feat: implement research command with enhanced context gathering - Add comprehensive research command with AI-powered queries - Implement ContextGatherer utility for reusable context extraction - Support multiple context types: tasks, files, custom text, project tree - Add fuzzy search integration for automatic task discovery - Implement detailed token breakdown display with syntax highlighting - Add enhanced UI with boxed output and code block formatting - Support different detail levels (low, medium, high) for responses - Include project-specific context for more relevant AI responses - Add token counting with gpt-tokens library integration - Create reusable patterns for future context-aware commands - Task 94.4 completed

scripts/modules/commands.js

@@ -1444,7 +1444,7 @@ function registerCommands(programInstance) {
 			'Additional custom context to include in the research prompt'
 		)
 		.option(
-			'-t, --tree',
+			'--project-tree',
 			'Include project file tree structure in the research context'
 		)
 		.option(
@@ -1578,7 +1578,7 @@ function registerCommands(programInstance) {
 				taskIds: taskIds,
 				filePaths: filePaths,
 				customContext: options.context ? options.context.trim() : null,
-				includeProjectTree: !!options.tree,
+				includeProjectTree: !!options.projectTree,
 				saveTarget: options.save ? options.save.trim() : null,
 				detailLevel: options.detail ? options.detail.toLowerCase() : 'medium',
 				tasksPath: tasksPath,

scripts/modules/task-manager.js

@@ -50,7 +50,7 @@ export {
 	taskExists,
 	isTaskDependentOn,
 	moveTask,
-	performResearch,
 	readComplexityReport,
-	migrateProject
+	migrateProject,
+	performResearch
 };

scripts/modules/ui.js

@@ -924,6 +924,11 @@ function displayHelp() {
 					name: 'expand --all',
 					args: '[--force] [--research]',
 					desc: 'Expand all pending tasks with subtasks'
+				},
+				{
+					name: 'research',
+					args: '"<prompt>" [-i=<task_ids>] [-f=<file_paths>] [-c="<context>"] [--project-tree] [-s=<save_file>] [-d=<detail_level>]',
+					desc: 'Perform AI-powered research queries with project context'
 				}
 			]
 		},

scripts/modules/utils/fuzzyTaskSearch.js

@@ -276,11 +276,7 @@ export class FuzzyTaskSearch {
 	 * @returns {Array<string>} Array of task ID strings
 	 */
 	getTaskIds(searchResults) {
-		return searchResults.results.map((task) => {
-			// Use searchableId if available (for flattened tasks with subtasks)
-			// Otherwise fall back to regular id
-			return task.searchableId || task.id.toString();
-		});
+		return searchResults.results.map((task) => task.id.toString());
 	}
 
 	/**