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-tasks.js

@@ -8,6 +8,7 @@ import {
 	enableSilentMode,
 	disableSilentMode
 } from '../../../../scripts/modules/utils.js';
+import { createLogWrapper } from '../../tools/utils.js';
 
 /**
  * Direct function wrapper for updating tasks based on new context/prompt.
@@ -88,6 +89,9 @@ export async function updateTasksDirect(args, log, context = {}) {
 
 	enableSilentMode(); // Enable silent mode
 	try {
+		// Create logger wrapper using the utility
+		const mcpLog = createLogWrapper(log);
+
 		// Execute core updateTasks function, passing session context
 		await updateTasks(
 			tasksJsonPath,
@@ -95,7 +99,7 @@ export async function updateTasksDirect(args, log, context = {}) {
 			prompt,
 			useResearch,
 			// Pass context with logger wrapper and session
-			{ mcpLog: logWrapper, session },
+			{ mcpLog, session },
 			'json' // Explicitly request JSON format for MCP
 		);