fix(tags): Resolve critical tag deletion and migration notice bugs

Major Issues Fixed:

1. Tag Deletion Bug: Fixed critical issue where creating subtasks would delete other tags

   - Root cause: writeJSON function wasn't accepting projectRoot/tag parameters

   - Fixed writeJSON signature and logic to handle tagged data structure

   - Added proper merging of resolved tag data back into full tagged structure

2. Persistent Migration Notice: Fixed FYI notice showing after every command

   - Root cause: markMigrationForNotice was resetting migrationNoticeShown to false

   - Fixed migration logic to only trigger on actual legacy->tagged migrations

   - Added proper _rawTaggedData checks to prevent false migration detection

3. Data Corruption Prevention: Enhanced data integrity safeguards

   - Fixed writeJSON to filter out internal properties

   - Added automatic cleanup of rogue properties

   - Improved hasTaggedStructure detection logic

Commands Fixed: add-subtask, remove-subtask, and all commands now preserve tags correctly

scripts/modules/task-manager/add-subtask.js

@@ -11,6 +11,7 @@ import generateTaskFiles from './generate-task-files.js';
  * @param {number|string|null} existingTaskId - ID of an existing task to convert to subtask (optional)
  * @param {Object} newSubtaskData - Data for creating a new subtask (used if existingTaskId is null)
  * @param {boolean} generateFiles - Whether to regenerate task files after adding the subtask
+ * @param {Object} context - Context object containing projectRoot and tag information
  * @returns {Object} The newly created or converted subtask
  */
 async function addSubtask(
@@ -18,13 +19,14 @@ async function addSubtask(
 	parentId,
 	existingTaskId = null,
 	newSubtaskData = null,
-	generateFiles = true
+	generateFiles = true,
+	context = {}
 ) {
 	try {
 		log('info', `Adding subtask to parent task ${parentId}...`);
 
-		// Read the existing tasks
-		const data = readJSON(tasksPath);
+		// Read the existing tasks with proper context
+		const data = readJSON(tasksPath, context.projectRoot, context.tag);
 		if (!data || !data.tasks) {
 			throw new Error(`Invalid or missing tasks file at ${tasksPath}`);
 		}
@@ -134,13 +136,13 @@ async function addSubtask(
 			);
 		}
 
-		// Write the updated tasks back to the file
-		writeJSON(tasksPath, data);
+		// Write the updated tasks back to the file with proper context
+		writeJSON(tasksPath, data, context.projectRoot, context.tag);
 
 		// Generate task files if requested
 		if (generateFiles) {
 			log('info', 'Regenerating task files...');
-			await generateTaskFiles(tasksPath, path.dirname(tasksPath));
+			await generateTaskFiles(tasksPath, path.dirname(tasksPath), context);
 		}
 
 		return newSubtask;

scripts/modules/task-manager/add-task.js

@@ -226,12 +226,18 @@ async function addTask(
 		}
 
 		// Handle legacy format migration using utilities
-		if (rawData && Array.isArray(rawData.tasks)) {
-			report('Migrating legacy tasks.json format to tagged format...', 'info');
-			const legacyTasks = rawData.tasks;
+		if (rawData && Array.isArray(rawData.tasks) && !rawData._rawTaggedData) {
+			report('Legacy format detected. Migrating to tagged format...', 'info');
+
+			// This is legacy format - migrate it to tagged format
 			rawData = {
 				master: {
-					tasks: legacyTasks
+					tasks: rawData.tasks,
+					metadata: rawData.metadata || {
+						created: new Date().toISOString(),
+						updated: new Date().toISOString(),
+						description: 'Tasks for master context'
+					}
 				}
 			};
 			// Ensure proper metadata using utility

scripts/modules/task-manager/generate-task-files.js

@@ -11,7 +11,7 @@ import { getDebugFlag } from '../config-manager.js';
  * Generate individual task files from tasks.json
  * @param {string} tasksPath - Path to the tasks.json file
  * @param {string} outputDir - Output directory for task files
- * @param {Object} options - Additional options (mcpLog for MCP mode)
+ * @param {Object} options - Additional options (mcpLog for MCP mode, projectRoot, tag)
  * @returns {Object|undefined} Result object in MCP mode, undefined in CLI mode
  */
 function generateTaskFiles(tasksPath, outputDir, options = {}) {
@@ -19,7 +19,7 @@ function generateTaskFiles(tasksPath, outputDir, options = {}) {
 		// Determine if we're in MCP mode by checking for mcpLog
 		const isMcpMode = !!options?.mcpLog;
 
-		const data = readJSON(tasksPath);
+		const data = readJSON(tasksPath, options.projectRoot, options.tag);
 		if (!data || !data.tasks) {
 			throw new Error(`No valid tasks found in ${tasksPath}`);
 		}
@@ -33,7 +33,12 @@ function generateTaskFiles(tasksPath, outputDir, options = {}) {
 
 		// Validate and fix dependencies before generating files
 		log('info', `Validating and fixing dependencies`);
-		validateAndFixDependencies(data, tasksPath);
+		validateAndFixDependencies(
+			data,
+			tasksPath,
+			options.projectRoot,
+			options.tag
+		);
 
 		// Get valid task IDs from tasks.json
 		const validTaskIds = data.tasks.map((task) => task.id);

scripts/modules/task-manager/tag-management.js

@@ -566,10 +566,10 @@ async function tags(
 			tagList.push({
 				name: tagName,
 				isCurrent: tagName === currentTag,
-				taskCount: tasks.length,
 				completedTasks: tasks.filter(
 					(t) => t.status === 'done' || t.status === 'completed'
 				).length,
+				tasks: tasks || [],
 				created: metadata.created || 'Unknown',
 				description: metadata.description || 'No description'
 			});
@@ -634,7 +634,7 @@ async function tags(
 				row.push(tagDisplay);
 
 				if (showTaskCounts) {
-					row.push(chalk.white(tag.taskCount.toString()));
+					row.push(chalk.white(tag.tasks.length.toString()));
 					row.push(chalk.green(tag.completedTasks.toString()));
 				}
 
@@ -1034,8 +1034,7 @@ async function copyTag(
 					`Copy of "${sourceName}" created on ${new Date().toLocaleDateString()}`,
 				copiedFrom: {
 					tag: sourceName,
-					date: new Date().toISOString(),
-					taskCount: sourceTasks.length
+					date: new Date().toISOString()
 				}
 			}
 		};
@@ -1061,7 +1060,6 @@ async function copyTag(
 				sourceName,
 				targetName,
 				copied: true,
-				taskCount: sourceTasks.length,
 				description:
 					description ||
 					`Copy of "${sourceName}" created on ${new Date().toLocaleDateString()}`
@@ -1091,7 +1089,6 @@ async function copyTag(
 			sourceName,
 			targetName,
 			copied: true,
-			taskCount: sourceTasks.length,
 			description:
 				description ||
 				`Copy of "${sourceName}" created on ${new Date().toLocaleDateString()}`