test: fix missing getAllowedTools mock in gemini.tsx tests

Removes the unnecessary setTimeout wrapper when emitting the allowedTools
deprecation warning, leveraging the built-in event backlog mechanism of
CoreEventEmitter.

packages/cli/src/config/config.ts

@@ -177,7 +177,8 @@ export async function parseArguments(
           type: 'array',
           string: true,
           nargs: 1,
-          description: 'Tools that are allowed to run without confirmation',
+          description:
+            '[DEPRECATED: Use Policy Engine instead See https://geminicli.com/docs/core/policy-engine] Tools that are allowed to run without confirmation.',
           coerce: (tools: string[]) =>
             // Handle comma-separated values
             tools.flatMap((tool) => tool.split(',').map((t) => t.trim())),

packages/cli/src/gemini.test.tsx

@@ -538,6 +538,7 @@ describe('gemini.tsx main function kitty protocol', () => {
 
     const mockConfig = createMockConfig({
       isInteractive: () => false,
+      getAllowedTools: vi.fn(),
       getQuestion: () => '',
       getSandbox: () => undefined,
       getListExtensions: () => flag === 'listExtensions',
@@ -614,6 +615,7 @@ describe('gemini.tsx main function kitty protocol', () => {
 
     const mockConfig = createMockConfig({
       isInteractive: () => false,
+      getAllowedTools: vi.fn(),
       getQuestion: () => '',
       getSandbox: () => ({ command: 'docker', image: 'test-image' }),
     });

packages/cli/src/gemini.tsx

@@ -518,6 +518,14 @@ export async function main() {
 
     adminControlsListner.setConfig(config);
 
+    // Show deprecation warning only for allowedTools as that's the only one set by the user currently via command line args
+    if (config.getAllowedTools() !== undefined) {
+      coreEvents.emitFeedback(
+        'warning',
+        `The allowed-tools cli argument is deprecated and will be removed in Gemini CLI 1.0: Please use the Policy Engine to manage tool permissions instead: https://geminicli.com/docs/core/policy-engine/`,
+      );
+    }
+
     if (config.isInteractive() && config.storage && config.getDebugMode()) {
       const { registerActivityLogger } = await import(
         './utils/activityLogger.js'

packages/cli/src/gemini_cleanup.test.tsx

@@ -78,6 +78,7 @@ vi.mock('./config/config.js', () => ({
     getQuestion: vi.fn(() => ''),
     isInteractive: () => false,
     storage: { initialize: vi.fn().mockResolvedValue(undefined) },
+    getAllowedTools: vi.fn(),
   } as unknown as Config),
   parseArguments: vi.fn().mockResolvedValue({}),
   isDebugMode: vi.fn(() => false),
@@ -188,6 +189,7 @@ describe('gemini.tsx main function cleanup', () => {
     } as any); // eslint-disable-line @typescript-eslint/no-explicit-any
     vi.mocked(loadCliConfig).mockResolvedValue({
       isInteractive: vi.fn(() => false),
+      getAllowedTools: vi.fn(),
       getQuestion: vi.fn(() => 'test'),
       getSandbox: vi.fn(() => false),
       getDebugMode: vi.fn(() => false),

packages/core/src/config/config.ts

@@ -376,8 +376,11 @@ export interface ConfigParameters {
   debugMode: boolean;
   question?: string;
 
+  /** @deprecated Use the Policy System instead. See https://geminicli.com/docs/core/policy-engine/ */
   coreTools?: string[];
+  /** @deprecated Use the Policy System instead. See https://geminicli.com/docs/core/policy-engine/ */
   allowedTools?: string[];
+  /** @deprecated Use the Policy System instead. See https://geminicli.com/docs/core/policy-engine/ */
   excludeTools?: string[];
   toolDiscoveryCommand?: string;
   toolCallCommand?: string;