fix: improve docs and command help for analzye-complexity

Co-authored-by: Ralph Khreish <35776126+Crunchyman-ralph@users.noreply.github.com>

.changeset/chore-fix-docs.md

@@ -0,0 +1,5 @@
+---
+"task-master-ai": patch
+---
+
+Improve `analyze-complexity` cli docs and `--research` flag documentation

.changeset/mcp-timeout-configuration.md

@@ -0,0 +1,13 @@
+---
+"task-master-ai": minor
+---
+
+Enhanced Roo Code profile with MCP timeout configuration for improved reliability during long-running AI operations. The Roo profile now automatically configures a 300-second timeout for MCP server operations, preventing timeouts during complex tasks like `parse-prd`, `expand-all`, `analyze-complexity`, and `research` operations. This change also replaces static MCP configuration files with programmatic generation for better maintainability.
+
+**What's New:**
+- 300-second timeout for MCP operations (up from default 60 seconds)
+- Programmatic MCP configuration generation (replaces static asset files)
+- Enhanced reliability for AI-powered operations
+- Consistent with other AI coding assistant profiles
+
+**Migration:** No user action required - existing Roo Code installations will automatically receive the enhanced MCP configuration on next initialization.

.changeset/petite-ideas-grab.md

@@ -0,0 +1,5 @@
+---
+"task-master-ai": patch
+---
+
+Fix Claude Code settings validation for pathToClaudeCodeExecutable

apps/docs/capabilities/cli-root-commands.mdx

@@ -156,7 +156,7 @@ sidebarTitle: "CLI Commands"
     # Use an alternative tasks file
     task-master analyze-complexity --file=custom-tasks.json
 
-    # Use Perplexity AI for research-backed complexity analysis
+    # Use your configured research model for research-backed complexity analysis
     task-master analyze-complexity --research
     ```
   </Accordion>
@@ -206,25 +206,4 @@ sidebarTitle: "CLI Commands"
     task-master init
     ```
   </Accordion>
-
-  <Accordion title="Start Working on Tasks">
-    ```bash
-    # Start working on a specific task with Claude Code
-    task-master start <task-id>
-
-    # Start working on the next available task automatically
-    task-master start
-
-    # Example: Start working on task 1.2
-    task-master start 1.2
-    ```
-
-    The `start` command automatically launches Claude Code with a comprehensive prompt containing:
-    - Complete task details and context
-    - Implementation guidelines and best practices
-    - Relevant codebase information
-    - Dependencies and requirements
-
-    When no task ID is provided, it automatically detects and starts the next available task.
-  </Accordion>
 </AccordionGroup>

apps/docs/getting-started/quick-start/configuration-quick.mdx

@@ -30,8 +30,7 @@ For MCP/Cursor usage: Configure keys in the env section of your .cursor/mcp.json
 				"MISTRAL_API_KEY": "MISTRAL_API_KEY_HERE",
 				"AZURE_OPENAI_API_KEY": "AZURE_OPENAI_API_KEY_HERE",
 				"OLLAMA_API_KEY": "OLLAMA_API_KEY_HERE",
-				"GITHUB_API_KEY": "GITHUB_API_KEY_HERE",
-				"GROK_CLI_API_KEY": "GROK_CLI_API_KEY_HERE"
+				"GITHUB_API_KEY": "GITHUB_API_KEY_HERE"
 			}
 		}
 	}
@@ -63,50 +62,8 @@ PERPLEXITY_API_KEY=pplx-your-key-here
 
 # Google Vertex AI Configuration (Required if using 'vertex' provider)
 # VERTEX_PROJECT_ID=your-gcp-project-id
-
-# Grok CLI Configuration (Required if using 'grok-cli' provider)
-# GROK_CLI_API_KEY=your-grok-api-key-here
-
-# Codebase Analysis Feature Control
-# TASKMASTER_ENABLE_CODEBASE_ANALYSIS=true  # Enable codebase analysis features (default: true)
 ```
 
-## Grok Provider Setup
-
-Task Master now supports Grok models from xAI with full codebase context awareness. This is especially useful for AI operations that benefit from understanding your entire project structure.
-
-### Getting Started with Grok
-
-1. **Get your Grok API key** from [console.x.ai](https://console.x.ai)
-2. **Set the environment variable**:
-   ```bash
-   export GROK_CLI_API_KEY="your-api-key-here"
-   ```
-3. **Configure Task Master to use Grok**:
-   ```bash
-   task-master models --set-main grok-beta
-   # or
-   task-master models --set-research grok-beta
-   # or  
-   task-master models --set-fallback grok-beta
-   ```
-
-### Key Features
-
-- **Full codebase context**: Grok models can analyze your entire project when generating tasks or parsing PRDs
-- **xAI model access**: Support for latest Grok models (grok-2, grok-3, grok-4, etc.)
-- **Code-aware task generation**: Create more accurate and contextual tasks based on your actual codebase
-- **Intelligent PRD parsing**: Parse requirements with understanding of your existing code structure
-
-### Available Models
-
-- `grok-beta` - Latest Grok model with codebase context
-- `grok-vision-beta` - Grok with vision capabilities and codebase context
-
-<Note>
-The Grok CLI provider integrates with xAI's Grok models via [grok-cli](https://github.com/superagent-ai/grok-cli) by Superagent AI and can also use the local Grok CLI configuration file (`~/.grok/user-settings.json`) if available.
-</Note>
-
 ## What Else Can Be Configured?
 
 The main configuration file (`.taskmaster/config.json`) allows you to control nearly every aspect of Task Master’s behavior. Here’s a high-level look at what you can customize:
@@ -132,13 +89,6 @@ You don’t need to configure everything up front. Most settings can be left as
 - `defaultSubtasks`: Number of subtasks to auto-generate
 - `defaultPriority`: Priority level for new tasks
 
-### Codebase Analysis Control
-- `TASKMASTER_ENABLE_CODEBASE_ANALYSIS`: Control whether codebase analysis features are enabled
-  - Can be set via environment variables, MCP configuration, or project config files
-  - Priority order: `.env` > MCP session env > `.taskmaster/config.json`
-  - Default: `true`
-  - When enabled, allows providers like Claude Code and Gemini CLI to analyze your project structure for more contextual task generation
-
 ### API Endpoint Overrides
 - `ollamaBaseURL`: Custom Ollama server URL
 - `azureBaseURL`: Global Azure endpoint

apps/docs/getting-started/quick-start/tasks-quick.mdx

@@ -61,9 +61,25 @@ Task Master can provide a complexity report which can be helpful to read before
 Can you analyze the complexity of our tasks to help me understand which ones need to be broken down further?
 ```
 
+The agent will use the `analyze_project_complexity` MCP tool, or you can run it directly with the CLI command:
+```bash
+task-master analyze-complexity
+```
+
+For more comprehensive analysis using your configured research model, you can use:
+```bash
+task-master analyze-complexity --research
+```
+
+<Tip>
+The `--research` flag uses whatever research model you have configured in `.taskmaster/config.json` (configurable via `task-master models --setup`) for research-backed complexity analysis, providing more informed recommendations.
+</Tip>
+
 You can view the report in a friendly table using:
 ```
 Can you show me the complexity report in a more readable format?
 ```
 
+For more detailed CLI options, see the [Analyze Task Complexity](/docs/capabilities/cli-root-commands#analyze-task-complexity) section.
+
 <Check>Now you are ready to begin [executing tasks](/docs/getting-started/quick-start/execute-quick)</Check>

apps/docs/whats-new.mdx

@@ -3,78 +3,4 @@ title: "What's New"
 sidebarTitle: "What's New"
 ---
 
-## Version 0.27.0 - Latest Release
-
-### New Features
-
-#### `task-master start` Command
-- **Automated Task Execution**: New command that automatically launches Claude Code with comprehensive task context
-- **Smart Task Detection**: When no task ID is provided, automatically detects and starts the next available task
-- **Rich Context**: Provides complete task details, implementation guidelines, and codebase information to Claude Code
-
-#### Grok Provider Integration
-- **Full Codebase Context**: Grok models can now analyze your entire project when generating tasks or parsing PRDs
-- **xAI Model Support**: Access to latest Grok models (grok-2, grok-3, grok-4, etc.) via the grok-cli integration
-- **Code-Aware Generation**: More accurate and contextual task creation based on your actual codebase structure
-- **Available Models**: 
-  - `grok-beta` - Latest Grok model with codebase context
-  - `grok-vision-beta` - Grok with vision capabilities and codebase context
-
-### Improvements
-
-#### Enhanced Provider Defaults
-- **Main Model**: Upgraded from Claude 3.5 Sonnet to **Claude Sonnet 4** for better performance
-- **Fallback Model**: Improved from Claude 3.5 Sonnet to **Claude 3.7** for enhanced reliability
-
-#### MCP Server Simplification
-- **No More --package Flag**: Removed the need for `--package=task-master-ai` in MCP server configuration
-- **Bundled Package**: The entire package is now bundled, eliminating common configuration issues
-
-#### Auto-Update Functionality
-- **CLI Auto-Updates**: Every CLI command now includes auto-update functionality to keep you on the latest version
-
-#### Codebase Analysis Feature Control
-- **Configurable Analysis**: New `TASKMASTER_ENABLE_CODEBASE_ANALYSIS` environment variable to control codebase analysis features
-- **Multiple Configuration Sources**: Can be set via `.env`, MCP configuration, or project config files
-- **Priority System**: Environment variables > MCP session env > `.taskmaster/config.json`
-
-### TypeScript Migration
-- **Improved Development**: Moving from JavaScript to TypeScript environment for better development experience
-- **Gradual Migration**: JavaScript commands are being incrementally moved to TypeScript
-
-## Getting Started with New Features
-
-### Using the Start Command
-```bash
-# Start working on a specific task
-task-master start 1.2
-
-# Auto-detect and start next available task  
-task-master start
-```
-
-### Setting up Grok
-```bash
-# Set your API key
-export GROK_CLI_API_KEY="your-api-key-here"
-
-# Configure Grok as your main provider
-task-master models --set-main grok-beta
-```
-
-### Simplified MCP Configuration
-```json
-{
-  "mcpServers": {
-    "task-master-ai": {
-      "command": "npx",
-      "args": ["-y", "task-master-ai"],
-      "env": {
-        "ANTHROPIC_API_KEY": "your-key-here"
-      }
-    }
-  }
-}
-```
-
-For detailed setup instructions and configuration options, see our [Configuration Guide](/docs/getting-started/quick-start/configuration-quick).
+An easy way to see the latest releases

docs/configuration.md

@@ -235,6 +235,60 @@ node scripts/init.js
    - "MCP provider requires session context" → Ensure running in MCP environment
    - See the [MCP Provider Guide](./mcp-provider-guide.md) for detailed troubleshooting
 
+### MCP Timeout Configuration
+
+Long-running AI operations in taskmaster-ai can exceed the default 60-second MCP timeout. Operations like `parse_prd`, `expand_task`, `research`, and `analyze_project_complexity` may take 2-5 minutes to complete.
+
+#### Adding Timeout Configuration
+
+Add a `timeout` parameter to your MCP configuration to extend the timeout limit. The timeout configuration works identically across MCP clients including Cursor, Windsurf, and RooCode:
+
+```json
+{
+  "mcpServers": {
+    "task-master-ai": {
+      "command": "npx",
+      "args": ["-y", "--package=task-master-ai", "task-master-ai"],
+      "timeout": 300,
+      "env": {
+        "ANTHROPIC_API_KEY": "your-anthropic-api-key"
+      }
+    }
+  }
+}
+```
+
+**Configuration Details:**
+- **`timeout: 300`** - Sets timeout to 300 seconds (5 minutes)
+- **Value range**: 1-3600 seconds (1 second to 1 hour)
+- **Recommended**: 300 seconds provides sufficient time for most AI operations
+- **Format**: Integer value in seconds (not milliseconds)
+
+#### Automatic Setup
+
+When adding taskmaster rules for supported editors, the timeout configuration is automatically included:
+
+```bash
+# Automatically includes timeout configuration
+task-master rules add cursor
+task-master rules add roo
+task-master rules add windsurf
+task-master rules add vscode
+```
+
+#### Troubleshooting Timeouts
+
+If you're still experiencing timeout errors:
+
+1. **Verify configuration**: Check that `timeout: 300` is present in your MCP config
+2. **Restart editor**: Restart your editor after making configuration changes
+3. **Increase timeout**: For very complex operations, try `timeout: 600` (10 minutes)
+4. **Check API keys**: Ensure required API keys are properly configured
+
+**Expected behavior:**
+- **Before fix**: Operations fail after 60 seconds with `MCP request timed out after 60000ms`
+- **After fix**: Operations complete successfully within the configured timeout limit
+
 ### Google Vertex AI Configuration
 
 Google Vertex AI is Google Cloud's enterprise AI platform and requires specific configuration:

scripts/modules/commands.js

@@ -1847,7 +1847,7 @@ function registerCommands(programInstance) {
 		)
 		.option(
 			'-r, --research',
-			'Use Perplexity AI for research-backed complexity analysis'
+			'Use configured research model for research-backed complexity analysis'
 		)
 		.option(
 			'-i, --id <ids>',

scripts/modules/config-manager.js

@@ -310,6 +310,7 @@ function validateProviderModelCombination(providerName, modelId) {
 function validateClaudeCodeSettings(settings) {
 	// Define the base settings schema without commandSpecific first
 	const BaseSettingsSchema = z.object({
+		pathToClaudeCodeExecutable: z.string().optional(),
 		maxTurns: z.number().int().positive().optional(),
 		customSystemPrompt: z.string().optional(),
 		appendSystemPrompt: z.string().optional(),

src/profiles/roo.js

@@ -5,6 +5,40 @@ import { isSilentMode, log } from '../../scripts/modules/utils.js';
 import { createProfile, COMMON_TOOL_MAPPINGS } from './base-profile.js';
 import { ROO_MODES } from '../constants/profiles.js';
 
+// Import the shared MCP configuration helper
+import { formatJSONWithTabs } from '../utils/create-mcp-config.js';
+
+// Roo-specific MCP configuration enhancements
+function enhanceRooMCPConfiguration(mcpPath) {
+	if (!fs.existsSync(mcpPath)) {
+		log('warn', `[Roo] MCP configuration file not found at ${mcpPath}`);
+		return;
+	}
+
+	try {
+		// Read the existing configuration
+		const mcpConfig = JSON.parse(fs.readFileSync(mcpPath, 'utf8'));
+
+		if (mcpConfig.mcpServers && mcpConfig.mcpServers['task-master-ai']) {
+			const server = mcpConfig.mcpServers['task-master-ai'];
+
+			// Add Roo-specific timeout enhancement for long-running AI operations
+			server.timeout = 300;
+
+			// Write the enhanced configuration back
+			fs.writeFileSync(mcpPath, formatJSONWithTabs(mcpConfig) + '\n');
+			log(
+				'debug',
+				`[Roo] Enhanced MCP configuration with timeout at ${mcpPath}`
+			);
+		} else {
+			log('warn', `[Roo] task-master-ai server not found in MCP configuration`);
+		}
+	} catch (error) {
+		log('error', `[Roo] Failed to enhance MCP configuration: ${error.message}`);
+	}
+}
+
 // Lifecycle functions for Roo profile
 function onAddRulesProfile(targetDir, assetsDir) {
 	// Use the provided assets directory to find the roocode directory
@@ -32,6 +66,9 @@ function onAddRulesProfile(targetDir, assetsDir) {
 		}
 	}
 
+	// Note: MCP configuration is now handled by the base profile system
+	// The base profile will call setupMCPConfiguration, and we enhance it in onPostConvert
+
 	for (const mode of ROO_MODES) {
 		const src = path.join(rooModesDir, `rules-${mode}`, `${mode}-rules`);
 		const dest = path.join(targetDir, '.roo', `rules-${mode}`, `${mode}-rules`);
@@ -78,6 +115,15 @@ function onRemoveRulesProfile(targetDir) {
 
 	const rooDir = path.join(targetDir, '.roo');
 	if (fs.existsSync(rooDir)) {
+		// Remove MCP configuration
+		const mcpPath = path.join(rooDir, 'mcp.json');
+		try {
+			fs.rmSync(mcpPath, { force: true });
+			log('debug', `[Roo] Removed MCP configuration from ${mcpPath}`);
+		} catch (err) {
+			log('error', `[Roo] Failed to remove MCP configuration: ${err.message}`);
+		}
+
 		fs.readdirSync(rooDir).forEach((entry) => {
 			if (entry.startsWith('rules-')) {
 				const modeDir = path.join(rooDir, entry);
@@ -101,7 +147,13 @@ function onRemoveRulesProfile(targetDir) {
 }
 
 function onPostConvertRulesProfile(targetDir, assetsDir) {
-	onAddRulesProfile(targetDir, assetsDir);
+	// Enhance the MCP configuration with Roo-specific features after base setup
+	const mcpPath = path.join(targetDir, '.roo', 'mcp.json');
+	try {
+		enhanceRooMCPConfiguration(mcpPath);
+	} catch (err) {
+		log('error', `[Roo] Failed to enhance MCP configuration: ${err.message}`);
+	}
 }
 
 // Create and export roo profile using the base factory
@@ -111,6 +163,7 @@ export const rooProfile = createProfile({
 	url: 'roocode.com',
 	docsUrl: 'docs.roocode.com',
 	toolMappings: COMMON_TOOL_MAPPINGS.ROO_STYLE,
+	mcpConfig: true, // Enable MCP config - we enhance it with Roo-specific features
 	onAdd: onAddRulesProfile,
 	onRemove: onRemoveRulesProfile,
 	onPostConvert: onPostConvertRulesProfile

src/utils/create-mcp-config.js

@@ -262,3 +262,6 @@ export function removeTaskMasterMCPConfiguration(projectRoot, mcpConfigPath) {
 
 	return result;
 }
+
+// Export the formatting function for use by other modules
+export { formatJSONWithTabs };

tests/integration/profiles/roo-init-functionality.test.js

@@ -26,7 +26,7 @@ describe('Roo Profile Initialization Functionality', () => {
 		expect(rooProfile.displayName).toBe('Roo Code');
 		expect(rooProfile.profileDir).toBe('.roo'); // default
 		expect(rooProfile.rulesDir).toBe('.roo/rules'); // default
-		expect(rooProfile.mcpConfig).toBe(true); // default
+		expect(rooProfile.mcpConfig).toBe(true); // now uses standard MCP configuration with Roo enhancements
 	});
 
 	test('roo.js uses custom ROO_STYLE tool mappings', () => {

tests/unit/profiles/mcp-config-validation.test.js

@@ -266,10 +266,10 @@ describe('MCP Configuration Validation', () => {
 			expect(mcpEnabledProfiles).toContain('cursor');
 			expect(mcpEnabledProfiles).toContain('gemini');
 			expect(mcpEnabledProfiles).toContain('opencode');
-			expect(mcpEnabledProfiles).toContain('roo');
 			expect(mcpEnabledProfiles).toContain('vscode');
 			expect(mcpEnabledProfiles).toContain('windsurf');
 			expect(mcpEnabledProfiles).toContain('zed');
+			expect(mcpEnabledProfiles).toContain('roo');
 			expect(mcpEnabledProfiles).not.toContain('cline');
 			expect(mcpEnabledProfiles).not.toContain('codex');
 			expect(mcpEnabledProfiles).not.toContain('trae');
@@ -384,6 +384,7 @@ describe('MCP Configuration Validation', () => {
 			'claude',
 			'cursor',
 			'gemini',
+			'kiro',
 			'opencode',
 			'roo',
 			'windsurf',