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_services.py

@@ -1,14 +1,11 @@
 """Tests for service classes."""
 
-import asyncio
 from pathlib import Path
-from unittest.mock import AsyncMock, MagicMock, patch
+from unittest.mock import patch
 
 import pytest
 
-from clide.models.git import GitBranch, GitChange, GitCommit, GitStatus
-from clide.models.problems import Problem, Severity
-from clide.models.todos import TodoItem, TodoType
+from clide.models.todos import TodoType
 from clide.services.file_service import FileService
 from clide.services.git_service import GitService
 from clide.services.linter_service import LinterService