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`.

scripts/modules/dependency-manager.js

@@ -6,8 +6,6 @@
 import path from 'path';
 import chalk from 'chalk';
 import boxen from 'boxen';
-// Remove Anthropic import if client is no longer initialized globally
-// import { Anthropic } from '@anthropic-ai/sdk';
 
 import {
 	log,
@@ -23,11 +21,6 @@ import { displayBanner } from './ui.js';
 
 import { generateTaskFiles } from './task-manager.js';
 
-// Remove global Anthropic client initialization
-// const anthropic = new Anthropic({
-// 	apiKey: process.env.ANTHROPIC_API_KEY
-// });
-
 /**
  * Add a dependency to a task
  * @param {string} tasksPath - Path to the tasks.json file