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/unit/test_app.py

@@ -1,9 +1,6 @@
 """Tests for ClideApp."""
 
 from pathlib import Path
-from unittest.mock import AsyncMock, MagicMock, patch
-
-import pytest
 
 from clide.models.config import ClideSettings