Restructure project and add user settings persistence

- Move src/clide/ to clide/ (flatten directory structure)
- Add SettingsService for persistent user preferences
- Settings stored in ~/.clide/settings.json
- Persist theme, panel visibility, and compact mode state
- Fix terminal rendering glitch with throttled refresh (~60fps)
- Update pyproject.toml, Makefile, and tests for new structure

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

tests/conftest.py

@@ -1,8 +1,7 @@
 """Shared pytest fixtures for Clide tests."""
 
+from collections.abc import AsyncGenerator, Generator
 from pathlib import Path
-from typing import AsyncGenerator, Generator
-from unittest.mock import MagicMock
 
 import pytest
 from textual.pilot import Pilot