fix(cli): Use correct defaults for file filtering (#11426)

packages/cli/src/config/config.test.ts

@@ -8,6 +8,7 @@ import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
 import * as os from 'node:os';
 import * as path from 'node:path';
 import {
+  DEFAULT_FILE_FILTERING_OPTIONS,
   DEFAULT_GEMINI_MODEL,
   DEFAULT_GEMINI_MODEL_AUTO,
   OutputFormat,
@@ -583,6 +584,19 @@ describe('loadCliConfig', () => {
       });
     });
   });
+
+  it('should use default fileFilter options when unconfigured', async () => {
+    process.argv = ['node', 'script.js'];
+    const argv = await parseArguments({} as Settings);
+    const settings: Settings = {};
+    const config = await loadCliConfig(settings, [], 'test-session', argv);
+    expect(config.getFileFilteringRespectGitIgnore()).toBe(
+      DEFAULT_FILE_FILTERING_OPTIONS.respectGitIgnore,
+    );
+    expect(config.getFileFilteringRespectGeminiIgnore()).toBe(
+      DEFAULT_FILE_FILTERING_OPTIONS.respectGeminiIgnore,
+    );
+  });
 });
 
 describe('Hierarchical Memory Loading (config.ts) - Placeholder Suite', () => {

packages/cli/src/config/config.ts

@@ -27,6 +27,7 @@ import {
   DEFAULT_GEMINI_MODEL,
   DEFAULT_GEMINI_MODEL_AUTO,
   DEFAULT_GEMINI_EMBEDDING_MODEL,
+  DEFAULT_FILE_FILTERING_OPTIONS,
   DEFAULT_MEMORY_FILE_FILTERING_OPTIONS,
   FileDiscoveryService,
   WRITE_FILE_TOOL_NAME,
@@ -394,11 +395,16 @@ export async function loadCliConfig(
 
   const fileService = new FileDiscoveryService(cwd);
 
-  const fileFiltering = {
+  const memoryFileFiltering = {
     ...DEFAULT_MEMORY_FILE_FILTERING_OPTIONS,
     ...settings.context?.fileFiltering,
   };
 
+  const fileFiltering = {
+    ...DEFAULT_FILE_FILTERING_OPTIONS,
+    ...settings.context?.fileFiltering,
+  };
+
   const includeDirectories = (settings.context?.includeDirectories || [])
     .map(resolvePath)
     .concat((argv.includeDirectories || []).map(resolvePath));
@@ -416,7 +422,7 @@ export async function loadCliConfig(
       allExtensions,
       trustedFolder,
       memoryImportFormat,
-      fileFiltering,
+      memoryFileFiltering,
     );
 
   let mcpServers = mergeMcpServers(settings, allExtensions);