chore: remove broken link from readme

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

.changeset/silly-pandas-find.md

@@ -0,0 +1,5 @@
+---
+"task-master-ai": patch
+---
+
+Fix sonar deep research model failing, should be called `sonar-deep-research`

README.md

@@ -60,6 +60,19 @@ The following documentation is also available in the `docs` directory:
 
 > **Note:** After clicking the link, you'll still need to add your API keys to the configuration. The link installs the MCP server with placeholder keys that you'll need to replace with your actual API keys.
 
+#### Claude Code Quick Install
+
+For Claude Code users:
+
+```bash
+claude mcp add taskmaster-ai -- npx -y task-master-ai
+```
+
+Don't forget to add your API keys to the configuration:
+- in the root .env of your Project
+- in the "env" section of your mcp config for taskmaster-ai
+
+
 ## Requirements
 
 Taskmaster utilizes AI across several commands, and those require a separate API key. You can use a variety of models from different AI providers provided you add your API keys. For example, if you want to use Claude 3.7, you'll need an Anthropic API key.

apps/docs/README.md

@@ -1,22 +1,24 @@
 # Task Master Documentation
 
-Welcome to the Task Master documentation. Use the links below to navigate to the information you need:
+Welcome to the Task Master documentation. This documentation site provides comprehensive guides for getting started with Task Master.
 
 ## Getting Started
 
-- [Configuration Guide](archive/configuration.md) - Set up environment variables and customize Task Master
+- [Quick Start Guide](/getting-started/quick-start) - Complete setup and first-time usage guide
-- [Tutorial](archive/ctutorial.md) - Step-by-step guide to getting started with Task Master
+- [Requirements](/getting-started/quick-start/requirements) - What you need to get started
+- [Installation](/getting-started/quick-start/installation) - How to install Task Master
 
-## Reference
+## Core Capabilities
 
-- [Command Reference](archive/ccommand-reference.md) - Complete list of all available commands
+- [MCP Tools](/capabilities/mcp) - Model Control Protocol integration
-- [Task Structure](archive/ctask-structure.md) - Understanding the task format and features
+- [CLI Commands](/capabilities/cli-root-commands) - Command line interface reference
+- [Task Structure](/capabilities/task-structure) - Understanding tasks and subtasks
 
-## Examples & Licensing
+## Best Practices
 
-- [Example Interactions](archive/cexamples.md) - Common Cursor AI interaction examples
+- [Advanced Configuration](/best-practices/configuration-advanced) - Detailed configuration options
-- [Licensing Information](archive/clicensing.md) - Detailed information about the license
+- [Advanced Tasks](/best-practices/advanced-tasks) - Working with complex task structures
 
 ## Need More Help?
 
-If you can't find what you're looking for in these docs, please check the [main README](../README.md) or visit our [GitHub repository](https://github.com/eyaltoledano/claude-task-master).
+If you can't find what you're looking for in these docs, please check the root README.md or visit our [GitHub repository](https://github.com/eyaltoledano/claude-task-master).

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>

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

@@ -108,5 +108,5 @@ You don’t need to configure everything up front. Most settings can be left as
 </Accordion>
 
 <Note>
-For advanced configuration options and detailed customization, see our [Advanced Configuration Guide](/docs/best-practices/configuration-advanced) page.
+For advanced configuration options and detailed customization, see our [Advanced Configuration Guide](/best-practices/configuration-advanced) page.
 </Note>

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

@@ -56,4 +56,4 @@ If you ran into problems and had to debug errors you can create new rules as you
 
 By now you have all you need to get started executing code faster and smarter with Task Master.
 
-If you have any questions please check out [Frequently Asked Questions](/docs/getting-started/faq)
+If you have any questions please check out [Frequently Asked Questions](/getting-started/faq)

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

@@ -30,6 +30,19 @@ cursor://anysphere.cursor-deeplink/mcp/install?name=taskmaster-ai&config=eyJjb21
 ```
 
 > **Note:** After clicking the link, you'll still need to add your API keys to the configuration. The link installs the MCP server with placeholder keys that you'll need to replace with your actual API keys.
+
+### Claude Code Quick Install
+
+For Claude Code users:
+
+```bash
+claude mcp add taskmaster-ai -- npx -y task-master-ai
+```
+
+Don't forget to add your API keys to the configuration:
+- in the root .env of your Project
+- in the "env" section of your mcp config for taskmaster-ai
+
 </Accordion>
 ## Installation Options
 

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

@@ -6,13 +6,13 @@ sidebarTitle: "Quick Start"
 This guide is for new users who want to start using Task Master with minimal setup time.
 
 It covers:
-- [Requirements](/docs/getting-started/quick-start/requirements): You will need Node.js and an AI model API Key.
+- [Requirements](/getting-started/quick-start/requirements): You will need Node.js and an AI model API Key.
-- [Installation](/docs/getting-started/quick-start/installation): How to Install Task Master.
+- [Installation](/getting-started/quick-start/installation): How to Install Task Master.
-- [Configuration](/docs/getting-started/quick-start/configuration-quick): Setting up your API Key, MCP, and more.
+- [Configuration](/getting-started/quick-start/configuration-quick): Setting up your API Key, MCP, and more.
-- [PRD](/docs/getting-started/quick-start/prd-quick): Writing and parsing your first PRD.
+- [PRD](/getting-started/quick-start/prd-quick): Writing and parsing your first PRD.
-- [Task Setup](/docs/getting-started/quick-start/tasks-quick): Preparing your tasks for execution.
+- [Task Setup](/getting-started/quick-start/tasks-quick): Preparing your tasks for execution.
-- [Executing Tasks](/docs/getting-started/quick-start/execute-quick): Using Task Master to execute tasks.
+- [Executing Tasks](/getting-started/quick-start/execute-quick): Using Task Master to execute tasks.
-- [Rules & Context](/docs/getting-started/quick-start/rules-quick): Learn how and why to build context in your project over time.
+- [Rules & Context](/getting-started/quick-start/rules-quick): Learn how and why to build context in your project over time.
 
 <Tip>
 By the end of this guide, you'll have everything you need to begin working productively with Task Master.

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?
 ```
 
-<Check>Now you are ready to begin [executing tasks](/docs/getting-started/quick-start/execute-quick)</Check>
+For more detailed CLI options, see the [Analyze Task Complexity](/capabilities/cli-root-commands#analyze-task-complexity) section.
+
+<Check>Now you are ready to begin [executing tasks](/getting-started/quick-start/execute-quick)</Check>

apps/docs/introduction.mdx

@@ -4,7 +4,7 @@ Welcome to v1 of the Task Master Docs. Expect weekly updates as we expand and re
 
 We've organized the docs into three sections depending on your experience level and goals:
 
-### Getting Started - Jump in to [Quick Start](/docs/getting-started/quick-start)
+### Getting Started - Jump in to [Quick Start](/getting-started/quick-start)
 Designed for first-time users. Get set up, create your first PRD, and run your first task.
 
 ### Best Practices

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:

docs/models.md

@@ -1,4 +1,4 @@
-# Available Models as of September 19, 2025
+# Available Models as of September 23, 2025
 
 ## Main Models
 
@@ -119,7 +119,7 @@
 | groq        | deepseek-r1-distill-llama-70b                | 0.52      | 0.75       | 0.99        |
 | perplexity  | sonar-pro                                    | —         | 3          | 15          |
 | perplexity  | sonar                                        | —         | 1          | 1           |
-| perplexity  | deep-research                                | 0.211     | 2          | 8           |
+| perplexity  | sonar-deep-research                          | 0.211     | 2          | 8           |
 | perplexity  | sonar-reasoning-pro                          | 0.211     | 2          | 8           |
 | perplexity  | sonar-reasoning                              | 0.211     | 1          | 5           |
 | bedrock     | us.anthropic.claude-3-opus-20240229-v1:0     | 0.725     | 15         | 75          |

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(),

scripts/modules/supported-models.json

@@ -522,7 +522,7 @@
 			"supported": true
 		},
 		{
-			"id": "deep-research",
+			"id": "sonar-deep-research",
 			"swe_score": 0.211,
 			"cost_per_1m_tokens": {
 				"input": 2,

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',