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/task-manager/analyze-task-complexity.js

@@ -44,7 +44,6 @@ Do not include any explanatory text, markdown formatting, or code block markers
  * @param {Object} options Command options
  * @param {string} options.file - Path to tasks file
  * @param {string} options.output - Path to report output file
- * @param {string} [options.model] - Deprecated: Model override (ignored)
  * @param {string|number} [options.threshold] - Complexity threshold
  * @param {boolean} [options.research] - Use research role
  * @param {Object} [options._filteredTasksData] - Pre-filtered task data (internal use)