Refactor: Improve MCP logging, update E2E & tests

Refactors MCP server logging and updates testing infrastructure.

- MCP Server:

  - Replaced manual logger wrappers with centralized `createLogWrapper` utility.

  - Updated direct function calls to use `{ session, mcpLog }` context.

  - Removed deprecated `model` parameter from analyze, expand-all, expand-task tools.

  - Adjusted MCP tool import paths and parameter descriptions.

- Documentation:

  - Modified `docs/configuration.md`.

  - Modified `docs/tutorial.md`.

- Testing:

  - E2E Script (`run_e2e.sh`):

    - Removed `set -e`.

    - Added LLM analysis function (`analyze_log_with_llm`) & integration.

    - Adjusted test run directory creation timing.

    - Added debug echo statements.

  - Deleted Unit Tests: Removed `ai-client-factory.test.js`, `ai-client-utils.test.js`, `ai-services.test.js`.

  - Modified Fixtures: Updated `scripts/task-complexity-report.json`.

- Dev Scripts:

  - Modified `scripts/dev.js`.

mcp-server/src/core/direct-functions/update-subtask-by-id.js

@@ -8,6 +8,7 @@ import {
 	enableSilentMode,
 	disableSilentMode
 } from '../../../../scripts/modules/utils.js';
+import { createLogWrapper } from '../../tools/utils.js';
 
 /**
  * Direct function wrapper for updateSubtaskById with error handling.
@@ -95,15 +96,8 @@ export async function updateSubtaskByIdDirect(args, log, context = {}) {
 			// Enable silent mode to prevent console logs from interfering with JSON response
 			enableSilentMode();
 
-			// Create a logger wrapper object to handle logging without breaking the mcpLog[level] calls
-			// This ensures outputFormat is set to 'json' while still supporting proper logging
-			const logWrapper = {
-				info: (message) => log.info(message),
-				warn: (message) => log.warn(message),
-				error: (message) => log.error(message),
-				debug: (message) => log.debug && log.debug(message),
-				success: (message) => log.info(message) // Map success to info if needed
-			};
+			// Create the logger wrapper using the utility function
+			const mcpLog = createLogWrapper(log);
 
 			// Execute core updateSubtaskById function
 			// Pass both session and logWrapper as mcpLog to ensure outputFormat is 'json'
@@ -114,7 +108,7 @@ export async function updateSubtaskByIdDirect(args, log, context = {}) {
 				useResearch,
 				{
 					session,
-					mcpLog: logWrapper
+					mcpLog
 				}
 			);