks/slashCommandProcessor.test.ts
@@ -74,11 +74,12 @@ describe('useSlashCommandProcessor', () => {
   const mockSetQuittingMessages = vi.fn();
 
   const mockConfig = {
-    getProjectRoot: () => '/mock/cwd',
-    getSessionId: () => 'test-session',
-    getGeminiClient: () => ({
+    getProjectRoot: vi.fn(() => '/mock/cwd'),
+    getSessionId: vi.fn(() => 'test-session'),
+    getGeminiClient: vi.fn(() => ({
       setHistory: vi.fn().mockResolvedValue(undefined),
-    }),
+    })),
+    getExtensions: vi.fn(() => []),
   } as unknown as Config;
 
   const mockSettings = {} as LoadedSettings;