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/integration/test_files_view.py

@@ -4,7 +4,6 @@ from pathlib import Path
 
 import pytest
 from textual.app import App, ComposeResult
-from textual.widgets import Static
 
 from clide.widgets.components.files_view import FilesView