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/tools/analyze.js

@@ -26,12 +26,6 @@ export function registerAnalyzeTool(server) {
 				.describe(
 					'Output file path relative to project root (default: scripts/task-complexity-report.json)'
 				),
-			model: z
-				.string()
-				.optional()
-				.describe(
-					'Deprecated: LLM model override (model is determined by configured role)'
-				),
 			threshold: z.coerce
 				.number()
 				.min(1)
@@ -44,7 +38,7 @@ export function registerAnalyzeTool(server) {
 				.string()
 				.optional()
 				.describe(
-					'Path to the tasks file relative to project root (default: tasks/tasks.json)'
+					'Absolute path to the tasks file in the /tasks folder inside the project root (default: tasks/tasks.json)'
 				),
 			research: z
 				.boolean()