fix merge conflicts to prep for merge with branch next

- Enhance E2E testing and LLM analysis report and:
  - Add --analyze-log flag to run_e2e.sh to re-run LLM analysis on existing logs.
  - Add test:e2e and analyze-log scripts to package.json for easier execution.

- Correct display errors and dependency validation output:
  - Update chalk usage in add-task.js to use bracket notation (chalk[color]) compatible with v5, resolving 'chalk.keyword is not a function' error.
  - Modify fix-dependencies command output to show red failure box with issue count instead of green success box when validation fails.

- Refactor interactive model setup:
  - Verify inclusion of 'No change' option during interactive model setup flow (task-master models --setup).

- Update model definitions:
  - Add max_tokens field for gpt-4o in supported-models.json.

- Remove unused scripts:
  - Delete prepare-package.js and rule-transformer.test.js.

Release candidate

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

@@ -10,7 +10,7 @@ import os from 'os'; // Import os module for home directory check
 /**
  * Direct function wrapper for initializing a project.
  * Derives target directory from session, sets CWD, and calls core init logic.
- * @param {object} args - Arguments containing project details and options (projectName, projectDescription, yes, etc.)
+ * @param {object} args - Arguments containing initialization options (addAliases, skipInstall, yes, projectRoot)
  * @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.
@@ -92,12 +92,8 @@ export async function initializeProjectDirect(args, log, context = {}) {
 	try {
 		// Always force yes: true when called via MCP to avoid interactive prompts
 		const options = {
-			name: args.projectName,
-			description: args.projectDescription,
-			version: args.projectVersion,
-			author: args.authorName,
-			skipInstall: args.skipInstall,
 			aliases: args.addAliases,
+			skipInstall: args.skipInstall,
 			yes: true // Force yes mode
 		};
 

mcp-server/src/core/direct-functions/parse-prd.js

@@ -101,8 +101,12 @@ export async function parsePRDDirect(args, log, context = {}) {
 			}
 		}
 
+		// Extract the append flag from args
+		const append = Boolean(args.append) === true;
+
+		// Log key parameters including append flag
 		log.info(
-			`Preparing to parse PRD from ${inputPath} and output to ${outputPath} with ${numTasks} tasks`
+			`Preparing to parse PRD from ${inputPath} and output to ${outputPath} with ${numTasks} tasks, append mode: ${append}`
 		);
 
 		// --- Logger Wrapper ---
@@ -117,29 +121,61 @@ export async function parsePRDDirect(args, log, context = {}) {
 		// Enable silent mode to prevent console logs from interfering with JSON response
 		enableSilentMode();
 		try {
-			// Execute core parsePRD function - It now handles AI internally
-			const tasksDataResult = await parsePRD(inputPath, numTasks, options);
-
-			// Check the result from the core function (assuming it might return data or null/undefined)
-			if (!tasksDataResult || !tasksDataResult.tasks) {
-				throw new Error(
-					'Core parsePRD function did not return valid task data.'
-				);
+			// Make sure the output directory exists
+			const outputDir = path.dirname(outputPath);
+			if (!fs.existsSync(outputDir)) {
+				log.info(`Creating output directory: ${outputDir}`);
+				fs.mkdirSync(outputDir, { recursive: true });
 			}
 
-			log.info(
-				`Successfully parsed PRD and generated ${tasksDataResult.tasks?.length || 0} tasks`
+			// Execute core parsePRD function with AI client
+			const tasksDataResult = await parsePRD(
+				inputPath,
+				outputPath,
+				numTasks,
+				{
+					mcpLog: logWrapper,
+					session,
+					append
+				},
+				aiClient,
+				modelConfig
 			);
 
-			return {
-				success: true,
-				data: {
-					message: `Successfully generated ${tasksDataResult.tasks?.length || 0} tasks from PRD`,
-					taskCount: tasksDataResult.tasks?.length || 0,
-					outputPath
-				},
-				fromCache: false // This operation always modifies state
-			};
+			// Since parsePRD doesn't return a value but writes to a file, we'll read the result
+			// to return it to the caller
+			if (fs.existsSync(outputPath)) {
+				const tasksData = JSON.parse(fs.readFileSync(outputPath, 'utf8'));
+				const actionVerb = append ? 'appended' : 'generated';
+				const message = `Successfully ${actionVerb} ${tasksData.tasks?.length || 0} tasks from PRD`;
+
+				if (!tasksDataResult || !tasksDataResult.tasks || !tasksData) {
+					throw new Error(
+						'Core parsePRD function did not return valid task data.'
+					);
+				}
+
+				log.info(message);
+
+				return {
+					success: true,
+					data: {
+						message,
+						taskCount: tasksDataResult.tasks?.length || 0,
+						outputPath,
+						appended: append
+					},
+					fromCache: false // This operation always modifies state and should never be cached
+				};
+			} else {
+				const errorMessage = `Tasks file was not created at ${outputPath}`;
+				log.error(errorMessage);
+				return {
+					success: false,
+					error: { code: 'OUTPUT_FILE_NOT_CREATED', message: errorMessage },
+					fromCache: false
+				};
+			}
 		} finally {
 			// Always restore normal logging
 			disableSilentMode();

mcp-server/src/core/direct-functions/remove-task.js

@@ -3,18 +3,23 @@
  * Direct function implementation for removing a task
  */
 
-import { removeTask } from '../../../../scripts/modules/task-manager.js';
+import {
+	removeTask,
+	taskExists
+} from '../../../../scripts/modules/task-manager.js';
 import {
 	enableSilentMode,
-	disableSilentMode
+	disableSilentMode,
+	readJSON
 } from '../../../../scripts/modules/utils.js';
 
 /**
  * Direct function wrapper for removeTask with error handling.
+ * Supports removing multiple tasks at once with comma-separated IDs.
  *
  * @param {Object} args - Command arguments
  * @param {string} args.tasksJsonPath - Explicit path to the tasks.json file.
- * @param {string} args.id - The ID of the task or subtask to remove.
+ * @param {string} args.id - The ID(s) of the task(s) or subtask(s) to remove (comma-separated for multiple).
  * @param {Object} log - Logger object
  * @returns {Promise<Object>} - Remove task result { success: boolean, data?: any, error?: { code: string, message: string }, fromCache: false }
  */
@@ -36,8 +41,7 @@ export async function removeTaskDirect(args, log) {
 		}
 
 		// Validate task ID parameter
-		const taskId = id;
-		if (!taskId) {
+		if (!id) {
 			log.error('Task ID is required');
 			return {
 				success: false,
@@ -49,46 +53,103 @@ export async function removeTaskDirect(args, log) {
 			};
 		}
 
-		// Skip confirmation in the direct function since it's handled by the client
-		log.info(`Removing task with ID: ${taskId} from ${tasksJsonPath}`);
+		// Split task IDs if comma-separated
+		const taskIdArray = id.split(',').map((taskId) => taskId.trim());
 
-		try {
-			// Enable silent mode to prevent console logs from interfering with JSON response
-			enableSilentMode();
+		log.info(
+			`Removing ${taskIdArray.length} task(s) with ID(s): ${taskIdArray.join(', ')} from ${tasksJsonPath}`
+		);
 
-			// Call the core removeTask function using the provided path
-			const result = await removeTask(tasksJsonPath, taskId);
-
-			// Restore normal logging
-			disableSilentMode();
-
-			log.info(`Successfully removed task: ${taskId}`);
-
-			// Return the result
-			return {
-				success: true,
-				data: {
-					message: result.message,
-					taskId: taskId,
-					tasksPath: tasksJsonPath,
-					removedTask: result.removedTask
-				},
-				fromCache: false
-			};
-		} catch (error) {
-			// Make sure to restore normal logging even if there's an error
-			disableSilentMode();
-
-			log.error(`Error removing task: ${error.message}`);
+		// Validate all task IDs exist before proceeding
+		const data = readJSON(tasksJsonPath);
+		if (!data || !data.tasks) {
 			return {
 				success: false,
 				error: {
-					code: error.code || 'REMOVE_TASK_ERROR',
-					message: error.message || 'Failed to remove task'
+					code: 'INVALID_TASKS_FILE',
+					message: `No valid tasks found in ${tasksJsonPath}`
 				},
 				fromCache: false
 			};
 		}
+
+		const invalidTasks = taskIdArray.filter(
+			(taskId) => !taskExists(data.tasks, taskId)
+		);
+
+		if (invalidTasks.length > 0) {
+			return {
+				success: false,
+				error: {
+					code: 'INVALID_TASK_ID',
+					message: `The following tasks were not found: ${invalidTasks.join(', ')}`
+				},
+				fromCache: false
+			};
+		}
+
+		// Remove tasks one by one
+		const results = [];
+
+		// Enable silent mode to prevent console logs from interfering with JSON response
+		enableSilentMode();
+
+		try {
+			for (const taskId of taskIdArray) {
+				try {
+					const result = await removeTask(tasksJsonPath, taskId);
+					results.push({
+						taskId,
+						success: true,
+						message: result.message,
+						removedTask: result.removedTask
+					});
+					log.info(`Successfully removed task: ${taskId}`);
+				} catch (error) {
+					results.push({
+						taskId,
+						success: false,
+						error: error.message
+					});
+					log.error(`Error removing task ${taskId}: ${error.message}`);
+				}
+			}
+		} finally {
+			// Restore normal logging
+			disableSilentMode();
+		}
+
+		// Check if all tasks were successfully removed
+		const successfulRemovals = results.filter((r) => r.success);
+		const failedRemovals = results.filter((r) => !r.success);
+
+		if (successfulRemovals.length === 0) {
+			// All removals failed
+			return {
+				success: false,
+				error: {
+					code: 'REMOVE_TASK_ERROR',
+					message: 'Failed to remove any tasks',
+					details: failedRemovals
+						.map((r) => `${r.taskId}: ${r.error}`)
+						.join('; ')
+				},
+				fromCache: false
+			};
+		}
+
+		// At least some tasks were removed successfully
+		return {
+			success: true,
+			data: {
+				totalTasks: taskIdArray.length,
+				successful: successfulRemovals.length,
+				failed: failedRemovals.length,
+				results: results,
+				tasksPath: tasksJsonPath
+			},
+			fromCache: false
+		};
 	} catch (error) {
 		// Ensure silent mode is disabled even if an outer error occurs
 		disableSilentMode();