docs: auto-update documentation based on changes in next branch

This PR was automatically generated to update documentation based on recent changes.

  Original commit: feat: add MCP timeout configuration for long-running operations (#1112)\n\n\n

  Co-authored-by: Claude <claude-assistant@anthropic.com>

.changeset/petite-ideas-grab.md

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

.changeset/silly-pandas-find.md

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

apps/docs/best-practices/configuration-advanced.mdx

@@ -66,6 +66,32 @@ Taskmaster uses two primary methods for configuration:
 - **Location:**
   - For CLI usage: Create a `.env` file in your project root.
   - For MCP/Cursor usage: Configure keys in the `env` section of your `.cursor/mcp.json` file.
+
+## MCP Timeout Configuration
+
+For MCP usage, it's important to configure appropriate timeouts for long-running AI operations:
+
+```json
+{
+  "mcpServers": {
+    "task-master-ai": {
+      "command": "npx",
+      "args": ["-y", "task-master-ai"],
+      "timeout": 300,
+      "env": {
+        "ANTHROPIC_API_KEY": "your-api-key-here"
+      }
+    }
+  }
+}
+```
+
+**Key points:**
+- **Default MCP timeout**: 60 seconds (often insufficient for AI operations)
+- **Recommended timeout**: 300 seconds (5 minutes) 
+- **Operations that benefit**: `parse_prd`, `expand_task`, `analyze_project_complexity`, `research`
+- **Automatic setup**: Included when using `task-master rules add` for supported editors
+
 - **Required API Keys (Depending on configured providers):**
   - `ANTHROPIC_API_KEY`: Your Anthropic API key.
   - `PERPLEXITY_API_KEY`: Your Perplexity API key.

apps/docs/capabilities/mcp.mdx

@@ -7,6 +7,60 @@ sidebarTitle: "MCP Tools"
 
 This document provides an overview of the MCP (Machine-to-Machine Communication Protocol) interface for the Task Master application. The MCP interface is defined in the `mcp-server/` directory and exposes the application's core functionalities as a set of tools that can be called remotely.
 
+## MCP Timeout Configuration
+
+Long-running AI operations in Task Master can exceed the default 60-second MCP timeout. Operations like `parse_prd`, `expand_task`, `analyze_project_complexity`, and `research` may take 2-5 minutes to complete.
+
+### Adding Timeout Configuration
+
+Add a `timeout` parameter to your MCP configuration to extend the timeout limit:
+
+```json
+{
+  "mcpServers": {
+    "task-master-ai": {
+      "command": "npx",
+      "args": ["-y", "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 using supported AI coding assistants, the timeout configuration is automatically included when you add Task Master rules:
+
+```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
+
 ## Core Concepts
 
 The MCP interface is built on top of the `fastmcp` library and registers a set of tools that correspond to the core functionalities of the Task Master application. These tools are defined in the `mcp-server/src/tools/` directory and are registered with the MCP server in `mcp-server/src/tools/index.js`.

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

@@ -20,6 +20,7 @@ For MCP/Cursor usage: Configure keys in the env section of your .cursor/mcp.json
 		"task-master-ai": {
 			"command": "npx",
 			"args": ["-y", "task-master-ai"],
+			"timeout": 300,
 			"env": {
 				"ANTHROPIC_API_KEY": "ANTHROPIC_API_KEY_HERE",
 				"PERPLEXITY_API_KEY": "PERPLEXITY_API_KEY_HERE",
@@ -37,6 +38,10 @@ For MCP/Cursor usage: Configure keys in the env section of your .cursor/mcp.json
 }
 ```
 
+<Note>
+The `timeout: 300` setting (5 minutes) is recommended for long-running AI operations like `parse-prd`, `expand-all`, and `analyze-complexity`. This prevents timeout errors during complex tasks.
+</Note>
+
 ### CLI Usage: `.env` File
 
 Create a `.env` file in your project root and include the keys for the providers you plan to use:

docs/models.md

@@ -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  | sonar-deep-research                          | 0.211     | 2          | 8           |
+| perplexity  | 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/config-manager.js

@@ -310,7 +310,6 @@ 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": "sonar-deep-research",
+			"id": "deep-research",
 			"swe_score": 0.211,
 			"cost_per_1m_tokens": {
 				"input": 2,

src/profiles/roo.js

@@ -14,23 +14,20 @@ function enhanceRooMCPConfiguration(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}`
-			);
+			log('debug', `[Roo] Enhanced MCP configuration with timeout at ${mcpPath}`);
 		} else {
 			log('warn', `[Roo] task-master-ai server not found in MCP configuration`);
 		}