fix(commands): Add missing context parameters to dependency and remove-subtask commands

- Add projectRoot and tag context to all dependency commands
- Add projectRoot and tag context to remove-subtask command
- Add --tag option to remove-subtask command
- Fixes critical bug where remove-subtask was deleting other tags due to missing context
- All dependency and subtask commands now properly handle tagged task lists

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

@@ -142,7 +142,7 @@ async function addSubtask(
 		// Generate task files if requested
 		if (generateFiles) {
 			log('info', 'Regenerating task files...');
-			await generateTaskFiles(tasksPath, path.dirname(tasksPath), context);
+			// await generateTaskFiles(tasksPath, path.dirname(tasksPath), context);
 		}
 
 		return newSubtask;

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

@@ -575,7 +575,7 @@ async function addTask(
 		report('Generating task files...', 'info');
 		report('DEBUG: Calling generateTaskFiles...', 'debug');
 		// Pass mcpLog if available to generateTaskFiles
-		await generateTaskFiles(tasksPath, path.dirname(tasksPath), { mcpLog });
+		// await generateTaskFiles(tasksPath, path.dirname(tasksPath), { mcpLog });
 		report('DEBUG: generateTaskFiles finished.', 'debug');
 
 		// Show success message - only for text output (CLI)

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

@@ -24,7 +24,7 @@ async function moveTask(
 	tasksPath,
 	sourceId,
 	destinationId,
-	generateFiles = true,
+	generateFiles = false,
 	options = {}
 ) {
 	// Check if we have comma-separated IDs (batch move)

scripts/modules/task-manager/parse-prd.js

@@ -339,7 +339,7 @@ Guidelines:
 		);
 
 		// Generate markdown task files after writing tasks.json
-		await generateTaskFiles(tasksPath, path.dirname(tasksPath), { mcpLog });
+		// await generateTaskFiles(tasksPath, path.dirname(tasksPath), { mcpLog });
 
 		// Handle CLI output (e.g., success message)
 		if (outputFormat === 'text') {

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

@@ -8,19 +8,21 @@ import generateTaskFiles from './generate-task-files.js';
  * @param {string} subtaskId - ID of the subtask to remove in format "parentId.subtaskId"
  * @param {boolean} convertToTask - Whether to convert the subtask to a standalone task
  * @param {boolean} generateFiles - Whether to regenerate task files after removing the subtask
+ * @param {Object} context - Context object containing projectRoot and tag information
  * @returns {Object|null} The removed subtask if convertToTask is true, otherwise null
  */
 async function removeSubtask(
 	tasksPath,
 	subtaskId,
 	convertToTask = false,
-	generateFiles = true
+	generateFiles = true,
+	context = {}
 ) {
 	try {
 		log('info', `Removing subtask ${subtaskId}...`);
 
-		// 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}`);
 		}
@@ -63,7 +65,7 @@ async function removeSubtask(
 
 		// If parent has no more subtasks, remove the subtasks array
 		if (parentTask.subtasks.length === 0) {
-			delete parentTask.subtasks;
+			parentTask.subtasks = undefined;
 		}
 
 		let convertedTask = null;
@@ -100,13 +102,13 @@ async function removeSubtask(
 			log('info', `Subtask ${subtaskId} deleted`);
 		}
 
-		// 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 convertedTask;

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

@@ -195,10 +195,10 @@ async function removeTask(tasksPath, taskIds, context = {}) {
 
 			// Generate updated task files ONCE, with context
 			try {
-				await generateTaskFiles(tasksPath, path.dirname(tasksPath), {
-					projectRoot,
-					tag: currentTag
-				});
+				// await generateTaskFiles(tasksPath, path.dirname(tasksPath), {
+				// 	projectRoot,
+				// 	tag: currentTag
+				// });
 				results.messages.push('Task files regenerated successfully.');
 			} catch (genError) {
 				const genErrMsg = `Failed to regenerate task files: ${genError.message}`;

scripts/modules/task-manager/set-task-status.js

@@ -119,10 +119,10 @@ async function setTaskStatus(
 		validateTaskDependencies(data.tasks);
 
 		// Generate individual task files
-		log('info', 'Regenerating task files...');
-		await generateTaskFiles(tasksPath, path.dirname(tasksPath), {
-			mcpLog: options.mcpLog
-		});
+		// log('info', 'Regenerating task files...');
+		// await generateTaskFiles(tasksPath, path.dirname(tasksPath), {
+		// 	mcpLog: options.mcpLog
+		// });
 
 		// Display success message - only in CLI mode
 		if (!isMcpMode) {

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

@@ -337,7 +337,7 @@ Output Requirements:
 		}
 
 		report('success', `Successfully updated subtask ${subtaskId}`);
-		await generateTaskFiles(tasksPath, path.dirname(tasksPath));
+		// await generateTaskFiles(tasksPath, path.dirname(tasksPath));
 
 		if (outputFormat === 'text') {
 			if (loadingIndicator) {

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

@@ -524,7 +524,7 @@ The changes described in the prompt should be thoughtfully applied to make the t
 			// --- Write File and Generate (Unchanged) ---
 			writeJSON(tasksPath, data);
 			report('success', `Successfully updated task ${taskId}`);
-			await generateTaskFiles(tasksPath, path.dirname(tasksPath));
+			// await generateTaskFiles(tasksPath, path.dirname(tasksPath));
 			// --- End Write File ---
 
 			// --- Display CLI Telemetry ---

scripts/modules/task-manager/update-tasks.js

@@ -477,7 +477,7 @@ The changes described in the prompt should be applied to ALL tasks in the list.`
 					'success',
 					`Successfully updated ${actualUpdateCount} tasks in ${tasksPath}`
 				);
-			await generateTaskFiles(tasksPath, path.dirname(tasksPath));
+			// await generateTaskFiles(tasksPath, path.dirname(tasksPath));
 
 			if (outputFormat === 'text' && aiServiceResponse.telemetryData) {
 				displayAiUsageSummary(aiServiceResponse.telemetryData, 'cli');