chore: cleanup and apply requested changes

apps/cli/biome.json

@@ -1,7 +0,0 @@
-{
-	"$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
-	"extends": ["../../biome.json"],
-	"files": {
-		"include": ["src/**/*.ts", "src/**/*.tsx"]
-	}
-}

apps/cli/src/commands/list.command.ts

@@ -93,7 +93,10 @@ export class ListTasksCommand extends Command {
 				this.displayResults(result, options);
 			}
 		} catch (error: any) {
-			console.error(chalk.red(`Error: ${error.message}`));
+			const msg = error?.getSanitizedDetails?.() ?? {
+				message: error?.message ?? String(error)
+			};
+			console.error(chalk.red(`Error: ${msg.message || 'Unexpected error'}`));
 			if (error.stack && process.env.DEBUG) {
 				console.error(chalk.gray(error.stack));
 			}

package-lock.json

@@ -77,7 +77,8 @@
 				"prettier": "^3.5.3",
 				"supertest": "^7.1.0",
 				"tsup": "^8.5.0",
-				"tsx": "^4.16.2"
+				"tsx": "^4.16.2",
+				"typescript": "^5.9.2"
 			},
 			"engines": {
 				"node": ">=18.0.0"
@@ -24783,7 +24784,9 @@
 			}
 		},
 		"node_modules/typescript": {
-			"version": "5.8.3",
+			"version": "5.9.2",
+			"resolved": "https://registry.npmjs.org/typescript/-/typescript-5.9.2.tgz",
+			"integrity": "sha512-CWBzXQrc/qOkhidw1OzBTQuYRbfyxDXJMVJ1XNwUHGROVmuaeiEm3OslpZ1RV96d7SKKjZKrSJu3+t/xlw3R9A==",
 			"dev": true,
 			"license": "Apache-2.0",
 			"bin": {

package.json

@@ -136,6 +136,7 @@
 		"prettier": "^3.5.3",
 		"supertest": "^7.1.0",
 		"tsup": "^8.5.0",
-		"tsx": "^4.16.2"
+		"tsx": "^4.16.2",
+		"typescript": "^5.9.2"
 	}
 }

packages/tm-core/biome.json

@@ -1,104 +0,0 @@
-{
-	"$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
-	"vcs": {
-		"enabled": true,
-		"clientKind": "git",
-		"useIgnoreFile": true,
-		"defaultBranch": "main"
-	},
-	"files": {
-		"include": ["src/**/*.ts", "tests/**/*.ts", "*.ts", "*.js", "*.json"],
-		"ignore": [
-			"**/node_modules",
-			"**/dist",
-			"**/.git",
-			"**/coverage",
-			"**/*.d.ts"
-		]
-	},
-	"formatter": {
-		"enabled": true,
-		"formatWithErrors": false,
-		"indentStyle": "tab",
-		"indentWidth": 2,
-		"lineEnding": "lf",
-		"lineWidth": 100,
-		"attributePosition": "auto"
-	},
-	"organizeImports": {
-		"enabled": true
-	},
-	"linter": {
-		"enabled": true,
-		"rules": {
-			"recommended": true,
-			"style": {
-				"noNonNullAssertion": "off",
-				"useConst": "error",
-				"useImportType": "warn",
-				"useTemplate": "warn",
-				"noUselessElse": "warn",
-				"noVar": "error"
-			},
-			"correctness": {
-				"noUnusedVariables": "warn",
-				"noUnusedImports": "error",
-				"useExhaustiveDependencies": "warn"
-			},
-			"complexity": {
-				"noBannedTypes": "error",
-				"noForEach": "off",
-				"noStaticOnlyClass": "warn",
-				"noUselessConstructor": "error",
-				"noUselessTypeConstraint": "error",
-				"useArrowFunction": "off"
-			},
-			"suspicious": {
-				"noExplicitAny": "warn",
-				"noImplicitAnyLet": "error",
-				"noArrayIndexKey": "warn",
-				"noAsyncPromiseExecutor": "error",
-				"noDoubleEquals": "warn",
-				"noRedundantUseStrict": "error"
-			},
-			"security": {
-				"noGlobalEval": "error"
-			},
-			"performance": {
-				"noAccumulatingSpread": "warn",
-				"noDelete": "warn"
-			},
-			"a11y": {
-				"recommended": false
-			}
-		}
-	},
-	"javascript": {
-		"formatter": {
-			"enabled": true,
-			"quoteStyle": "single",
-			"jsxQuoteStyle": "double",
-			"quoteProperties": "asNeeded",
-			"trailingCommas": "none",
-			"semicolons": "always",
-			"arrowParentheses": "always",
-			"bracketSpacing": true,
-			"bracketSameLine": false
-		},
-		"parser": {
-			"unsafeParameterDecoratorsEnabled": true
-		}
-	},
-	"json": {
-		"formatter": {
-			"enabled": true,
-			"indentStyle": "tab",
-			"lineWidth": 100,
-			"trailingCommas": "none"
-		},
-		"parser": {
-			"allowComments": true,
-			"allowTrailingCommas": false
-		}
-	}
-}

packages/tm-core/src/errors/index.ts

@@ -3,6 +3,15 @@
  * This file exports all custom error types and error handling utilities
  */
 
+// Export the main TaskMasterError class
+export {
+	TaskMasterError,
+	ERROR_CODES,
+	type ErrorCode,
+	type ErrorContext,
+	type SerializableError
+} from './task-master-error.js';
+
 // Error implementations will be defined here
 // export * from './task-errors.js';
 // export * from './storage-errors.js';

packages/tm-core/src/storage/file-storage/file-operations.ts

@@ -32,7 +32,10 @@ export class FileOperations {
 	/**
 	 * Write JSON file with atomic operation and locking
 	 */
-	async writeJson(filePath: string, data: FileStorageData | any): Promise<void> {
+	async writeJson(
+		filePath: string,
+		data: FileStorageData | any
+	): Promise<void> {
 		// Use file locking to prevent concurrent writes
 		const lockKey = filePath;
 		const existingLock = this.fileLocks.get(lockKey);
@@ -109,7 +112,9 @@ export class FileOperations {
 		try {
 			await fs.mkdir(dirPath, { recursive: true });
 		} catch (error: any) {
-			throw new Error(`Failed to create directory ${dirPath}: ${error.message}`);
+			throw new Error(
+				`Failed to create directory ${dirPath}: ${error.message}`
+			);
 		}
 	}
 
@@ -133,7 +138,9 @@ export class FileOperations {
 		try {
 			await fs.rename(oldPath, newPath);
 		} catch (error: any) {
-			throw new Error(`Failed to move file from ${oldPath} to ${newPath}: ${error.message}`);
+			throw new Error(
+				`Failed to move file from ${oldPath} to ${newPath}: ${error.message}`
+			);
 		}
 	}
 
@@ -144,7 +151,9 @@ export class FileOperations {
 		try {
 			await fs.copyFile(srcPath, destPath);
 		} catch (error: any) {
-			throw new Error(`Failed to copy file from ${srcPath} to ${destPath}: ${error.message}`);
+			throw new Error(
+				`Failed to copy file from ${srcPath} to ${destPath}: ${error.message}`
+			);
 		}
 	}
 

packages/tm-core/src/storage/file-storage/file-storage.ts

@@ -136,7 +136,12 @@ export class FileStorage implements IStorage {
 		const normalizedTasks = this.normalizeTaskIds(tasks);
 
 		// Update the specific tag in the existing data structure
-		if (this.formatHandler.detectFormat(existingData) === 'legacy' || Object.keys(existingData).some(key => key !== 'tasks' && key !== 'metadata')) {
+		if (
+			this.formatHandler.detectFormat(existingData) === 'legacy' ||
+			Object.keys(existingData).some(
+				(key) => key !== 'tasks' && key !== 'metadata'
+			)
+		) {
 			// Legacy format - update/add the tag
 			existingData[resolvedTag] = {
 				tasks: normalizedTasks,
@@ -177,7 +182,8 @@ export class FileStorage implements IStorage {
 			...task,
 			id: String(task.id), // Task IDs are strings
 			dependencies: task.dependencies?.map((dep) => String(dep)) || [],
-			subtasks: task.subtasks?.map((subtask) => ({
+			subtasks:
+				task.subtasks?.map((subtask) => ({
 					...subtask,
 					id: Number(subtask.id), // Subtask IDs are numbers
 					parentId: String(subtask.parentId) // Parent ID is string (Task ID)

packages/tm-core/src/storage/file-storage/format-handler.ts

@@ -27,7 +27,9 @@ export class FormatHandler {
 
 		// Check if this uses the legacy format with tag keys
 		// Legacy format has keys that are not 'tasks' or 'metadata'
-		const hasLegacyFormat = keys.some(key => key !== 'tasks' && key !== 'metadata');
+		const hasLegacyFormat = keys.some(
+			(key) => key !== 'tasks' && key !== 'metadata'
+		);
 
 		return hasLegacyFormat ? 'legacy' : 'standard';
 	}
@@ -60,7 +62,9 @@ export class FormatHandler {
 		}
 
 		// If we're looking for 'master' tag but it doesn't exist, try the first available tag
-		const availableKeys = Object.keys(data).filter(key => key !== 'tasks' && key !== 'metadata');
+		const availableKeys = Object.keys(data).filter(
+			(key) => key !== 'tasks' && key !== 'metadata'
+		);
 		if (tag === 'master' && availableKeys.length > 0) {
 			const firstTag = availableKeys[0];
 			const tagData = data[firstTag];
@@ -97,7 +101,10 @@ export class FormatHandler {
 	/**
 	 * Extract metadata from legacy format
 	 */
-	private extractMetadataFromLegacy(data: any, tag: string): TaskMetadata | null {
+	private extractMetadataFromLegacy(
+		data: any,
+		tag: string
+	): TaskMetadata | null {
 		if (tag in data) {
 			const tagData = data[tag];
 			// Generate metadata if not present in legacy format
@@ -108,7 +115,9 @@ export class FormatHandler {
 		}
 
 		// If we're looking for 'master' tag but it doesn't exist, try the first available tag
-		const availableKeys = Object.keys(data).filter(key => key !== 'tasks' && key !== 'metadata');
+		const availableKeys = Object.keys(data).filter(
+			(key) => key !== 'tasks' && key !== 'metadata'
+		);
 		if (tag === 'master' && availableKeys.length > 0) {
 			const firstTag = availableKeys[0];
 			const tagData = data[firstTag];
@@ -141,7 +150,7 @@ export class FormatHandler {
 		if (format === 'legacy') {
 			// Return all tag keys from legacy format
 			const keys = Object.keys(data);
-			return keys.filter(key => key !== 'tasks' && key !== 'metadata');
+			return keys.filter((key) => key !== 'tasks' && key !== 'metadata');
 		}
 
 		// Standard format - just has 'master' tag
@@ -215,7 +224,8 @@ export class FormatHandler {
 			...task,
 			id: String(task.id), // Task IDs are strings
 			dependencies: task.dependencies?.map((dep) => String(dep)) || [],
-			subtasks: task.subtasks?.map((subtask) => ({
+			subtasks:
+				task.subtasks?.map((subtask) => ({
 					...subtask,
 					id: Number(subtask.id), // Subtask IDs are numbers
 					parentId: String(subtask.parentId) // Parent ID is string (Task ID)

packages/tm-core/src/storage/file-storage/index.ts

@@ -2,7 +2,11 @@
  * @fileoverview Exports for file storage components
  */
 
-export { FormatHandler, type FileStorageData, type FileFormat } from './format-handler.js';
+export {
+	FormatHandler,
+	type FileStorageData,
+	type FileFormat
+} from './format-handler.js';
 export { FileOperations } from './file-operations.js';
 export { PathResolver } from './path-resolver.js';
 

packages/tm-core/tsconfig.json

@@ -28,12 +28,12 @@
 		"isolatedModules": true,
 		"paths": {
 			"@/*": ["./src/*"],
-			"@/types": ["./src/types/index"],
+			"@/types": ["./src/types"],
-			"@/providers": ["./src/providers/index"],
+			"@/providers": ["./src/providers"],
-			"@/storage": ["./src/storage/index"],
+			"@/storage": ["./src/storage"],
-			"@/parser": ["./src/parser/index"],
+			"@/parser": ["./src/parser"],
-			"@/utils": ["./src/utils/index"],
+			"@/utils": ["./src/utils"],
-			"@/errors": ["./src/errors/index"]
+			"@/errors": ["./src/errors"]
 		}
 	},
 	"include": ["src/**/*"],

packages/tm-core/vitest.config.ts

@@ -1,6 +1,11 @@
 import path from 'node:path';
+import { fileURLToPath } from 'node:url';
 import { defineConfig } from 'vitest/config';
 
+// __dirname in ESM
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
+
 export default defineConfig({
 	test: {
 		globals: true,
@@ -8,6 +13,7 @@ export default defineConfig({
 		include: [
 			'tests/**/*.test.ts',
 			'tests/**/*.spec.ts',
+			'tests/{unit,integration,e2e}/**/*.{test,spec}.ts',
 			'src/**/*.test.ts',
 			'src/**/*.spec.ts'
 		],
@@ -22,7 +28,7 @@ export default defineConfig({
 				'**/*.test.ts',
 				'**/*.spec.ts',
 				'**/*.d.ts',
-				'**/index.ts'
+				'src/index.ts'
 			],
 			thresholds: {
 				branches: 80,

tsconfig.json

@@ -3,6 +3,8 @@
 		"target": "ES2022",
 		"module": "ESNext",
 		"moduleResolution": "bundler",
+		"lib": ["ES2022"],
+		"types": ["node"],
 		"allowJs": true,
 		"resolveJsonModule": true,
 		"esModuleInterop": true,
@@ -10,13 +12,7 @@
 		"strict": true,
 		"skipLibCheck": true,
 		"noEmit": true,
-		"baseUrl": ".",
+		"baseUrl": "."
-		"paths": {
-			"@tm/core": ["packages/tm-core/src/index.ts"],
-			"@tm/core/*": ["packages/tm-core/src/*"],
-			"@tm/cli": ["apps/cli/src/index.ts"],
-			"@tm/cli/*": ["apps/cli/src/*"]
-		}
 	},
 	"tsx": {
 		"tsconfig": {

tsup.config.ts

@@ -10,8 +10,6 @@ export default defineConfig({
 	splitting: false,
 	sourcemap: true,
 	clean: true,
-	shims: true,
-	dts: true,
 	bundle: true, // Bundle everything into one file
 	outDir: 'dist',
 	// Handle TypeScript imports transparently