diff --git a/packages/tm-core/src/auth/auth-manager.test.ts b/packages/tm-core/src/auth/auth-manager.test.ts
index e7238921..04178764 100644
--- a/packages/tm-core/src/auth/auth-manager.test.ts
+++ b/packages/tm-core/src/auth/auth-manager.test.ts
@@ -21,6 +21,7 @@ describe('AuthManager Singleton', () => {
 	beforeEach(() => {
 		// Reset singleton before each test
 		AuthManager.resetInstance();
+		vi.clearAllMocks();
 	});
 
 	it('should return the same instance on multiple calls', () => {
@@ -39,6 +40,12 @@ describe('AuthManager Singleton', () => {
 
 		const instance = AuthManager.getInstance(config);
 		expect(instance).toBeDefined();
+		
+		// Verify the config is passed to internal components
+		// This would be observable when attempting operations that use the config
+		// For example, getCredentials would look in the configured file path
+		const credentials = instance.getCredentials();
+		expect(credentials).toBeNull(); // File doesn't exist, but it should check the right path
 	});
 
 	it('should warn when config is provided after initialization', () => {
diff --git a/packages/tm-core/src/auth/auth-manager.ts b/packages/tm-core/src/auth/auth-manager.ts
index f59931cf..1d678906 100644
--- a/packages/tm-core/src/auth/auth-manager.ts
+++ b/packages/tm-core/src/auth/auth-manager.ts
@@ -41,7 +41,7 @@ export class AuthManager {
 				'getInstance called with config after initialization; config is ignored.'
 			);
 		}
-		return AuthManager.instance;
+		return AuthManager.instance!;
 	}
 
 	/**
@@ -74,29 +74,6 @@ export class AuthManager {
 		return this.oauthService.getAuthorizationUrl();
 	}
 
-	/**
-	 * Authenticate with API key
-	 * Note: This would require a custom implementation or Supabase RLS policies
-	 */
-	async authenticateWithApiKey(apiKey: string): Promise<AuthCredentials> {
-		const token = apiKey.trim();
-		if (!token || token.length < 10) {
-			throw new AuthenticationError('Invalid API key', 'INVALID_API_KEY');
-		}
-
-		const authData: AuthCredentials = {
-			token,
-			tokenType: 'api_key',
-			userId: 'api-user',
-			email: undefined,
-			expiresAt: undefined, // API keys don't expire
-			savedAt: new Date().toISOString()
-		};
-
-		this.credentialStore.saveCredentials(authData);
-		return authData;
-	}
-
 	/**
 	 * Refresh authentication token
 	 */
diff --git a/packages/tm-core/src/auth/credential-store.test.ts b/packages/tm-core/src/auth/credential-store.test.ts
new file mode 100644
index 00000000..93330521
--- /dev/null
+++ b/packages/tm-core/src/auth/credential-store.test.ts
@@ -0,0 +1,414 @@
+/**
+ * Tests for CredentialStore with numeric and string timestamp handling
+ */
+
+import { describe, it, expect, beforeEach, vi, afterEach } from 'vitest';
+import { CredentialStore } from './credential-store.js';
+import { AuthenticationError } from './types.js';
+import type { AuthCredentials } from './types.js';
+import fs from 'fs';
+import path from 'path';
+import os from 'os';
+
+// Mock fs module
+vi.mock('fs');
+
+// Mock logger
+const mockLogger = {
+	warn: vi.fn(),
+	info: vi.fn(),
+	debug: vi.fn(),
+	error: vi.fn()
+};
+
+vi.mock('../logger/index.js', () => ({
+	getLogger: () => mockLogger
+}));
+
+describe('CredentialStore', () => {
+	let store: CredentialStore;
+	const testDir = '/test/config';
+	const configFile = '/test/config/auth.json';
+
+	beforeEach(() => {
+		vi.clearAllMocks();
+		store = new CredentialStore({
+			configDir: testDir,
+			configFile: configFile,
+			baseUrl: 'https://api.test.com'
+		});
+	});
+
+	afterEach(() => {
+		vi.restoreAllMocks();
+	});
+
+	describe('getCredentials with timestamp migration', () => {
+		it('should handle string ISO timestamp correctly', () => {
+			const futureDate = new Date(Date.now() + 3600000); // 1 hour from now
+			const mockCredentials: AuthCredentials = {
+				token: 'test-token',
+				userId: 'user-123',
+				email: 'test@example.com',
+				expiresAt: futureDate.toISOString(),
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify(mockCredentials));
+
+			const result = store.getCredentials();
+
+			expect(result).not.toBeNull();
+			expect(result?.token).toBe('test-token');
+			// The timestamp should be normalized to numeric milliseconds
+			expect(typeof result?.expiresAt).toBe('number');
+			expect(result?.expiresAt).toBe(futureDate.getTime());
+		});
+
+		it('should handle numeric timestamp correctly', () => {
+			const futureTimestamp = Date.now() + 7200000; // 2 hours from now
+			const mockCredentials = {
+				token: 'test-token',
+				userId: 'user-456',
+				email: 'test2@example.com',
+				expiresAt: futureTimestamp,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify(mockCredentials));
+
+			const result = store.getCredentials();
+
+			expect(result).not.toBeNull();
+			expect(result?.token).toBe('test-token');
+			// Numeric timestamp should remain as-is
+			expect(typeof result?.expiresAt).toBe('number');
+			expect(result?.expiresAt).toBe(futureTimestamp);
+		});
+
+		it('should reject invalid string timestamp', () => {
+			const mockCredentials = {
+				token: 'test-token',
+				userId: 'user-789',
+				expiresAt: 'invalid-date-string',
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify(mockCredentials));
+
+			const result = store.getCredentials();
+
+			expect(result).toBeNull();
+			expect(mockLogger.warn).toHaveBeenCalledWith(
+				'No valid expiration time provided for token'
+			);
+		});
+
+		it('should reject NaN timestamp', () => {
+			const mockCredentials = {
+				token: 'test-token',
+				userId: 'user-nan',
+				expiresAt: NaN,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify(mockCredentials));
+
+			const result = store.getCredentials();
+
+			expect(result).toBeNull();
+			expect(mockLogger.warn).toHaveBeenCalledWith(
+				'No valid expiration time provided for token'
+			);
+		});
+
+		it('should reject Infinity timestamp', () => {
+			const mockCredentials = {
+				token: 'test-token',
+				userId: 'user-inf',
+				expiresAt: Infinity,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify(mockCredentials));
+
+			const result = store.getCredentials();
+
+			expect(result).toBeNull();
+			expect(mockLogger.warn).toHaveBeenCalledWith(
+				'No valid expiration time provided for token'
+			);
+		});
+
+		it('should handle missing expiresAt field', () => {
+			const mockCredentials = {
+				token: 'test-token',
+				userId: 'user-no-expiry',
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+				// No expiresAt field
+			};
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify(mockCredentials));
+
+			const result = store.getCredentials();
+
+			expect(result).toBeNull();
+			expect(mockLogger.warn).toHaveBeenCalledWith(
+				'No valid expiration time provided for token'
+			);
+		});
+
+		it('should check token expiration correctly', () => {
+			const expiredTimestamp = Date.now() - 3600000; // 1 hour ago
+			const mockCredentials = {
+				token: 'expired-token',
+				userId: 'user-expired',
+				expiresAt: expiredTimestamp,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify(mockCredentials));
+
+			const result = store.getCredentials();
+
+			expect(result).toBeNull();
+			expect(mockLogger.warn).toHaveBeenCalledWith(
+				expect.stringContaining('Authentication token has expired'),
+				expect.any(Object)
+			);
+		});
+
+		it('should allow expired tokens when requested', () => {
+			const expiredTimestamp = Date.now() - 3600000; // 1 hour ago
+			const mockCredentials = {
+				token: 'expired-token',
+				userId: 'user-expired',
+				expiresAt: expiredTimestamp,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue(JSON.stringify(mockCredentials));
+
+			const result = store.getCredentials({ allowExpired: true });
+
+			expect(result).not.toBeNull();
+			expect(result?.token).toBe('expired-token');
+		});
+	});
+
+	describe('saveCredentials with timestamp normalization', () => {
+		beforeEach(() => {
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.mkdirSync).mockImplementation(() => undefined);
+			vi.mocked(fs.writeFileSync).mockImplementation(() => undefined);
+			vi.mocked(fs.renameSync).mockImplementation(() => undefined);
+		});
+
+		it('should normalize string timestamp to ISO string when saving', () => {
+			const futureDate = new Date(Date.now() + 3600000);
+			const credentials: AuthCredentials = {
+				token: 'test-token',
+				userId: 'user-123',
+				expiresAt: futureDate.toISOString(),
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			store.saveCredentials(credentials);
+
+			expect(fs.writeFileSync).toHaveBeenCalledWith(
+				expect.stringContaining('.tmp'),
+				expect.stringContaining('"expiresAt":'),
+				expect.any(Object)
+			);
+
+			// Check that the written data contains a valid ISO string
+			const writtenData = vi.mocked(fs.writeFileSync).mock.calls[0][1] as string;
+			const parsed = JSON.parse(writtenData);
+			expect(typeof parsed.expiresAt).toBe('string');
+			expect(new Date(parsed.expiresAt).toISOString()).toBe(parsed.expiresAt);
+		});
+
+		it('should convert numeric timestamp to ISO string when saving', () => {
+			const futureTimestamp = Date.now() + 7200000;
+			const credentials: AuthCredentials = {
+				token: 'test-token',
+				userId: 'user-456',
+				expiresAt: futureTimestamp,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			store.saveCredentials(credentials);
+
+			const writtenData = vi.mocked(fs.writeFileSync).mock.calls[0][1] as string;
+			const parsed = JSON.parse(writtenData);
+			expect(typeof parsed.expiresAt).toBe('string');
+			expect(new Date(parsed.expiresAt).getTime()).toBe(futureTimestamp);
+		});
+
+		it('should reject invalid string timestamp when saving', () => {
+			const credentials: AuthCredentials = {
+				token: 'test-token',
+				userId: 'user-789',
+				expiresAt: 'invalid-date' as any,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			expect(() => store.saveCredentials(credentials)).toThrow(AuthenticationError);
+			expect(() => store.saveCredentials(credentials)).toThrow('Invalid expiresAt format');
+		});
+
+		it('should reject NaN timestamp when saving', () => {
+			const credentials: AuthCredentials = {
+				token: 'test-token',
+				userId: 'user-nan',
+				expiresAt: NaN as any,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			expect(() => store.saveCredentials(credentials)).toThrow(AuthenticationError);
+			expect(() => store.saveCredentials(credentials)).toThrow('Invalid expiresAt format');
+		});
+
+		it('should reject Infinity timestamp when saving', () => {
+			const credentials: AuthCredentials = {
+				token: 'test-token',
+				userId: 'user-inf',
+				expiresAt: Infinity as any,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			expect(() => store.saveCredentials(credentials)).toThrow(AuthenticationError);
+			expect(() => store.saveCredentials(credentials)).toThrow('Invalid expiresAt format');
+		});
+
+		it('should handle missing expiresAt when saving', () => {
+			const credentials: AuthCredentials = {
+				token: 'test-token',
+				userId: 'user-no-expiry',
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+				// No expiresAt
+			};
+
+			store.saveCredentials(credentials);
+
+			const writtenData = vi.mocked(fs.writeFileSync).mock.calls[0][1] as string;
+			const parsed = JSON.parse(writtenData);
+			expect(parsed.expiresAt).toBeUndefined();
+		});
+
+		it('should not mutate the original credentials object', () => {
+			const originalTimestamp = Date.now() + 3600000;
+			const credentials: AuthCredentials = {
+				token: 'test-token',
+				userId: 'user-123',
+				expiresAt: originalTimestamp,
+				tokenType: 'standard',
+				savedAt: new Date().toISOString()
+			};
+
+			const originalCredentialsCopy = { ...credentials };
+
+			store.saveCredentials(credentials);
+
+			// Original object should not be modified
+			expect(credentials).toEqual(originalCredentialsCopy);
+			expect(credentials.expiresAt).toBe(originalTimestamp);
+		});
+	});
+
+	describe('corrupt file handling', () => {
+		it('should quarantine corrupt file on JSON parse error', () => {
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue('invalid json {');
+			vi.mocked(fs.renameSync).mockImplementation(() => undefined);
+
+			const result = store.getCredentials();
+
+			expect(result).toBeNull();
+			expect(fs.renameSync).toHaveBeenCalledWith(
+				configFile,
+				expect.stringContaining('.corrupt-')
+			);
+			expect(mockLogger.warn).toHaveBeenCalledWith(
+				expect.stringContaining('Quarantined corrupt auth file')
+			);
+		});
+
+		it('should handle quarantine failure gracefully', () => {
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readFileSync).mockReturnValue('invalid json {');
+			vi.mocked(fs.renameSync).mockImplementation(() => {
+				throw new Error('Permission denied');
+			});
+
+			const result = store.getCredentials();
+
+			expect(result).toBeNull();
+			expect(mockLogger.debug).toHaveBeenCalledWith(
+				expect.stringContaining('Could not quarantine corrupt file')
+			);
+		});
+	});
+
+	describe('cleanupCorruptFiles', () => {
+		it('should remove old corrupt files', () => {
+			const now = Date.now();
+			const oldFile = 'auth.json.corrupt-' + (now - 8 * 24 * 60 * 60 * 1000); // 8 days old
+			const newFile = 'auth.json.corrupt-' + (now - 1000); // 1 second old
+
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readdirSync).mockReturnValue([
+				{ name: oldFile, isFile: () => true },
+				{ name: newFile, isFile: () => true },
+				{ name: 'auth.json', isFile: () => true }
+			] as any);
+			vi.mocked(fs.statSync).mockImplementation((filePath) => {
+				if (filePath.includes(oldFile)) {
+					return { mtimeMs: now - 8 * 24 * 60 * 60 * 1000 } as any;
+				}
+				return { mtimeMs: now - 1000 } as any;
+			});
+			vi.mocked(fs.unlinkSync).mockImplementation(() => undefined);
+
+			store.cleanupCorruptFiles();
+
+			expect(fs.unlinkSync).toHaveBeenCalledWith(expect.stringContaining(oldFile));
+			expect(fs.unlinkSync).not.toHaveBeenCalledWith(expect.stringContaining(newFile));
+		});
+
+		it('should handle cleanup errors gracefully', () => {
+			vi.mocked(fs.existsSync).mockReturnValue(true);
+			vi.mocked(fs.readdirSync).mockImplementation(() => {
+				throw new Error('Permission denied');
+			});
+
+			// Should not throw
+			expect(() => store.cleanupCorruptFiles()).not.toThrow();
+			expect(mockLogger.debug).toHaveBeenCalledWith(
+				expect.stringContaining('Error during corrupt file cleanup')
+			);
+		});
+	});
+});
\ No newline at end of file
diff --git a/packages/tm-core/src/auth/credential-store.ts b/packages/tm-core/src/auth/credential-store.ts
index c4d47f85..bb8fd015 100644
--- a/packages/tm-core/src/auth/credential-store.ts
+++ b/packages/tm-core/src/auth/credential-store.ts
@@ -29,30 +29,38 @@ export class CredentialStore {
 				fs.readFileSync(this.config.configFile, 'utf-8')
 			) as AuthCredentials;
 
-			// Parse expiration time for validation (expects ISO string format)
+			// Normalize/migrate timestamps to numeric (handles both number and ISO string)
 			let expiresAtMs: number | undefined;
-			
-			if (authData.expiresAt) {
-				expiresAtMs = Date.parse(authData.expiresAt);
-				if (isNaN(expiresAtMs)) {
-					// Invalid date string - treat as expired
-					this.logger.error(`Invalid expiresAt format: ${authData.expiresAt}`);
-					return null;
-				}
+			if (typeof authData.expiresAt === 'number') {
+				expiresAtMs = Number.isFinite(authData.expiresAt) ? authData.expiresAt : undefined;
+			} else if (typeof authData.expiresAt === 'string') {
+				const parsed = Date.parse(authData.expiresAt);
+				expiresAtMs = Number.isNaN(parsed) ? undefined : parsed;
+			} else {
+				expiresAtMs = undefined;
 			}
 
-			// Check if token is expired (API keys never expire)
-			const isApiKey = authData.tokenType === 'api_key';
-			if (
-				!isApiKey &&
-				expiresAtMs &&
-				expiresAtMs < Date.now() &&
-				!options?.allowExpired
-			) {
-				this.logger.warn('Authentication token has expired');
+			// Validate expiration time for tokens
+			if (expiresAtMs === undefined) {
+				this.logger.warn('No valid expiration time provided for token');
 				return null;
 			}
 
+			// Update the authData with normalized timestamp
+			authData.expiresAt = expiresAtMs;
+
+			// Check if the token has expired
+			const now = Date.now();
+			const allowExpired = options?.allowExpired ?? false;
+			if (now >= expiresAtMs && !allowExpired) {
+				this.logger.warn('Authentication token has expired', {
+					expiresAt: authData.expiresAt,
+					currentTime: new Date(now).toISOString()
+				});
+				return null;
+			}
+
+			// Return valid token
 			return authData;
 		} catch (error) {
 			this.logger.error(
@@ -87,18 +95,29 @@ export class CredentialStore {
 				fs.mkdirSync(this.config.configDir, { recursive: true, mode: 0o700 });
 			}
 
-			// Add timestamp
-			authData.savedAt = new Date().toISOString();
+			// Add timestamp without mutating caller's object
+			authData = { ...authData, savedAt: new Date().toISOString() };
 			
-			// Validate expiresAt is a valid ISO string if present
-			if (authData.expiresAt) {
-				const ms = Date.parse(authData.expiresAt);
-				if (isNaN(ms)) {
+			// Validate and normalize expiresAt timestamp
+			if (authData.expiresAt !== undefined) {
+				let validTimestamp: number | undefined;
+				
+				if (typeof authData.expiresAt === 'number') {
+					validTimestamp = Number.isFinite(authData.expiresAt) ? authData.expiresAt : undefined;
+				} else if (typeof authData.expiresAt === 'string') {
+					const parsed = Date.parse(authData.expiresAt);
+					validTimestamp = Number.isNaN(parsed) ? undefined : parsed;
+				}
+				
+				if (validTimestamp === undefined) {
 					throw new AuthenticationError(
 						`Invalid expiresAt format: ${authData.expiresAt}`,
 						'SAVE_FAILED'
 					);
 				}
+				
+				// Store as ISO string for consistency
+				authData.expiresAt = new Date(validTimestamp).toISOString();
 			}
 
 			// Save credentials atomically with secure permissions
@@ -156,16 +175,19 @@ export class CredentialStore {
 		try {
 			const dir = path.dirname(this.config.configFile);
 			const baseName = path.basename(this.config.configFile);
-			const corruptPattern = new RegExp(`^${baseName}\\.corrupt-\\d+$`);
+			const escapedBaseName = baseName.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+			const corruptPattern = new RegExp(`^${escapedBaseName}\\.corrupt-\\d+$`);
 
 			if (!fs.existsSync(dir)) {
 				return;
 			}
 
-			const files = fs.readdirSync(dir);
+			const entries = fs.readdirSync(dir, { withFileTypes: true });
 			const now = Date.now();
 
-			for (const file of files) {
+			for (const entry of entries) {
+				if (!entry.isFile()) continue;
+				const file = entry.name;
 				if (corruptPattern.test(file)) {
 					const filePath = path.join(dir, file);
 					try {
diff --git a/packages/tm-core/src/auth/types.ts b/packages/tm-core/src/auth/types.ts
index a86250aa..a2dc5d72 100644
--- a/packages/tm-core/src/auth/types.ts
+++ b/packages/tm-core/src/auth/types.ts
@@ -7,8 +7,8 @@ export interface AuthCredentials {
 	refreshToken?: string;
 	userId: string;
 	email?: string;
-	expiresAt?: string;
-	tokenType?: 'standard' | 'api_key';
+	expiresAt?: string | number;
+	tokenType?: 'standard';
 	savedAt: string;
 }
 
@@ -57,7 +57,6 @@ export type AuthErrorCode =
 	| 'INVALID_STATE'
 	| 'NO_TOKEN'
 	| 'TOKEN_EXCHANGE_FAILED'
-	| 'INVALID_API_KEY'
 	| 'INVALID_CREDENTIALS'
 	| 'NO_REFRESH_TOKEN'
 	| 'NOT_AUTHENTICATED'
@@ -65,7 +64,10 @@ export type AuthErrorCode =
 	| 'CONFIG_MISSING'
 	| 'SAVE_FAILED'
 	| 'CLEAR_FAILED'
-	| 'STORAGE_ERROR';
+	| 'STORAGE_ERROR'
+	| 'NOT_SUPPORTED'
+	| 'REFRESH_FAILED'
+	| 'INVALID_RESPONSE';
 
 /**
  * Authentication error class
diff --git a/packages/tm-core/src/config/config-manager.ts b/packages/tm-core/src/config/config-manager.ts
index 51867b63..5ef5003a 100644
--- a/packages/tm-core/src/config/config-manager.ts
+++ b/packages/tm-core/src/config/config-manager.ts
@@ -142,17 +142,23 @@ export class ConfigManager {
 
 		// Return the configured type (including 'auto')
 		const storageType = storage?.type || 'auto';
+		const basePath = storage?.basePath;
 
 		if (storageType === 'api' || storageType === 'auto') {
 			return {
 				type: storageType,
+				basePath,
 				apiEndpoint: storage?.apiEndpoint,
 				apiAccessToken: storage?.apiAccessToken,
 				apiConfigured: Boolean(storage?.apiEndpoint || storage?.apiAccessToken)
 			};
 		}
 
-		return { type: storageType, apiConfigured: false };
+		return { 
+			type: storageType, 
+			basePath, 
+			apiConfigured: false 
+		};
 	}
 
 	/**
@@ -183,9 +189,10 @@ export class ConfigManager {
 	}
 
 	/**
-	 * Check if using API storage
+	 * Check if explicitly configured to use API storage
+	 * Excludes 'auto' type 
 	 */
-	isUsingApiStorage(): boolean {
+	isApiExplicitlyConfigured(): boolean {
 		return this.getStorageConfig().type === 'api';
 	}
 
@@ -218,6 +225,7 @@ export class ConfigManager {
 		await this.persistence.saveConfig(this.config);
 
 		// Re-initialize to respect precedence
+		this.initialized = false;
 		await this.initialize();
 	}
 
diff --git a/packages/tm-core/src/interfaces/configuration.interface.ts b/packages/tm-core/src/interfaces/configuration.interface.ts
index b41e5717..eecad240 100644
--- a/packages/tm-core/src/interfaces/configuration.interface.ts
+++ b/packages/tm-core/src/interfaces/configuration.interface.ts
@@ -88,6 +88,8 @@ export type StorageType = 'file' | 'api' | 'auto';
 export interface RuntimeStorageConfig {
 	/** Storage backend type */
 	type: StorageType;
+	/** Base path for file storage (if configured) */
+	basePath?: string;
 	/** API endpoint for API storage (Hamster integration) */
 	apiEndpoint?: string;
 	/** Access token for API authentication */
@@ -107,19 +109,15 @@ export interface RuntimeStorageConfig {
 export interface StorageSettings
 	extends Omit<RuntimeStorageConfig, 'apiConfigured'> {
 	/** Storage backend type - 'auto' detects based on auth status */
-	type: 'file' | 'api' | 'auto';
+	type: StorageType;
 	/** Base path for file storage */
 	basePath?: string;
-	/** API endpoint for API storage (Hamster integration) */
-	apiEndpoint?: string;
-	/** Access token for API authentication */
-	apiAccessToken?: string;
-	/**
-	 * Indicates whether API is configured (has endpoint or token)
+	/** 
+	 * Indicates whether API is configured 
 	 * @computed Derived automatically from presence of apiEndpoint or apiAccessToken
 	 * @internal Should not be set manually in user config - computed by ConfigManager
 	 */
-	apiConfigured?: boolean;
+	readonly apiConfigured?: boolean;
 	/** Enable automatic backups */
 	enableBackup: boolean;
 	/** Maximum number of backups to retain */
diff --git a/packages/tm-core/src/storage/storage-factory.ts b/packages/tm-core/src/storage/storage-factory.ts
index 60546d3c..873ff0f6 100644
--- a/packages/tm-core/src/storage/storage-factory.ts
+++ b/packages/tm-core/src/storage/storage-factory.ts
@@ -28,9 +28,10 @@ export class StorageFactory {
 		storageConfig: RuntimeStorageConfig,
 		projectPath: string
 	): IStorage {
-		// Wrap the storage config in the expected format
+		// Wrap the storage config in the expected format, including projectPath
+		// This ensures ApiStorage receives the projectPath for projectId
 		return StorageFactory.create(
-			{ storage: storageConfig } as Partial<IConfiguration>,
+			{ storage: storageConfig, projectPath } as Partial<IConfiguration>,
 			projectPath
 		);
 	}