diff --git a/mcp-server/src/core/direct-functions/initialize-project.js b/mcp-server/src/core/direct-functions/initialize-project.js
index 43e43da2..01184112 100644
--- a/mcp-server/src/core/direct-functions/initialize-project.js
+++ b/mcp-server/src/core/direct-functions/initialize-project.js
@@ -9,14 +9,6 @@ import os from 'os'; // Import os module for home directory check
 /**
  * Direct function wrapper for initializing a project.
  * Derives target directory from session, sets CWD, and calls core init logic.
- * @param {object} args - Arguments containing initialization options (addAliases, skipInstall, yes, projectRoot)
- * @param {object} log - The FastMCP logger instance.
- * @param {object} context - The context object, must contain { session }.
- * @returns {Promise<{success: boolean, data?: any, error?: {code: string, message: string}}>} - Standard result object.
- */
-/**
- * Direct function wrapper for initializing a project.
- * Accepts a 'rules' array in args (e.g., ["cursor", "roo"]). If present, passes it as the --rules argument to the core init logic. Defaults to ["cursor"] if not provided.
  * @param {object} args - Arguments containing initialization options (addAliases, skipInstall, yes, projectRoot, rules)
  * @param {object} log - The FastMCP logger instance.
  * @param {object} context - The context object, must contain { session }.
diff --git a/mcp-server/src/tools/initialize-project.js b/mcp-server/src/tools/initialize-project.js
index 27e820fc..f4a286d4 100644
--- a/mcp-server/src/tools/initialize-project.js
+++ b/mcp-server/src/tools/initialize-project.js
@@ -24,6 +24,13 @@ export function registerInitializeProjectTool(server) {
 				.optional()
 				.default(false)
 				.describe('Add shell aliases (tm, taskmaster) to shell config file.'),
+			yes: z
+				.boolean()
+				.optional()
+				.default(true)
+				.describe(
+					'Skip prompts and use default values. Always set to true for MCP tools.'
+				),
 			projectRoot: z
 				.string()
 				.describe(
diff --git a/scripts/init.js b/scripts/init.js
index a661f49a..8b6d090f 100755
--- a/scripts/init.js
+++ b/scripts/init.js
@@ -222,7 +222,7 @@ function copyTemplateFile(templateName, targetPath, replacements = {}) {
 			break;
 			// case 'README-task-master.md':
 			// 	sourcePath = path.join(__dirname, '..', 'README-task-master.md');
-			break;
+			// break;
 
 		default:
 			// For other files like env.example, gitignore, etc. that don't have direct equivalents