feat: experimental, bundle our commands into bins in order to be able to remove --package

* Fix Cursor deeplink installation with copy-paste instructions (#723)

* detect git worktree

* add changeset

* add aliases and git flags

* add changeset

* rename and update test

* add store tasks in git functionality

* update changeset

* fix newline

* remove unused import

* update command wording

* update command option text

.changeset/nasty-berries-tan.md

@@ -1,5 +0,0 @@
----
-"task-master-ai": patch
----
-
-Fix issues with task creation/update where subtasks are being created like id: <parent_task>.<subtask> instead if just id: <subtask>

.changeset/vast-plants-exist.md

@@ -0,0 +1,22 @@
+---
+"task-master-ai": minor
+---
+
+- **Git Worktree Detection:**
+  - Now properly skips Git initialization when inside existing Git worktree
+  - Prevents accidental nested repository creation
+- **Flag System Overhaul:**
+  - `--git`/`--no-git` controls repository initialization
+  - `--aliases`/`--no-aliases` consistently manages shell alias creation
+  - `--git-tasks`/`--no-git-tasks` controls whether task files are stored in Git
+  - `--dry-run` accurately previews all initialization behaviors
+- **GitTasks Functionality:**
+  - New `--git-tasks` flag includes task files in Git (comments them out in .gitignore)
+  - New `--no-git-tasks` flag excludes task files from Git (default behavior)
+  - Supports both CLI and MCP interfaces with proper parameter passing
+
+**Implementation Details:**
+- Added explicit Git worktree detection before initialization
+- Refactored flag processing to ensure consistent behavior
+
+- Fixes #734

.cursor/rules/taskmaster.mdc

@@ -26,6 +26,7 @@ This document provides a detailed reference for interacting with Taskmaster, cov
     *   `--name <name>`: `Set the name for your project in Taskmaster's configuration.`
     *   `--description <text>`: `Provide a brief description for your project.`
     *   `--version <version>`: `Set the initial version for your project, e.g., '0.1.0'.`
+    *   `--no-git`: `Skip initializing a Git repository entirely.`
     *   `-y, --yes`: `Initialize Taskmaster quickly using default settings without interactive prompts.`
 *   **Usage:** Run this once at the beginning of a new project.
 *   **MCP Variant Description:** `Set up the basic Taskmaster file structure and configuration in the current directory for a new project by running the 'task-master init' command.`
@@ -36,6 +37,7 @@ This document provides a detailed reference for interacting with Taskmaster, cov
     *   `authorName`: `Author name.` (CLI: `--author <author>`)
     *   `skipInstall`: `Skip installing dependencies. Default is false.` (CLI: `--skip-install`)
     *   `addAliases`: `Add shell aliases tm and taskmaster. Default is false.` (CLI: `--aliases`)
+    *   `noGit`: `Skip initializing a Git repository entirely. Default is false.` (CLI: `--no-git`)
     *   `yes`: `Skip prompts and use defaults/provided arguments. Default is false.` (CLI: `-y, --yes`)
 *   **Usage:** Run this once at the beginning of a new project, typically via an integrated tool like Cursor. Operates on the current working directory of the MCP server. 
 *   **Important:** Once complete, you *MUST* parse a prd in order to generate tasks. There will be no tasks files until then. The next step after initializing should be to create a PRD using the example PRD in .taskmaster/templates/example_prd.txt. 

index.js

@@ -83,6 +83,11 @@ if (import.meta.url === `file://${process.argv[1]}`) {
 		.option('--skip-install', 'Skip installing dependencies')
 		.option('--dry-run', 'Show what would be done without making changes')
 		.option('--aliases', 'Add shell aliases (tm, taskmaster)')
+		.option('--no-aliases', 'Skip shell aliases (tm, taskmaster)')
+		.option('--git', 'Initialize Git repository')
+		.option('--no-git', 'Skip Git repository initialization')
+		.option('--git-tasks', 'Store tasks in Git')
+		.option('--no-git-tasks', 'No Git storage of tasks')
 		.action(async (cmdOptions) => {
 			try {
 				await runInitCLI(cmdOptions);

mcp-server/src/core/direct-functions/initialize-project.js

@@ -11,7 +11,7 @@ import { convertAllRulesToProfileRules } from '../../../../src/utils/rule-transf
 /**
  * Direct function wrapper for initializing a project.
  * Derives target directory from session, sets CWD, and calls core init logic.
- * @param {object} args - Arguments containing initialization options (addAliases, skipInstall, yes, projectRoot, rules)
+ * @param {object} args - Arguments containing initialization options (addAliases, initGit, storeTasksInGit, skipInstall, yes, projectRoot, rules)
  * @param {object} log - The FastMCP logger instance.
  * @param {object} context - The context object, must contain { session }.
  * @returns {Promise<{success: boolean, data?: any, error?: {code: string, message: string}}>} - Standard result object.
@@ -65,7 +65,9 @@ export async function initializeProjectDirect(args, log, context = {}) {
 		// Construct options ONLY from the relevant flags in args
 		// The core initializeProject operates in the current CWD, which we just set
 		const options = {
-			aliases: args.addAliases,
+			addAliases: args.addAliases,
+			initGit: args.initGit,
+			storeTasksInGit: args.storeTasksInGit,
 			skipInstall: args.skipInstall,
 			yes: true // Force yes mode
 		};

mcp-server/src/tools/initialize-project.js

@@ -23,8 +23,18 @@ export function registerInitializeProjectTool(server) {
 			addAliases: z
 				.boolean()
 				.optional()
-				.default(false)
+				.default(true)
 				.describe('Add shell aliases (tm, taskmaster) to shell config file.'),
+			initGit: z
+				.boolean()
+				.optional()
+				.default(true)
+				.describe('Initialize Git repository in project root.'),
+			storeTasksInGit: z
+				.boolean()
+				.optional()
+				.default(false)
+				.describe('Store tasks in Git (tasks.json and tasks/ directory).'),
 			yes: z
 				.boolean()
 				.optional()

package.json

@@ -1,13 +1,13 @@
 {
 	"name": "task-master-ai",
-	"version": "0.17.1",
+	"version": "0.17.1-test",
 	"description": "A task management system for ambitious AI-driven development that doesn't overwhelm and confuse Cursor.",
 	"main": "index.js",
 	"type": "module",
 	"bin": {
-		"task-master": "bin/task-master.js",
+		"task-master": "dist/task-master.cjs",
-		"task-master-mcp": "mcp-server/server.js",
+		"task-master-mcp": "dist/task-master-mcp.cjs",
-		"task-master-ai": "mcp-server/server.js"
+		"task-master-ai": "dist/task-master-mcp.cjs"
 	},
 	"scripts": {
 		"test": "node --experimental-vm-modules node_modules/.bin/jest",
@@ -22,7 +22,13 @@
 		"inspector": "npx @modelcontextprotocol/inspector node mcp-server/server.js",
 		"mcp-server": "node mcp-server/server.js",
 		"format-check": "biome format .",
-		"format": "biome format . --write"
+		"format": "biome format . --write",
+		"prebuild": "npm test",
+		"build": "vite build && npm run postbuild",
+		"postbuild": "node scripts/add-shebang.js",
+		"build:bundle": "npm run build",
+		"build:watch": "vite build --watch",
+		"test:build": "echo 'Testing bundled binaries:' && echo '🔧 CLI (task-master):' && node dist/task-master.cjs --version && echo '🔌 MCP (task-master-ai):' && node dist/task-master-mcp.cjs --help | head -5 && echo '✅ Both bundles work!'"
 	},
 	"keywords": [
 		"claude",
@@ -91,14 +97,11 @@
 		"url": "https://github.com/eyaltoledano/claude-task-master/issues"
 	},
 	"files": [
-		"scripts/**",
+		"dist/**",
-		"assets/**",
-		".cursor/**",
-		"README-task-master.md",
-		"index.js",
-		"bin/**",
 		"mcp-server/**",
-		"src/**"
+		"README-task-master.md",
+		".cursor/**",
+		"assets/**"
 	],
 	"overrides": {
 		"node-fetch": "^2.6.12",
@@ -108,15 +111,19 @@
 		"@biomejs/biome": "^1.9.4",
 		"@changesets/changelog-github": "^0.5.1",
 		"@changesets/cli": "^2.28.1",
+		"@rollup/plugin-json": "^6.1.0",
+		"@rollup/plugin-node-resolve": "^16.0.1",
 		"@types/jest": "^29.5.14",
 		"execa": "^8.0.1",
 		"ink": "^5.0.1",
 		"jest": "^29.7.0",
 		"jest-environment-node": "^29.7.0",
 		"mock-fs": "^5.5.0",
+		"pkg": "^5.8.1",
 		"prettier": "^3.5.3",
 		"react": "^18.3.1",
 		"supertest": "^7.1.0",
-		"tsx": "^4.16.2"
+		"tsx": "^4.16.2",
+		"vite": "^6.3.5"
 	}
-}
+}

scripts/add-shebang.js

@@ -0,0 +1,82 @@
+#!/usr/bin/env node
+
+import {
+	readFileSync,
+	writeFileSync,
+	chmodSync,
+	copyFileSync,
+	mkdirSync,
+	existsSync
+} from 'fs';
+import { join, dirname } from 'path';
+
+const bundlePaths = [
+	join(process.cwd(), 'dist/task-master.cjs'), // CLI tool
+	join(process.cwd(), 'dist/task-master-mcp.cjs') // MCP server
+];
+
+try {
+	// Copy necessary asset files to dist
+	const assetsToCopy = [
+		{
+			src: 'scripts/modules/supported-models.json',
+			dest: 'dist/supported-models.json'
+		},
+		{ src: 'README-task-master.md', dest: 'dist/README-task-master.md' }
+	];
+
+	console.log('📁 Copying assets...');
+	for (const asset of assetsToCopy) {
+		const srcPath = join(process.cwd(), asset.src);
+		const destPath = join(process.cwd(), asset.dest);
+
+		if (existsSync(srcPath)) {
+			// Ensure destination directory exists
+			const destDir = dirname(destPath);
+			if (!existsSync(destDir)) {
+				mkdirSync(destDir, { recursive: true });
+			}
+
+			copyFileSync(srcPath, destPath);
+			console.log(`  ✅ Copied ${asset.src} → ${asset.dest}`);
+		} else {
+			console.log(`  ⚠️  Source not found: ${asset.src}`);
+		}
+	}
+
+	// Process each bundle file
+	for (const bundlePath of bundlePaths) {
+		const fileName = bundlePath.split('/').pop();
+
+		if (!existsSync(bundlePath)) {
+			console.log(`⚠️  Bundle not found: ${fileName}`);
+			continue;
+		}
+
+		// Read the existing bundle
+		const bundleContent = readFileSync(bundlePath, 'utf8');
+
+		// Add shebang if it doesn't already exist
+		if (!bundleContent.startsWith('#!/usr/bin/env node')) {
+			const contentWithShebang = '#!/usr/bin/env node\n' + bundleContent;
+			writeFileSync(bundlePath, contentWithShebang);
+			console.log(`✅ Added shebang to ${fileName}`);
+		} else {
+			console.log(`✅ Shebang already exists in ${fileName}`);
+		}
+
+		// Make it executable
+		chmodSync(bundlePath, 0o755);
+		console.log(`✅ Made ${fileName} executable`);
+	}
+
+	console.log('📦 Both bundles ready:');
+	console.log('  🔧 CLI tool: dist/task-master.cjs');
+	console.log('  🔌 MCP server: dist/task-master-mcp.cjs');
+	console.log('🧪 Test with:');
+	console.log('  node dist/task-master.cjs --version');
+	console.log('  node dist/task-master-mcp.cjs --help');
+} catch (error) {
+	console.error('❌ Post-build failed:', error.message);
+	process.exit(1);
+}

scripts/init.js

@@ -23,6 +23,8 @@ import figlet from 'figlet';
 import boxen from 'boxen';
 import gradient from 'gradient-string';
 import { isSilentMode } from './modules/utils.js';
+import { insideGitWorkTree } from './modules/utils/git-utils.js';
+import { manageGitignoreFile } from '../src/utils/manage-gitignore.js';
 import { RULE_PROFILES } from '../src/constants/profiles.js';
 import {
 	convertAllRulesToProfileRules,
@@ -320,6 +322,30 @@ async function initializeProject(options = {}) {
 	// 	console.log('==================================================');
 	// }
 
+	// Handle boolean aliases flags
+	if (options.aliases === true) {
+		options.addAliases = true; // --aliases flag provided
+	} else if (options.aliases === false) {
+		options.addAliases = false; // --no-aliases flag provided
+	}
+	// If options.aliases and options.noAliases are undefined, we'll prompt for it
+
+	// Handle boolean git flags
+	if (options.git === true) {
+		options.initGit = true; // --git flag provided
+	} else if (options.git === false) {
+		options.initGit = false; // --no-git flag provided
+	}
+	// If options.git and options.noGit are undefined, we'll prompt for it
+
+	// Handle boolean gitTasks flags
+	if (options.gitTasks === true) {
+		options.storeTasksInGit = true; // --git-tasks flag provided
+	} else if (options.gitTasks === false) {
+		options.storeTasksInGit = false; // --no-git-tasks flag provided
+	}
+	// If options.gitTasks and options.noGitTasks are undefined, we'll prompt for it
+
 	const skipPrompts = options.yes || (options.name && options.description);
 
 	// if (!isSilentMode()) {
@@ -343,21 +369,44 @@ async function initializeProject(options = {}) {
 		const projectVersion = options.version || '0.1.0';
 		const authorName = options.author || 'Vibe coder';
 		const dryRun = options.dryRun || false;
-		const addAliases = options.aliases || false;
+		const addAliases =
+			options.addAliases !== undefined ? options.addAliases : true; // Default to true if not specified
+		const initGit = options.initGit !== undefined ? options.initGit : true; // Default to true if not specified
+		const storeTasksInGit =
+			options.storeTasksInGit !== undefined ? options.storeTasksInGit : false; // Default to false if not specified
 
 		if (dryRun) {
 			log('info', 'DRY RUN MODE: No files will be modified');
 			log('info', 'Would initialize Task Master project');
 			log('info', 'Would create/update necessary project files');
-			if (addAliases) {
+
-				log('info', 'Would add shell aliases for task-master');
+			// Show flag-specific behavior
-			}
+			log(
+				'info',
+				`${addAliases ? 'Would add shell aliases (tm, taskmaster)' : 'Would skip shell aliases'}`
+			);
+			log(
+				'info',
+				`${initGit ? 'Would initialize Git repository' : 'Would skip Git initialization'}`
+			);
+			log(
+				'info',
+				`${storeTasksInGit ? 'Would store tasks in Git' : 'Would exclude tasks from Git'}`
+			);
+
 			return {
 				dryRun: true
 			};
 		}
 
-		createProjectStructure(addAliases, dryRun, options, selectedRuleProfiles);
+		createProjectStructure(
+			addAliases,
+			initGit,
+			storeTasksInGit,
+			dryRun,
+			options,
+			selectedRuleProfiles
+		);
 	} else {
 		// Interactive logic
 		log('info', 'Required options not provided, proceeding with prompts.');
@@ -367,14 +416,45 @@ async function initializeProject(options = {}) {
 				input: process.stdin,
 				output: process.stdout
 			});
-			// Only prompt for shell aliases
+			// Prompt for shell aliases (skip if --aliases or --no-aliases flag was provided)
-			const addAliasesInput = await promptQuestion(
+			let addAliasesPrompted = true; // Default to true
-				rl,
+			if (options.addAliases !== undefined) {
-				chalk.cyan(
+				addAliasesPrompted = options.addAliases; // Use flag value if provided
-					'Add shell aliases for task-master? This lets you type "tm" instead of "task-master" (Y/n): '
+			} else {
-				)
+				const addAliasesInput = await promptQuestion(
-			);
+					rl,
-			const addAliasesPrompted = addAliasesInput.trim().toLowerCase() !== 'n';
+					chalk.cyan(
+						'Add shell aliases for task-master? This lets you type "tm" instead of "task-master" (Y/n): '
+					)
+				);
+				addAliasesPrompted = addAliasesInput.trim().toLowerCase() !== 'n';
+			}
+
+			// Prompt for Git initialization (skip if --git or --no-git flag was provided)
+			let initGitPrompted = true; // Default to true
+			if (options.initGit !== undefined) {
+				initGitPrompted = options.initGit; // Use flag value if provided
+			} else {
+				const gitInitInput = await promptQuestion(
+					rl,
+					chalk.cyan('Initialize a Git repository in project root? (Y/n): ')
+				);
+				initGitPrompted = gitInitInput.trim().toLowerCase() !== 'n';
+			}
+
+			// Prompt for Git tasks storage (skip if --git-tasks or --no-git-tasks flag was provided)
+			let storeGitPrompted = false; // Default to false
+			if (options.storeTasksInGit !== undefined) {
+				storeGitPrompted = options.storeTasksInGit; // Use flag value if provided
+			} else {
+				const gitTasksInput = await promptQuestion(
+					rl,
+					chalk.cyan(
+						'Store tasks in Git (tasks.json and tasks/ directory)? (y/N): '
+					)
+				);
+				storeGitPrompted = gitTasksInput.trim().toLowerCase() === 'y';
+			}
 
 			// Confirm settings...
 			console.log('\nTask Master Project settings:');
@@ -384,6 +464,14 @@ async function initializeProject(options = {}) {
 				),
 				chalk.white(addAliasesPrompted ? 'Yes' : 'No')
 			);
+			console.log(
+				chalk.blue('Initialize Git repository in project root:'),
+				chalk.white(initGitPrompted ? 'Yes' : 'No')
+			);
+			console.log(
+				chalk.blue('Store tasks in Git (tasks.json and tasks/ directory):'),
+				chalk.white(storeGitPrompted ? 'Yes' : 'No')
+			);
 
 			const confirmInput = await promptQuestion(
 				rl,
@@ -422,9 +510,21 @@ async function initializeProject(options = {}) {
 				log('info', 'DRY RUN MODE: No files will be modified');
 				log('info', 'Would initialize Task Master project');
 				log('info', 'Would create/update necessary project files');
-				if (addAliasesPrompted) {
+
-					log('info', 'Would add shell aliases for task-master');
+				// Show flag-specific behavior
-				}
+				log(
+					'info',
+					`${addAliasesPrompted ? 'Would add shell aliases (tm, taskmaster)' : 'Would skip shell aliases'}`
+				);
+				log(
+					'info',
+					`${initGitPrompted ? 'Would initialize Git repository' : 'Would skip Git initialization'}`
+				);
+				log(
+					'info',
+					`${storeGitPrompted ? 'Would store tasks in Git' : 'Would exclude tasks from Git'}`
+				);
+
 				return {
 					dryRun: true
 				};
@@ -433,6 +533,8 @@ async function initializeProject(options = {}) {
 			// Create structure using only necessary values
 			createProjectStructure(
 				addAliasesPrompted,
+				initGitPrompted,
+				storeGitPrompted,
 				dryRun,
 				options,
 				selectedRuleProfiles
@@ -458,6 +560,8 @@ function promptQuestion(rl, question) {
 // Function to create the project structure
 function createProjectStructure(
 	addAliases,
+	initGit,
+	storeTasksInGit,
 	dryRun,
 	options,
 	selectedRuleProfiles = RULE_PROFILES // Default to all rule profiles
@@ -507,18 +611,55 @@ function createProjectStructure(
 		}
 	);
 
-	// Copy .gitignore
+	// Copy .gitignore with GitTasks preference
-	copyTemplateFile('gitignore', path.join(targetDir, GITIGNORE_FILE));
+	try {
+		const gitignoreTemplatePath = path.join(
+			__dirname,
+			'..',
+			'assets',
+			'gitignore'
+		);
+		const templateContent = fs.readFileSync(gitignoreTemplatePath, 'utf8');
+		manageGitignoreFile(
+			path.join(targetDir, GITIGNORE_FILE),
+			templateContent,
+			storeTasksInGit,
+			log
+		);
+	} catch (error) {
+		log('error', `Failed to create .gitignore: ${error.message}`);
+	}
 
 	// Copy example_prd.txt to NEW location
 	copyTemplateFile('example_prd.txt', path.join(targetDir, EXAMPLE_PRD_FILE));
 
 	// Initialize git repository if git is available
 	try {
-		if (!fs.existsSync(path.join(targetDir, '.git'))) {
+		if (initGit === false) {
-			log('info', 'Initializing git repository...');
+			log('info', 'Git initialization skipped due to --no-git flag.');
-			execSync('git init', { stdio: 'ignore' });
+		} else if (initGit === true) {
-			log('success', 'Git repository initialized');
+			if (insideGitWorkTree()) {
+				log(
+					'info',
+					'Existing Git repository detected – skipping git init despite --git flag.'
+				);
+			} else {
+				log('info', 'Initializing Git repository due to --git flag...');
+				execSync('git init', { cwd: targetDir, stdio: 'ignore' });
+				log('success', 'Git repository initialized');
+			}
+		} else {
+			// Default behavior when no flag is provided (from interactive prompt)
+			if (insideGitWorkTree()) {
+				log('info', 'Existing Git repository detected – skipping git init.');
+			} else {
+				log(
+					'info',
+					'No Git repository detected. Initializing one in project root...'
+				);
+				execSync('git init', { cwd: targetDir, stdio: 'ignore' });
+				log('success', 'Git repository initialized');
+			}
 		}
 	} catch (error) {
 		log('warn', 'Git not available, skipping repository initialization');
@@ -599,6 +740,17 @@ function createProjectStructure(
 	}
 	// ====================================
 
+	// Add shell aliases if requested
+	if (addAliases && !dryRun) {
+		log('info', 'Adding shell aliases...');
+		const aliasResult = addShellAliases();
+		if (aliasResult) {
+			log('success', 'Shell aliases added successfully');
+		}
+	} else if (addAliases && dryRun) {
+		log('info', 'DRY RUN: Would add shell aliases (tm, taskmaster)');
+	}
+
 	// Display success message
 	if (!isSilentMode()) {
 		console.log(

scripts/modules/commands.js

@@ -3342,6 +3342,11 @@ ${result.result}
 		.option('--skip-install', 'Skip installing dependencies')
 		.option('--dry-run', 'Show what would be done without making changes')
 		.option('--aliases', 'Add shell aliases (tm, taskmaster)')
+		.option('--no-aliases', 'Skip shell aliases (tm, taskmaster)')
+		.option('--git', 'Initialize Git repository')
+		.option('--no-git', 'Skip Git repository initialization')
+		.option('--git-tasks', 'Store tasks in Git')
+		.option('--no-git-tasks', 'No Git storage of tasks')
 		.action(async (cmdOptions) => {
 			// cmdOptions contains parsed arguments
 			// Parse rules: accept space or comma separated, default to all available rules

scripts/modules/task-manager/update-task-by-id.js

@@ -39,23 +39,7 @@ const updatedTaskSchema = z
 		priority: z.string().optional(),
 		details: z.string().optional(),
 		testStrategy: z.string().optional(),
-		subtasks: z
+		subtasks: z.array(z.any()).optional()
-			.array(
-				z.object({
-					id: z
-						.number()
-						.int()
-						.positive()
-						.describe('Sequential subtask ID starting from 1'),
-					title: z.string(),
-					description: z.string(),
-					status: z.string(),
-					dependencies: z.array(z.number().int()).optional(),
-					details: z.string().optional(),
-					testStrategy: z.string().optional()
-				})
-			)
-			.optional()
 	})
 	.strip(); // Allows parsing even if AI adds extra fields, but validation focuses on schema
 
@@ -457,8 +441,6 @@ Guidelines:
 9. Instead, add a new subtask that clearly indicates what needs to be changed or replaced
 10. Use the existence of completed subtasks as an opportunity to make new subtasks more specific and targeted
 11. Ensure any new subtasks have unique IDs that don't conflict with existing ones
-12. CRITICAL: For subtask IDs, use ONLY numeric values (1, 2, 3, etc.) NOT strings ("1", "2", "3")
-13. CRITICAL: Subtask IDs should start from 1 and increment sequentially (1, 2, 3...) - do NOT use parent task ID as prefix
 
 The changes described in the prompt should be thoughtfully applied to make the task more accurate and actionable.`;
 
@@ -591,37 +573,6 @@ The changes described in the prompt should be thoughtfully applied to make the t
 				);
 				updatedTask.status = taskToUpdate.status;
 			}
-			// Fix subtask IDs if they exist (ensure they are numeric and sequential)
-			if (updatedTask.subtasks && Array.isArray(updatedTask.subtasks)) {
-				let currentSubtaskId = 1;
-				updatedTask.subtasks = updatedTask.subtasks.map((subtask) => {
-					// Fix AI-generated subtask IDs that might be strings or use parent ID as prefix
-					const correctedSubtask = {
-						...subtask,
-						id: currentSubtaskId, // Override AI-generated ID with correct sequential ID
-						dependencies: Array.isArray(subtask.dependencies)
-							? subtask.dependencies
-									.map((dep) =>
-										typeof dep === 'string' ? parseInt(dep, 10) : dep
-									)
-									.filter(
-										(depId) =>
-											!Number.isNaN(depId) &&
-											depId >= 1 &&
-											depId < currentSubtaskId
-									)
-							: [],
-						status: subtask.status || 'pending'
-					};
-					currentSubtaskId++;
-					return correctedSubtask;
-				});
-				report(
-					'info',
-					`Fixed ${updatedTask.subtasks.length} subtask IDs to be sequential numeric IDs.`
-				);
-			}
-
 			// Preserve completed subtasks (Keep existing logic)
 			if (taskToUpdate.subtasks?.length > 0) {
 				if (!updatedTask.subtasks) {

scripts/modules/utils/git-utils.js

@@ -349,6 +349,25 @@ function getCurrentBranchSync(projectRoot) {
 	}
 }
 
+/**
+ * Check if the current working directory is inside a Git work-tree.
+ * Uses `git rev-parse --is-inside-work-tree` which is more specific than --git-dir
+ * for detecting work-trees (excludes bare repos and .git directories).
+ * This is ideal for preventing accidental git init in existing work-trees.
+ * @returns {boolean} True if inside a Git work-tree, false otherwise.
+ */
+function insideGitWorkTree() {
+	try {
+		execSync('git rev-parse --is-inside-work-tree', {
+			stdio: 'ignore',
+			cwd: process.cwd()
+		});
+		return true;
+	} catch {
+		return false;
+	}
+}
+
 // Export all functions
 export {
 	isGitRepository,
@@ -366,5 +385,6 @@ export {
 	checkAndAutoSwitchGitTag,
 	checkAndAutoSwitchGitTagSync,
 	isGitRepositorySync,
-	getCurrentBranchSync
+	getCurrentBranchSync,
+	insideGitWorkTree
 };

src/utils/manage-gitignore.js

@@ -0,0 +1,293 @@
+// Utility to manage .gitignore files with task file preferences and template merging
+import fs from 'fs';
+import path from 'path';
+
+// Constants
+const TASK_FILES_COMMENT = '# Task files';
+const TASK_JSON_PATTERN = 'tasks.json';
+const TASK_DIR_PATTERN = 'tasks/';
+
+/**
+ * Normalizes a line by removing comments and trimming whitespace
+ * @param {string} line - Line to normalize
+ * @returns {string} Normalized line
+ */
+function normalizeLine(line) {
+	return line.trim().replace(/^#/, '').trim();
+}
+
+/**
+ * Checks if a line is task-related (tasks.json or tasks/)
+ * @param {string} line - Line to check
+ * @returns {boolean} True if line is task-related
+ */
+function isTaskLine(line) {
+	const normalized = normalizeLine(line);
+	return normalized === TASK_JSON_PATTERN || normalized === TASK_DIR_PATTERN;
+}
+
+/**
+ * Adjusts task-related lines in template based on storage preference
+ * @param {string[]} templateLines - Array of template lines
+ * @param {boolean} storeTasksInGit - Whether to comment out task lines
+ * @returns {string[]} Adjusted template lines
+ */
+function adjustTaskLinesInTemplate(templateLines, storeTasksInGit) {
+	return templateLines.map((line) => {
+		if (isTaskLine(line)) {
+			const normalized = normalizeLine(line);
+			// Preserve original trailing whitespace from the line
+			const originalTrailingSpace = line.match(/\s*$/)[0];
+			return storeTasksInGit
+				? `# ${normalized}${originalTrailingSpace}`
+				: `${normalized}${originalTrailingSpace}`;
+		}
+		return line;
+	});
+}
+
+/**
+ * Removes existing task files section from content
+ * @param {string[]} existingLines - Existing file lines
+ * @returns {string[]} Lines with task section removed
+ */
+function removeExistingTaskSection(existingLines) {
+	const cleanedLines = [];
+	let inTaskSection = false;
+
+	for (const line of existingLines) {
+		// Start of task files section
+		if (line.trim() === TASK_FILES_COMMENT) {
+			inTaskSection = true;
+			continue;
+		}
+
+		// Task lines (commented or not)
+		if (isTaskLine(line)) {
+			continue;
+		}
+
+		// Empty lines within task section
+		if (inTaskSection && !line.trim()) {
+			continue;
+		}
+
+		// End of task section (any non-empty, non-task line)
+		if (inTaskSection && line.trim() && !isTaskLine(line)) {
+			inTaskSection = false;
+		}
+
+		// Keep all other lines
+		if (!inTaskSection) {
+			cleanedLines.push(line);
+		}
+	}
+
+	return cleanedLines;
+}
+
+/**
+ * Filters template lines to only include new content not already present
+ * @param {string[]} templateLines - Template lines
+ * @param {Set<string>} existingLinesSet - Set of existing trimmed lines
+ * @returns {string[]} New lines to add
+ */
+function filterNewTemplateLines(templateLines, existingLinesSet) {
+	return templateLines.filter((line) => {
+		const trimmed = line.trim();
+		if (!trimmed) return false;
+
+		// Skip task-related lines (handled separately)
+		if (isTaskLine(line) || trimmed === TASK_FILES_COMMENT) {
+			return false;
+		}
+
+		// Include only if not already present
+		return !existingLinesSet.has(trimmed);
+	});
+}
+
+/**
+ * Builds the task files section based on storage preference
+ * @param {boolean} storeTasksInGit - Whether to comment out task lines
+ * @returns {string[]} Task files section lines
+ */
+function buildTaskFilesSection(storeTasksInGit) {
+	const section = [TASK_FILES_COMMENT];
+
+	if (storeTasksInGit) {
+		section.push(`# ${TASK_JSON_PATTERN}`, `# ${TASK_DIR_PATTERN} `);
+	} else {
+		section.push(TASK_JSON_PATTERN, `${TASK_DIR_PATTERN} `);
+	}
+
+	return section;
+}
+
+/**
+ * Adds a separator line if needed (avoids double spacing)
+ * @param {string[]} lines - Current lines array
+ */
+function addSeparatorIfNeeded(lines) {
+	if (lines.some((line) => line.trim())) {
+		const lastLine = lines[lines.length - 1];
+		if (lastLine && lastLine.trim()) {
+			lines.push('');
+		}
+	}
+}
+
+/**
+ * Validates input parameters
+ * @param {string} targetPath - Path to .gitignore file
+ * @param {string} content - Template content
+ * @param {boolean} storeTasksInGit - Storage preference
+ * @throws {Error} If validation fails
+ */
+function validateInputs(targetPath, content, storeTasksInGit) {
+	if (!targetPath || typeof targetPath !== 'string') {
+		throw new Error('targetPath must be a non-empty string');
+	}
+
+	if (!targetPath.endsWith('.gitignore')) {
+		throw new Error('targetPath must end with .gitignore');
+	}
+
+	if (!content || typeof content !== 'string') {
+		throw new Error('content must be a non-empty string');
+	}
+
+	if (typeof storeTasksInGit !== 'boolean') {
+		throw new Error('storeTasksInGit must be a boolean');
+	}
+}
+
+/**
+ * Creates a new .gitignore file from template
+ * @param {string} targetPath - Path to create file at
+ * @param {string[]} templateLines - Adjusted template lines
+ * @param {function} log - Logging function
+ */
+function createNewGitignoreFile(targetPath, templateLines, log) {
+	try {
+		fs.writeFileSync(targetPath, templateLines.join('\n'));
+		if (typeof log === 'function') {
+			log('success', `Created ${targetPath} with full template`);
+		}
+	} catch (error) {
+		if (typeof log === 'function') {
+			log('error', `Failed to create ${targetPath}: ${error.message}`);
+		}
+		throw error;
+	}
+}
+
+/**
+ * Merges template content with existing .gitignore file
+ * @param {string} targetPath - Path to existing file
+ * @param {string[]} templateLines - Adjusted template lines
+ * @param {boolean} storeTasksInGit - Storage preference
+ * @param {function} log - Logging function
+ */
+function mergeWithExistingFile(
+	targetPath,
+	templateLines,
+	storeTasksInGit,
+	log
+) {
+	try {
+		// Read and process existing file
+		const existingContent = fs.readFileSync(targetPath, 'utf8');
+		const existingLines = existingContent.split('\n');
+
+		// Remove existing task section
+		const cleanedExistingLines = removeExistingTaskSection(existingLines);
+
+		// Find new template lines to add
+		const existingLinesSet = new Set(
+			cleanedExistingLines.map((line) => line.trim()).filter((line) => line)
+		);
+		const newLines = filterNewTemplateLines(templateLines, existingLinesSet);
+
+		// Build final content
+		const finalLines = [...cleanedExistingLines];
+
+		// Add new template content
+		if (newLines.length > 0) {
+			addSeparatorIfNeeded(finalLines);
+			finalLines.push(...newLines);
+		}
+
+		// Add task files section
+		addSeparatorIfNeeded(finalLines);
+		finalLines.push(...buildTaskFilesSection(storeTasksInGit));
+
+		// Write result
+		fs.writeFileSync(targetPath, finalLines.join('\n'));
+
+		if (typeof log === 'function') {
+			const hasNewContent =
+				newLines.length > 0 ? ' and merged new content' : '';
+			log(
+				'success',
+				`Updated ${targetPath} according to user preference${hasNewContent}`
+			);
+		}
+	} catch (error) {
+		if (typeof log === 'function') {
+			log(
+				'error',
+				`Failed to merge content with ${targetPath}: ${error.message}`
+			);
+		}
+		throw error;
+	}
+}
+
+/**
+ * Manages .gitignore file creation and updates with task file preferences
+ * @param {string} targetPath - Path to the .gitignore file
+ * @param {string} content - Template content for .gitignore
+ * @param {boolean} storeTasksInGit - Whether to store tasks in git or not
+ * @param {function} log - Logging function (level, message)
+ * @throws {Error} If validation or file operations fail
+ */
+function manageGitignoreFile(
+	targetPath,
+	content,
+	storeTasksInGit = false,
+	log = null
+) {
+	// Validate inputs
+	validateInputs(targetPath, content, storeTasksInGit);
+
+	// Process template with task preference
+	const templateLines = content.split('\n');
+	const adjustedTemplateLines = adjustTaskLinesInTemplate(
+		templateLines,
+		storeTasksInGit
+	);
+
+	// Handle file creation or merging
+	if (!fs.existsSync(targetPath)) {
+		createNewGitignoreFile(targetPath, adjustedTemplateLines, log);
+	} else {
+		mergeWithExistingFile(
+			targetPath,
+			adjustedTemplateLines,
+			storeTasksInGit,
+			log
+		);
+	}
+}
+
+export default manageGitignoreFile;
+export {
+	manageGitignoreFile,
+	normalizeLine,
+	isTaskLine,
+	buildTaskFilesSection,
+	TASK_FILES_COMMENT,
+	TASK_JSON_PATTERN,
+	TASK_DIR_PATTERN
+};

tests/integration/manage-gitignore.test.js

@@ -0,0 +1,581 @@
+/**
+ * Integration tests for manage-gitignore.js module
+ * Tests actual file system operations in a temporary directory
+ */
+
+import fs from 'fs';
+import path from 'path';
+import os from 'os';
+import manageGitignoreFile from '../../src/utils/manage-gitignore.js';
+
+describe('manage-gitignore.js Integration Tests', () => {
+	let tempDir;
+	let testGitignorePath;
+
+	beforeEach(() => {
+		// Create a temporary directory for each test
+		tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gitignore-test-'));
+		testGitignorePath = path.join(tempDir, '.gitignore');
+	});
+
+	afterEach(() => {
+		// Clean up temporary directory after each test
+		if (fs.existsSync(tempDir)) {
+			fs.rmSync(tempDir, { recursive: true, force: true });
+		}
+	});
+
+	describe('New File Creation', () => {
+		const templateContent = `# Logs
+logs
+*.log
+npm-debug.log*
+
+# Dependencies
+node_modules/
+jspm_packages/
+
+# Environment variables
+.env
+.env.local
+
+# Task files
+tasks.json
+tasks/ `;
+
+		test('should create new .gitignore file with commented task lines (storeTasksInGit = true)', () => {
+			const logs = [];
+			const mockLog = (level, message) => logs.push({ level, message });
+
+			manageGitignoreFile(testGitignorePath, templateContent, true, mockLog);
+
+			// Verify file was created
+			expect(fs.existsSync(testGitignorePath)).toBe(true);
+
+			// Verify content
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+			expect(content).toContain('# Logs');
+			expect(content).toContain('logs');
+			expect(content).toContain('# Dependencies');
+			expect(content).toContain('node_modules/');
+			expect(content).toContain('# Task files');
+			expect(content).toContain('tasks.json');
+			expect(content).toContain('tasks/');
+
+			// Verify task lines are commented (storeTasksInGit = true)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+# tasks\.json\s*[\r\n]+# tasks\/ /
+			);
+
+			// Verify log message
+			expect(logs).toContainEqual({
+				level: 'success',
+				message: expect.stringContaining('Created')
+			});
+		});
+
+		test('should create new .gitignore file with uncommented task lines (storeTasksInGit = false)', () => {
+			const logs = [];
+			const mockLog = (level, message) => logs.push({ level, message });
+
+			manageGitignoreFile(testGitignorePath, templateContent, false, mockLog);
+
+			// Verify file was created
+			expect(fs.existsSync(testGitignorePath)).toBe(true);
+
+			// Verify content
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+			expect(content).toContain('# Task files');
+
+			// Verify task lines are uncommented (storeTasksInGit = false)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+tasks\.json\s*[\r\n]+tasks\/ /
+			);
+
+			// Verify log message
+			expect(logs).toContainEqual({
+				level: 'success',
+				message: expect.stringContaining('Created')
+			});
+		});
+
+		test('should work without log function', () => {
+			expect(() => {
+				manageGitignoreFile(testGitignorePath, templateContent, false);
+			}).not.toThrow();
+
+			expect(fs.existsSync(testGitignorePath)).toBe(true);
+		});
+	});
+
+	describe('File Merging', () => {
+		const templateContent = `# Logs
+logs
+*.log
+
+# Dependencies
+node_modules/
+
+# Environment variables
+.env
+
+# Task files
+tasks.json
+tasks/ `;
+
+		test('should merge template with existing file content', () => {
+			// Create existing .gitignore file
+			const existingContent = `# Existing content
+old-files.txt
+*.backup
+
+# Old task files (to be replaced)
+# Task files
+# tasks.json
+# tasks/ 
+
+# More existing content
+cache/`;
+
+			fs.writeFileSync(testGitignorePath, existingContent);
+
+			const logs = [];
+			const mockLog = (level, message) => logs.push({ level, message });
+
+			manageGitignoreFile(testGitignorePath, templateContent, false, mockLog);
+
+			// Verify file still exists
+			expect(fs.existsSync(testGitignorePath)).toBe(true);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+
+			// Should retain existing non-task content
+			expect(content).toContain('# Existing content');
+			expect(content).toContain('old-files.txt');
+			expect(content).toContain('*.backup');
+			expect(content).toContain('# More existing content');
+			expect(content).toContain('cache/');
+
+			// Should add new template content
+			expect(content).toContain('# Logs');
+			expect(content).toContain('logs');
+			expect(content).toContain('# Dependencies');
+			expect(content).toContain('node_modules/');
+			expect(content).toContain('# Environment variables');
+			expect(content).toContain('.env');
+
+			// Should replace task section with new preference (storeTasksInGit = false means uncommented)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+tasks\.json\s*[\r\n]+tasks\/ /
+			);
+
+			// Verify log message
+			expect(logs).toContainEqual({
+				level: 'success',
+				message: expect.stringContaining('Updated')
+			});
+		});
+
+		test('should handle switching task preferences from commented to uncommented', () => {
+			// Create existing file with commented task lines
+			const existingContent = `# Existing
+existing.txt
+
+# Task files
+# tasks.json
+# tasks/ `;
+
+			fs.writeFileSync(testGitignorePath, existingContent);
+
+			// Update with storeTasksInGit = true (commented)
+			manageGitignoreFile(testGitignorePath, templateContent, true);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+
+			// Should retain existing content
+			expect(content).toContain('# Existing');
+			expect(content).toContain('existing.txt');
+
+			// Should have commented task lines (storeTasksInGit = true)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+# tasks\.json\s*[\r\n]+# tasks\/ /
+			);
+		});
+
+		test('should handle switching task preferences from uncommented to commented', () => {
+			// Create existing file with uncommented task lines
+			const existingContent = `# Existing
+existing.txt
+
+# Task files
+tasks.json
+tasks/ `;
+
+			fs.writeFileSync(testGitignorePath, existingContent);
+
+			// Update with storeTasksInGit = false (uncommented)
+			manageGitignoreFile(testGitignorePath, templateContent, false);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+
+			// Should retain existing content
+			expect(content).toContain('# Existing');
+			expect(content).toContain('existing.txt');
+
+			// Should have uncommented task lines (storeTasksInGit = false)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+tasks\.json\s*[\r\n]+tasks\/ /
+			);
+		});
+
+		test('should not duplicate existing template content', () => {
+			// Create existing file that already has some template content
+			const existingContent = `# Logs
+logs
+*.log
+
+# Dependencies
+node_modules/
+
+# Custom content
+custom.txt
+
+# Task files
+# tasks.json
+# tasks/ `;
+
+			fs.writeFileSync(testGitignorePath, existingContent);
+
+			manageGitignoreFile(testGitignorePath, templateContent, false);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+
+			// Should not duplicate logs section
+			const logsMatches = content.match(/# Logs/g);
+			expect(logsMatches).toHaveLength(1);
+
+			// Should not duplicate dependencies section
+			const depsMatches = content.match(/# Dependencies/g);
+			expect(depsMatches).toHaveLength(1);
+
+			// Should retain custom content
+			expect(content).toContain('# Custom content');
+			expect(content).toContain('custom.txt');
+
+			// Should add new template content that wasn't present
+			expect(content).toContain('# Environment variables');
+			expect(content).toContain('.env');
+		});
+
+		test('should handle empty existing file', () => {
+			// Create empty file
+			fs.writeFileSync(testGitignorePath, '');
+
+			manageGitignoreFile(testGitignorePath, templateContent, false);
+
+			expect(fs.existsSync(testGitignorePath)).toBe(true);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+			expect(content).toContain('# Logs');
+			expect(content).toContain('# Task files');
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+tasks\.json\s*[\r\n]+tasks\/ /
+			);
+		});
+
+		test('should handle file with only whitespace', () => {
+			// Create file with only whitespace
+			fs.writeFileSync(testGitignorePath, '   \n\n  \n');
+
+			manageGitignoreFile(testGitignorePath, templateContent, true);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+			expect(content).toContain('# Logs');
+			expect(content).toContain('# Task files');
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+# tasks\.json\s*[\r\n]+# tasks\/ /
+			);
+		});
+	});
+
+	describe('Complex Task Section Handling', () => {
+		test('should remove task section with mixed comments and spacing', () => {
+			const existingContent = `# Dependencies
+node_modules/
+
+# Task files
+
+# tasks.json
+tasks/
+
+
+# More content
+more.txt`;
+
+			const templateContent = `# New content
+new.txt
+
+# Task files
+tasks.json
+tasks/ `;
+
+			fs.writeFileSync(testGitignorePath, existingContent);
+
+			manageGitignoreFile(testGitignorePath, templateContent, false);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+
+			// Should retain non-task content
+			expect(content).toContain('# Dependencies');
+			expect(content).toContain('node_modules/');
+			expect(content).toContain('# More content');
+			expect(content).toContain('more.txt');
+
+			// Should add new content
+			expect(content).toContain('# New content');
+			expect(content).toContain('new.txt');
+
+			// Should have clean task section (storeTasksInGit = false means uncommented)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+tasks\.json\s*[\r\n]+tasks\/ /
+			);
+		});
+
+		test('should handle multiple task file variations', () => {
+			const existingContent = `# Existing
+existing.txt
+
+# Task files
+tasks.json
+# tasks.json  
+# tasks/ 
+tasks/ 
+#tasks.json
+
+# More content
+more.txt`;
+
+			const templateContent = `# Task files
+tasks.json
+tasks/ `;
+
+			fs.writeFileSync(testGitignorePath, existingContent);
+
+			manageGitignoreFile(testGitignorePath, templateContent, true);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+
+			// Should retain non-task content
+			expect(content).toContain('# Existing');
+			expect(content).toContain('existing.txt');
+			expect(content).toContain('# More content');
+			expect(content).toContain('more.txt');
+
+			// Should have clean task section with preference applied (storeTasksInGit = true means commented)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+# tasks\.json\s*[\r\n]+# tasks\/ /
+			);
+
+			// Should not have multiple task sections
+			const taskFileMatches = content.match(/# Task files/g);
+			expect(taskFileMatches).toHaveLength(1);
+		});
+	});
+
+	describe('Error Handling', () => {
+		test('should handle permission errors gracefully', () => {
+			// Create a directory where we would create the file, then remove write permissions
+			const readOnlyDir = path.join(tempDir, 'readonly');
+			fs.mkdirSync(readOnlyDir);
+			fs.chmodSync(readOnlyDir, 0o444); // Read-only
+
+			const readOnlyGitignorePath = path.join(readOnlyDir, '.gitignore');
+			const templateContent = `# Test
+test.txt
+
+# Task files
+tasks.json
+tasks/ `;
+
+			const logs = [];
+			const mockLog = (level, message) => logs.push({ level, message });
+
+			expect(() => {
+				manageGitignoreFile(
+					readOnlyGitignorePath,
+					templateContent,
+					false,
+					mockLog
+				);
+			}).toThrow();
+
+			// Verify error was logged
+			expect(logs).toContainEqual({
+				level: 'error',
+				message: expect.stringContaining('Failed to create')
+			});
+
+			// Restore permissions for cleanup
+			fs.chmodSync(readOnlyDir, 0o755);
+		});
+
+		test('should handle read errors on existing files', () => {
+			// Create a file then remove read permissions
+			fs.writeFileSync(testGitignorePath, 'existing content');
+			fs.chmodSync(testGitignorePath, 0o000); // No permissions
+
+			const templateContent = `# Test
+test.txt
+
+# Task files
+tasks.json
+tasks/ `;
+
+			const logs = [];
+			const mockLog = (level, message) => logs.push({ level, message });
+
+			expect(() => {
+				manageGitignoreFile(testGitignorePath, templateContent, false, mockLog);
+			}).toThrow();
+
+			// Verify error was logged
+			expect(logs).toContainEqual({
+				level: 'error',
+				message: expect.stringContaining('Failed to merge content')
+			});
+
+			// Restore permissions for cleanup
+			fs.chmodSync(testGitignorePath, 0o644);
+		});
+	});
+
+	describe('Real-world Scenarios', () => {
+		test('should handle typical Node.js project .gitignore', () => {
+			const existingNodeGitignore = `# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# Optional npm cache directory
+.npm
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variables file
+.env
+
+# next.js build output
+.next`;
+
+			const taskMasterTemplate = `# Logs
+logs
+*.log
+
+# Dependencies  
+node_modules/
+
+# Environment variables
+.env
+
+# Build output
+dist/
+build/
+
+# Task files
+tasks.json
+tasks/ `;
+
+			fs.writeFileSync(testGitignorePath, existingNodeGitignore);
+
+			manageGitignoreFile(testGitignorePath, taskMasterTemplate, false);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+
+			// Should retain existing Node.js specific entries
+			expect(content).toContain('npm-debug.log*');
+			expect(content).toContain('yarn-debug.log*');
+			expect(content).toContain('*.pid');
+			expect(content).toContain('jspm_packages/');
+			expect(content).toContain('.npm');
+			expect(content).toContain('*.tgz');
+			expect(content).toContain('.yarn-integrity');
+			expect(content).toContain('.next');
+
+			// Should add new content from template that wasn't present
+			expect(content).toContain('dist/');
+			expect(content).toContain('build/');
+
+			// Should add task files section with correct preference (storeTasksInGit = false means uncommented)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+tasks\.json\s*[\r\n]+tasks\/ /
+			);
+
+			// Should not duplicate common entries
+			const nodeModulesMatches = content.match(/node_modules\//g);
+			expect(nodeModulesMatches).toHaveLength(1);
+
+			const logsMatches = content.match(/# Logs/g);
+			expect(logsMatches).toHaveLength(1);
+		});
+
+		test('should handle project with existing task files in git', () => {
+			const existingContent = `# Dependencies
+node_modules/
+
+# Logs
+*.log
+
+# Current task setup - keeping in git
+# Task files
+tasks.json
+tasks/ 
+
+# Build output
+dist/`;
+
+			const templateContent = `# New template
+# Dependencies
+node_modules/
+
+# Task files
+tasks.json
+tasks/ `;
+
+			fs.writeFileSync(testGitignorePath, existingContent);
+
+			// Change preference to exclude tasks from git (storeTasksInGit = false means uncommented/ignored)
+			manageGitignoreFile(testGitignorePath, templateContent, false);
+
+			const content = fs.readFileSync(testGitignorePath, 'utf8');
+
+			// Should retain existing content
+			expect(content).toContain('# Dependencies');
+			expect(content).toContain('node_modules/');
+			expect(content).toContain('# Logs');
+			expect(content).toContain('*.log');
+			expect(content).toContain('# Build output');
+			expect(content).toContain('dist/');
+
+			// Should update task preference to uncommented (storeTasksInGit = false)
+			expect(content).toMatch(
+				/# Task files\s*[\r\n]+tasks\.json\s*[\r\n]+tasks\/ /
+			);
+		});
+	});
+});

tests/unit/initialize-project.test.js

@@ -0,0 +1,538 @@
+import { jest } from '@jest/globals';
+import fs from 'fs';
+import path from 'path';
+import os from 'os';
+
+// Reduce noise in test output
+process.env.TASKMASTER_LOG_LEVEL = 'error';
+
+// === Mock everything early ===
+jest.mock('child_process', () => ({ execSync: jest.fn() }));
+jest.mock('fs', () => ({
+	...jest.requireActual('fs'),
+	mkdirSync: jest.fn(),
+	writeFileSync: jest.fn(),
+	readFileSync: jest.fn(),
+	appendFileSync: jest.fn(),
+	existsSync: jest.fn(),
+	mkdtempSync: jest.requireActual('fs').mkdtempSync,
+	rmSync: jest.requireActual('fs').rmSync
+}));
+
+// Mock console methods to suppress output
+const consoleMethods = ['log', 'info', 'warn', 'error', 'clear'];
+consoleMethods.forEach((method) => {
+	global.console[method] = jest.fn();
+});
+
+// Mock ES modules using unstable_mockModule
+jest.unstable_mockModule('../../scripts/modules/utils.js', () => ({
+	isSilentMode: jest.fn(() => true),
+	enableSilentMode: jest.fn(),
+	log: jest.fn(),
+	findProjectRoot: jest.fn(() => process.cwd())
+}));
+
+// Mock git-utils module
+jest.unstable_mockModule('../../scripts/modules/utils/git-utils.js', () => ({
+	insideGitWorkTree: jest.fn(() => false)
+}));
+
+// Mock rule transformer
+jest.unstable_mockModule('../../src/utils/rule-transformer.js', () => ({
+	convertAllRulesToProfileRules: jest.fn(),
+	getRulesProfile: jest.fn(() => ({
+		conversionConfig: {},
+		globalReplacements: []
+	}))
+}));
+
+// Mock any other modules that might output or do real operations
+jest.unstable_mockModule('../../scripts/modules/config-manager.js', () => ({
+	createDefaultConfig: jest.fn(() => ({ models: {}, project: {} })),
+	saveConfig: jest.fn()
+}));
+
+// Mock display libraries
+jest.mock('figlet', () => ({ textSync: jest.fn(() => 'MOCKED BANNER') }));
+jest.mock('boxen', () => jest.fn(() => 'MOCKED BOX'));
+jest.mock('gradient-string', () => jest.fn(() => jest.fn((text) => text)));
+jest.mock('chalk', () => ({
+	blue: jest.fn((text) => text),
+	green: jest.fn((text) => text),
+	red: jest.fn((text) => text),
+	yellow: jest.fn((text) => text),
+	cyan: jest.fn((text) => text),
+	white: jest.fn((text) => text),
+	dim: jest.fn((text) => text),
+	bold: jest.fn((text) => text),
+	underline: jest.fn((text) => text)
+}));
+
+const { execSync } = jest.requireMock('child_process');
+const mockFs = jest.requireMock('fs');
+
+// Import the mocked modules
+const mockUtils = await import('../../scripts/modules/utils.js');
+const mockGitUtils = await import('../../scripts/modules/utils/git-utils.js');
+const mockRuleTransformer = await import('../../src/utils/rule-transformer.js');
+
+// Import after mocks
+const { initializeProject } = await import('../../scripts/init.js');
+
+describe('initializeProject – Git / Alias flag logic', () => {
+	let tmpDir;
+	const origCwd = process.cwd();
+
+	// Standard non-interactive options for all tests
+	const baseOptions = {
+		yes: true,
+		skipInstall: true,
+		name: 'test-project',
+		description: 'Test project description',
+		version: '1.0.0',
+		author: 'Test Author'
+	};
+
+	beforeEach(() => {
+		jest.clearAllMocks();
+
+		// Set up basic fs mocks
+		mockFs.mkdirSync.mockImplementation(() => {});
+		mockFs.writeFileSync.mockImplementation(() => {});
+		mockFs.readFileSync.mockImplementation((filePath) => {
+			if (filePath.includes('assets') || filePath.includes('.cursor/rules')) {
+				return 'mock template content';
+			}
+			if (filePath.includes('.zshrc') || filePath.includes('.bashrc')) {
+				return '# existing config';
+			}
+			return '';
+		});
+		mockFs.appendFileSync.mockImplementation(() => {});
+		mockFs.existsSync.mockImplementation((filePath) => {
+			// Template source files exist
+			if (filePath.includes('assets') || filePath.includes('.cursor/rules')) {
+				return true;
+			}
+			// Shell config files exist by default
+			if (filePath.includes('.zshrc') || filePath.includes('.bashrc')) {
+				return true;
+			}
+			return false;
+		});
+
+		// Reset utils mocks
+		mockUtils.isSilentMode.mockReturnValue(true);
+		mockGitUtils.insideGitWorkTree.mockReturnValue(false);
+
+		// Default execSync mock
+		execSync.mockImplementation(() => '');
+
+		tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'tm-init-'));
+		process.chdir(tmpDir);
+	});
+
+	afterEach(() => {
+		process.chdir(origCwd);
+		fs.rmSync(tmpDir, { recursive: true, force: true });
+	});
+
+	describe('Git Flag Behavior', () => {
+		it('completes successfully with git:false in dry run', async () => {
+			const result = await initializeProject({
+				...baseOptions,
+				git: false,
+				aliases: false,
+				dryRun: true
+			});
+
+			expect(result.dryRun).toBe(true);
+		});
+
+		it('completes successfully with git:true when not inside repo', async () => {
+			mockGitUtils.insideGitWorkTree.mockReturnValue(false);
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: true,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('completes successfully when already inside repo', async () => {
+			mockGitUtils.insideGitWorkTree.mockReturnValue(true);
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: true,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('uses default git behavior without errors', async () => {
+			mockGitUtils.insideGitWorkTree.mockReturnValue(false);
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('handles git command failures gracefully', async () => {
+			mockGitUtils.insideGitWorkTree.mockReturnValue(false);
+			execSync.mockImplementation((cmd) => {
+				if (cmd.includes('git init')) {
+					throw new Error('git not found');
+				}
+				return '';
+			});
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: true,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+	});
+
+	describe('Alias Flag Behavior', () => {
+		it('completes successfully when aliases:true and environment is set up', async () => {
+			const originalShell = process.env.SHELL;
+			const originalHome = process.env.HOME;
+
+			process.env.SHELL = '/bin/zsh';
+			process.env.HOME = '/mock/home';
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false,
+					aliases: true,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+
+			process.env.SHELL = originalShell;
+			process.env.HOME = originalHome;
+		});
+
+		it('completes successfully when aliases:false', async () => {
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('handles missing shell gracefully', async () => {
+			const originalShell = process.env.SHELL;
+			const originalHome = process.env.HOME;
+
+			delete process.env.SHELL; // Remove shell env var
+			process.env.HOME = '/mock/home';
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false,
+					aliases: true,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+
+			process.env.SHELL = originalShell;
+			process.env.HOME = originalHome;
+		});
+
+		it('handles missing shell config file gracefully', async () => {
+			const originalShell = process.env.SHELL;
+			const originalHome = process.env.HOME;
+
+			process.env.SHELL = '/bin/zsh';
+			process.env.HOME = '/mock/home';
+
+			// Shell config doesn't exist
+			mockFs.existsSync.mockImplementation((filePath) => {
+				if (filePath.includes('.zshrc') || filePath.includes('.bashrc')) {
+					return false;
+				}
+				if (filePath.includes('assets') || filePath.includes('.cursor/rules')) {
+					return true;
+				}
+				return false;
+			});
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false,
+					aliases: true,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+
+			process.env.SHELL = originalShell;
+			process.env.HOME = originalHome;
+		});
+	});
+
+	describe('Flag Combinations', () => {
+		it.each`
+			git      | aliases  | description
+			${true}  | ${true}  | ${'git & aliases enabled'}
+			${true}  | ${false} | ${'git enabled, aliases disabled'}
+			${false} | ${true}  | ${'git disabled, aliases enabled'}
+			${false} | ${false} | ${'git & aliases disabled'}
+		`('handles $description without errors', async ({ git, aliases }) => {
+			const originalShell = process.env.SHELL;
+			const originalHome = process.env.HOME;
+
+			if (aliases) {
+				process.env.SHELL = '/bin/zsh';
+				process.env.HOME = '/mock/home';
+			}
+
+			if (git) {
+				mockGitUtils.insideGitWorkTree.mockReturnValue(false);
+			}
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git,
+					aliases,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+
+			process.env.SHELL = originalShell;
+			process.env.HOME = originalHome;
+		});
+	});
+
+	describe('Dry Run Mode', () => {
+		it('returns dry run result and performs no operations', async () => {
+			const result = await initializeProject({
+				...baseOptions,
+				git: true,
+				aliases: true,
+				dryRun: true
+			});
+
+			expect(result.dryRun).toBe(true);
+		});
+
+		it.each`
+			git      | aliases  | description
+			${true}  | ${false} | ${'git-specific behavior'}
+			${false} | ${false} | ${'no-git behavior'}
+			${false} | ${true}  | ${'alias behavior'}
+		`('shows $description in dry run', async ({ git, aliases }) => {
+			const result = await initializeProject({
+				...baseOptions,
+				git,
+				aliases,
+				dryRun: true
+			});
+
+			expect(result.dryRun).toBe(true);
+		});
+	});
+
+	describe('Error Handling', () => {
+		it('handles npm install failures gracefully', async () => {
+			execSync.mockImplementation((cmd) => {
+				if (cmd.includes('npm install')) {
+					throw new Error('npm failed');
+				}
+				return '';
+			});
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false,
+					aliases: false,
+					skipInstall: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('handles git failures gracefully', async () => {
+			mockGitUtils.insideGitWorkTree.mockReturnValue(false);
+			execSync.mockImplementation((cmd) => {
+				if (cmd.includes('git init')) {
+					throw new Error('git failed');
+				}
+				return '';
+			});
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: true,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('handles file system errors gracefully', async () => {
+			mockFs.mkdirSync.mockImplementation(() => {
+				throw new Error('Permission denied');
+			});
+
+			// Should handle file system errors gracefully
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+	});
+
+	describe('Non-Interactive Mode', () => {
+		it('bypasses prompts with yes:true', async () => {
+			const result = await initializeProject({
+				...baseOptions,
+				git: true,
+				aliases: true,
+				dryRun: true
+			});
+
+			expect(result).toEqual({ dryRun: true });
+		});
+
+		it('completes without hanging', async () => {
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('handles all flag combinations without hanging', async () => {
+			const flagCombinations = [
+				{ git: true, aliases: true },
+				{ git: true, aliases: false },
+				{ git: false, aliases: true },
+				{ git: false, aliases: false },
+				{} // No flags (uses defaults)
+			];
+
+			for (const flags of flagCombinations) {
+				await expect(
+					initializeProject({
+						...baseOptions,
+						...flags,
+						dryRun: true // Use dry run for speed
+					})
+				).resolves.not.toThrow();
+			}
+		});
+
+		it('accepts complete project details', async () => {
+			await expect(
+				initializeProject({
+					name: 'test-project',
+					description: 'test description',
+					version: '2.0.0',
+					author: 'Test User',
+					git: false,
+					aliases: false,
+					dryRun: true
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('works with skipInstall option', async () => {
+			await expect(
+				initializeProject({
+					...baseOptions,
+					skipInstall: true,
+					git: false,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+	});
+
+	describe('Function Integration', () => {
+		it('calls utility functions without errors', async () => {
+			await initializeProject({
+				...baseOptions,
+				git: false,
+				aliases: false,
+				dryRun: false
+			});
+
+			// Verify that utility functions were called
+			expect(mockUtils.isSilentMode).toHaveBeenCalled();
+			expect(
+				mockRuleTransformer.convertAllRulesToProfileRules
+			).toHaveBeenCalled();
+		});
+
+		it('handles template operations gracefully', async () => {
+			// Make file operations throw errors
+			mockFs.writeFileSync.mockImplementation(() => {
+				throw new Error('Write failed');
+			});
+
+			// Should complete despite file operation failures
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false,
+					aliases: false,
+					dryRun: false
+				})
+			).resolves.not.toThrow();
+		});
+
+		it('validates boolean flag conversion', async () => {
+			// Test the boolean flag handling specifically
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: true, // Should convert to initGit: true
+					aliases: false, // Should convert to addAliases: false
+					dryRun: true
+				})
+			).resolves.not.toThrow();
+
+			await expect(
+				initializeProject({
+					...baseOptions,
+					git: false, // Should convert to initGit: false
+					aliases: true, // Should convert to addAliases: true
+					dryRun: true
+				})
+			).resolves.not.toThrow();
+		});
+	});
+});

tests/unit/manage-gitignore.test.js

@@ -0,0 +1,439 @@
+/**
+ * Unit tests for manage-gitignore.js module
+ * Tests the logic with Jest spies instead of mocked modules
+ */
+
+import { jest } from '@jest/globals';
+import fs from 'fs';
+import path from 'path';
+import os from 'os';
+
+// Import the module under test and its exports
+import manageGitignoreFile, {
+	normalizeLine,
+	isTaskLine,
+	buildTaskFilesSection,
+	TASK_FILES_COMMENT,
+	TASK_JSON_PATTERN,
+	TASK_DIR_PATTERN
+} from '../../src/utils/manage-gitignore.js';
+
+describe('manage-gitignore.js Unit Tests', () => {
+	let tempDir;
+
+	beforeEach(() => {
+		jest.clearAllMocks();
+
+		// Create a temporary directory for testing
+		tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'manage-gitignore-test-'));
+	});
+
+	afterEach(() => {
+		// Clean up the temporary directory
+		try {
+			fs.rmSync(tempDir, { recursive: true, force: true });
+		} catch (err) {
+			// Ignore cleanup errors
+		}
+	});
+
+	describe('Constants', () => {
+		test('should have correct constant values', () => {
+			expect(TASK_FILES_COMMENT).toBe('# Task files');
+			expect(TASK_JSON_PATTERN).toBe('tasks.json');
+			expect(TASK_DIR_PATTERN).toBe('tasks/');
+		});
+	});
+
+	describe('normalizeLine function', () => {
+		test('should remove leading/trailing whitespace', () => {
+			expect(normalizeLine('  test  ')).toBe('test');
+		});
+
+		test('should remove comment hash and trim', () => {
+			expect(normalizeLine('# tasks.json')).toBe('tasks.json');
+			expect(normalizeLine('#tasks/')).toBe('tasks/');
+		});
+
+		test('should handle empty strings', () => {
+			expect(normalizeLine('')).toBe('');
+			expect(normalizeLine('   ')).toBe('');
+		});
+
+		test('should handle lines without comments', () => {
+			expect(normalizeLine('tasks.json')).toBe('tasks.json');
+		});
+	});
+
+	describe('isTaskLine function', () => {
+		test('should identify task.json patterns', () => {
+			expect(isTaskLine('tasks.json')).toBe(true);
+			expect(isTaskLine('# tasks.json')).toBe(true);
+			expect(isTaskLine('  # tasks.json  ')).toBe(true);
+		});
+
+		test('should identify tasks/ patterns', () => {
+			expect(isTaskLine('tasks/')).toBe(true);
+			expect(isTaskLine('# tasks/')).toBe(true);
+			expect(isTaskLine('  # tasks/  ')).toBe(true);
+		});
+
+		test('should reject non-task patterns', () => {
+			expect(isTaskLine('node_modules/')).toBe(false);
+			expect(isTaskLine('# Some comment')).toBe(false);
+			expect(isTaskLine('')).toBe(false);
+			expect(isTaskLine('tasks.txt')).toBe(false);
+		});
+	});
+
+	describe('buildTaskFilesSection function', () => {
+		test('should build commented section when storeTasksInGit is true (tasks stored in git)', () => {
+			const result = buildTaskFilesSection(true);
+			expect(result).toEqual(['# Task files', '# tasks.json', '# tasks/ ']);
+		});
+
+		test('should build uncommented section when storeTasksInGit is false (tasks ignored)', () => {
+			const result = buildTaskFilesSection(false);
+			expect(result).toEqual(['# Task files', 'tasks.json', 'tasks/ ']);
+		});
+	});
+
+	describe('manageGitignoreFile function - Input Validation', () => {
+		test('should throw error for invalid targetPath', () => {
+			expect(() => {
+				manageGitignoreFile('', 'content', false);
+			}).toThrow('targetPath must be a non-empty string');
+
+			expect(() => {
+				manageGitignoreFile(null, 'content', false);
+			}).toThrow('targetPath must be a non-empty string');
+
+			expect(() => {
+				manageGitignoreFile('invalid.txt', 'content', false);
+			}).toThrow('targetPath must end with .gitignore');
+		});
+
+		test('should throw error for invalid content', () => {
+			expect(() => {
+				manageGitignoreFile('.gitignore', '', false);
+			}).toThrow('content must be a non-empty string');
+
+			expect(() => {
+				manageGitignoreFile('.gitignore', null, false);
+			}).toThrow('content must be a non-empty string');
+		});
+
+		test('should throw error for invalid storeTasksInGit', () => {
+			expect(() => {
+				manageGitignoreFile('.gitignore', 'content', 'not-boolean');
+			}).toThrow('storeTasksInGit must be a boolean');
+		});
+	});
+
+	describe('manageGitignoreFile function - File Operations with Spies', () => {
+		let writeFileSyncSpy;
+		let readFileSyncSpy;
+		let existsSyncSpy;
+		let mockLog;
+
+		beforeEach(() => {
+			// Set up spies
+			writeFileSyncSpy = jest
+				.spyOn(fs, 'writeFileSync')
+				.mockImplementation(() => {});
+			readFileSyncSpy = jest
+				.spyOn(fs, 'readFileSync')
+				.mockImplementation(() => '');
+			existsSyncSpy = jest
+				.spyOn(fs, 'existsSync')
+				.mockImplementation(() => false);
+			mockLog = jest.fn();
+		});
+
+		afterEach(() => {
+			// Restore original implementations
+			writeFileSyncSpy.mockRestore();
+			readFileSyncSpy.mockRestore();
+			existsSyncSpy.mockRestore();
+		});
+
+		describe('New File Creation', () => {
+			const templateContent = `# Logs
+logs
+*.log
+
+# Task files
+tasks.json
+tasks/ `;
+
+			test('should create new file with commented task lines when storeTasksInGit is true', () => {
+				existsSyncSpy.mockReturnValue(false); // File doesn't exist
+
+				manageGitignoreFile('.gitignore', templateContent, true, mockLog);
+
+				expect(writeFileSyncSpy).toHaveBeenCalledWith(
+					'.gitignore',
+					`# Logs
+logs
+*.log
+
+# Task files
+# tasks.json
+# tasks/ `
+				);
+				expect(mockLog).toHaveBeenCalledWith(
+					'success',
+					'Created .gitignore with full template'
+				);
+			});
+
+			test('should create new file with uncommented task lines when storeTasksInGit is false', () => {
+				existsSyncSpy.mockReturnValue(false); // File doesn't exist
+
+				manageGitignoreFile('.gitignore', templateContent, false, mockLog);
+
+				expect(writeFileSyncSpy).toHaveBeenCalledWith(
+					'.gitignore',
+					`# Logs
+logs
+*.log
+
+# Task files
+tasks.json
+tasks/ `
+				);
+				expect(mockLog).toHaveBeenCalledWith(
+					'success',
+					'Created .gitignore with full template'
+				);
+			});
+
+			test('should handle write errors gracefully', () => {
+				existsSyncSpy.mockReturnValue(false);
+				const writeError = new Error('Permission denied');
+				writeFileSyncSpy.mockImplementation(() => {
+					throw writeError;
+				});
+
+				expect(() => {
+					manageGitignoreFile('.gitignore', templateContent, false, mockLog);
+				}).toThrow('Permission denied');
+
+				expect(mockLog).toHaveBeenCalledWith(
+					'error',
+					'Failed to create .gitignore: Permission denied'
+				);
+			});
+		});
+
+		describe('File Merging', () => {
+			const templateContent = `# Logs
+logs
+*.log
+
+# Dependencies
+node_modules/
+
+# Task files
+tasks.json
+tasks/ `;
+
+			test('should merge with existing file and add new content', () => {
+				const existingContent = `# Old content
+old-file.txt
+
+# Task files
+# tasks.json
+# tasks/`;
+
+				existsSyncSpy.mockReturnValue(true); // File exists
+				readFileSyncSpy.mockReturnValue(existingContent);
+
+				manageGitignoreFile('.gitignore', templateContent, false, mockLog);
+
+				expect(writeFileSyncSpy).toHaveBeenCalledWith(
+					'.gitignore',
+					expect.stringContaining('# Old content')
+				);
+				expect(writeFileSyncSpy).toHaveBeenCalledWith(
+					'.gitignore',
+					expect.stringContaining('# Logs')
+				);
+				expect(writeFileSyncSpy).toHaveBeenCalledWith(
+					'.gitignore',
+					expect.stringContaining('# Dependencies')
+				);
+				expect(writeFileSyncSpy).toHaveBeenCalledWith(
+					'.gitignore',
+					expect.stringContaining('# Task files')
+				);
+			});
+
+			test('should remove existing task section and replace with new preferences', () => {
+				const existingContent = `# Existing
+existing.txt
+
+# Task files
+tasks.json
+tasks/
+
+# More content
+more.txt`;
+
+				existsSyncSpy.mockReturnValue(true);
+				readFileSyncSpy.mockReturnValue(existingContent);
+
+				manageGitignoreFile('.gitignore', templateContent, false, mockLog);
+
+				const writtenContent = writeFileSyncSpy.mock.calls[0][1];
+
+				// Should contain existing non-task content
+				expect(writtenContent).toContain('# Existing');
+				expect(writtenContent).toContain('existing.txt');
+				expect(writtenContent).toContain('# More content');
+				expect(writtenContent).toContain('more.txt');
+
+				// Should contain new template content
+				expect(writtenContent).toContain('# Logs');
+				expect(writtenContent).toContain('# Dependencies');
+
+				// Should have uncommented task lines (storeTasksInGit = false means ignore tasks)
+				expect(writtenContent).toMatch(
+					/# Task files\s*[\r\n]+tasks\.json\s*[\r\n]+tasks\/ /
+				);
+			});
+
+			test('should handle different task preferences correctly', () => {
+				const existingContent = `# Existing
+existing.txt
+
+# Task files
+# tasks.json
+# tasks/`;
+
+				existsSyncSpy.mockReturnValue(true);
+				readFileSyncSpy.mockReturnValue(existingContent);
+
+				// Test with storeTasksInGit = true (commented)
+				manageGitignoreFile('.gitignore', templateContent, true, mockLog);
+
+				const writtenContent = writeFileSyncSpy.mock.calls[0][1];
+				expect(writtenContent).toMatch(
+					/# Task files\s*[\r\n]+# tasks\.json\s*[\r\n]+# tasks\/ /
+				);
+			});
+
+			test('should not duplicate existing template content', () => {
+				const existingContent = `# Logs
+logs
+*.log
+
+# Dependencies  
+node_modules/
+
+# Task files
+# tasks.json
+# tasks/`;
+
+				existsSyncSpy.mockReturnValue(true);
+				readFileSyncSpy.mockReturnValue(existingContent);
+
+				manageGitignoreFile('.gitignore', templateContent, false, mockLog);
+
+				const writtenContent = writeFileSyncSpy.mock.calls[0][1];
+
+				// Should not duplicate the logs section
+				const logsCount = (writtenContent.match(/# Logs/g) || []).length;
+				expect(logsCount).toBe(1);
+
+				// Should not duplicate dependencies
+				const depsCount = (writtenContent.match(/# Dependencies/g) || [])
+					.length;
+				expect(depsCount).toBe(1);
+			});
+
+			test('should handle read errors gracefully', () => {
+				existsSyncSpy.mockReturnValue(true);
+				const readError = new Error('File not readable');
+				readFileSyncSpy.mockImplementation(() => {
+					throw readError;
+				});
+
+				expect(() => {
+					manageGitignoreFile('.gitignore', templateContent, false, mockLog);
+				}).toThrow('File not readable');
+
+				expect(mockLog).toHaveBeenCalledWith(
+					'error',
+					'Failed to merge content with .gitignore: File not readable'
+				);
+			});
+
+			test('should handle write errors during merge gracefully', () => {
+				existsSyncSpy.mockReturnValue(true);
+				readFileSyncSpy.mockReturnValue('existing content');
+
+				const writeError = new Error('Disk full');
+				writeFileSyncSpy.mockImplementation(() => {
+					throw writeError;
+				});
+
+				expect(() => {
+					manageGitignoreFile('.gitignore', templateContent, false, mockLog);
+				}).toThrow('Disk full');
+
+				expect(mockLog).toHaveBeenCalledWith(
+					'error',
+					'Failed to merge content with .gitignore: Disk full'
+				);
+			});
+		});
+
+		describe('Edge Cases', () => {
+			test('should work without log function', () => {
+				existsSyncSpy.mockReturnValue(false);
+				const templateContent = `# Test
+test.txt
+
+# Task files
+tasks.json
+tasks/`;
+
+				expect(() => {
+					manageGitignoreFile('.gitignore', templateContent, false);
+				}).not.toThrow();
+
+				expect(writeFileSyncSpy).toHaveBeenCalled();
+			});
+
+			test('should handle empty existing file', () => {
+				existsSyncSpy.mockReturnValue(true);
+				readFileSyncSpy.mockReturnValue('');
+
+				const templateContent = `# Task files
+tasks.json
+tasks/`;
+
+				manageGitignoreFile('.gitignore', templateContent, false, mockLog);
+
+				expect(writeFileSyncSpy).toHaveBeenCalled();
+				const writtenContent = writeFileSyncSpy.mock.calls[0][1];
+				expect(writtenContent).toContain('# Task files');
+			});
+
+			test('should handle template with only task files', () => {
+				existsSyncSpy.mockReturnValue(false);
+				const templateContent = `# Task files
+tasks.json
+tasks/ `;
+
+				manageGitignoreFile('.gitignore', templateContent, true, mockLog);
+
+				const writtenContent = writeFileSyncSpy.mock.calls[0][1];
+				expect(writtenContent).toBe(`# Task files
+# tasks.json
+# tasks/ `);
+			});
+		});
+	});
+});

vite.config.js

@@ -0,0 +1,72 @@
+import { defineConfig } from 'vite';
+import { resolve } from 'path';
+import { nodeResolve } from '@rollup/plugin-node-resolve';
+
+export default defineConfig({
+	build: {
+		ssr: true, // Use SSR mode for Node.js
+		rollupOptions: {
+			// Multiple entry points for different applications
+			input: {
+				'task-master': resolve(__dirname, 'bin/task-master.js'), // CLI tool
+				'task-master-mcp': resolve(__dirname, 'mcp-server/server.js') // MCP server
+			},
+			// Bundle everything except Node.js built-ins
+			external: [
+				// Node.js built-in modules
+				'fs',
+				'fs/promises',
+				'path',
+				'os',
+				'crypto',
+				'http',
+				'https',
+				'net',
+				'tls',
+				'child_process',
+				'util',
+				'events',
+				'stream',
+				'url',
+				'querystring',
+				'buffer',
+				'module',
+				'worker_threads',
+				'readline',
+				'process',
+				'assert',
+				'zlib',
+				'dns',
+				'perf_hooks',
+				// Optional dependencies that might not be available
+				'@anthropic-ai/claude-code'
+			],
+			output: {
+				// Generate separate files for each entry
+				dir: 'dist',
+				format: 'cjs', // CommonJS for Node.js compatibility
+				entryFileNames: '[name].cjs',
+				chunkFileNames: 'chunks/[name]-[hash].cjs',
+				assetFileNames: 'assets/[name].[ext]'
+			},
+			plugins: [
+				nodeResolve({
+					preferBuiltins: true,
+					exportConditions: ['node']
+				})
+			]
+		},
+		target: 'node18',
+		outDir: 'dist',
+		minify: false, // Keep readable for debugging
+		sourcemap: false
+	},
+	define: {
+		// Define any environment variables if needed
+		'process.env.NODE_ENV': '"production"'
+	},
+	ssr: {
+		// Don't externalize any dependencies - bundle them all
+		noExternal: true
+	}
+});