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diff --git a/packages/cli/src/config/config.integration.test.ts b/packages/cli/src/config/config.integration.test.ts
new file mode 100644
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+++ b/packages/cli/src/config/config.integration.test.ts
@@ -0,0 +1,213 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, beforeEach, vi, afterEach } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import { tmpdir } from 'os';
+import { Config, ConfigParameters } from '@gemini-code/core';
+
+// Mock file discovery service and tool registry
+vi.mock('@gemini-code/core', async () => {
+  const actual = await vi.importActual('@gemini-code/core');
+  return {
+    ...actual,
+    FileDiscoveryService: vi.fn().mockImplementation(() => ({
+      initialize: vi.fn(),
+    })),
+    createToolRegistry: vi.fn().mockResolvedValue({}),
+  };
+});
+
+describe('Configuration Integration Tests', () => {
+  let tempDir: string;
+  let originalEnv: NodeJS.ProcessEnv;
+
+  beforeEach(() => {
+    tempDir = fs.mkdtempSync(path.join(tmpdir(), 'gemini-cli-test-'));
+    originalEnv = { ...process.env };
+    process.env.GEMINI_API_KEY = 'test-api-key';
+    vi.clearAllMocks();
+  });
+
+  afterEach(() => {
+    process.env = originalEnv;
+    if (fs.existsSync(tempDir)) {
+      fs.rmSync(tempDir, { recursive: true });
+    }
+  });
+
+  describe('File Filtering Configuration', () => {
+    it('should load default file filtering settings', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        fileFilteringRespectGitIgnore: undefined, // Should default to true
+        fileFilteringAllowBuildArtifacts: undefined, // Should default to false
+      };
+
+      const config = new Config(configParams);
+
+      expect(config.getFileFilteringRespectGitIgnore()).toBe(true);
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(false);
+    });
+
+    it('should load custom file filtering settings from configuration', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        fileFilteringRespectGitIgnore: false,
+        fileFilteringAllowBuildArtifacts: true,
+      };
+
+      const config = new Config(configParams);
+
+      expect(config.getFileFilteringRespectGitIgnore()).toBe(false);
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(true);
+    });
+
+    it('should merge user and workspace file filtering settings', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        fileFilteringRespectGitIgnore: true,
+        fileFilteringAllowBuildArtifacts: true,
+      };
+
+      const config = new Config(configParams);
+
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(true);
+      expect(config.getFileFilteringRespectGitIgnore()).toBe(true);
+    });
+  });
+
+  describe('Configuration Integration', () => {
+    it('should handle partial configuration objects gracefully', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        fileFilteringRespectGitIgnore: false,
+        fileFilteringAllowBuildArtifacts: undefined, // Should default to false
+      };
+
+      const config = new Config(configParams);
+
+      // Specified settings should be applied
+      expect(config.getFileFilteringRespectGitIgnore()).toBe(false);
+
+      // Missing settings should use defaults
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(false);
+    });
+
+    it('should handle empty configuration objects gracefully', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        fileFilteringRespectGitIgnore: undefined,
+        fileFilteringAllowBuildArtifacts: undefined,
+      };
+
+      const config = new Config(configParams);
+
+      // All settings should use defaults
+      expect(config.getFileFilteringRespectGitIgnore()).toBe(true);
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(false);
+    });
+
+    it('should handle missing configuration sections gracefully', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        // Missing fileFiltering configuration
+      };
+
+      const config = new Config(configParams);
+
+      // All git-aware settings should use defaults
+      expect(config.getFileFilteringRespectGitIgnore()).toBe(true);
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(false);
+    });
+  });
+
+  describe('Real-world Configuration Scenarios', () => {
+    it('should handle a security-focused configuration', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        fileFilteringRespectGitIgnore: true,
+        fileFilteringAllowBuildArtifacts: false,
+      };
+
+      const config = new Config(configParams);
+
+      expect(config.getFileFilteringRespectGitIgnore()).toBe(true);
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(false);
+    });
+
+    it('should handle a development-focused configuration', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        fileFilteringRespectGitIgnore: true,
+        fileFilteringAllowBuildArtifacts: true,
+      };
+
+      const config = new Config(configParams);
+
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(true);
+    });
+
+    it('should handle a CI/CD environment configuration', async () => {
+      const configParams: ConfigParameters = {
+        apiKey: 'test-key',
+        model: 'test-model',
+        sandbox: false,
+        targetDir: tempDir,
+        debugMode: false,
+        userAgent: 'test-agent',
+        fileFilteringRespectGitIgnore: false, // CI might need to see all files
+        fileFilteringAllowBuildArtifacts: true,
+      };
+
+      const config = new Config(configParams);
+
+      expect(config.getFileFilteringRespectGitIgnore()).toBe(false);
+      expect(config.getFileFilteringAllowBuildArtifacts()).toBe(true);
+    });
+  });
+});