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`.

tasks/task_074.txt

@@ -0,0 +1,19 @@
+# Task ID: 74
+# Title: PR Review: better-model-management
+# Status: done
+# Dependencies: None
+# Priority: medium
+# Description: will add subtasks
+# Details:
+
+
+# Test Strategy:
+
+
+# Subtasks:
+## 1. pull out logWrapper into utils [done]
+### Dependencies: None
+### Description: its being used a lot across direct functions and repeated right now
+### Details:
+
+