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_widgets.py

@@ -1,13 +1,11 @@
 """Tests for widget components."""
 
 from pathlib import Path
-from unittest.mock import MagicMock, patch
+from unittest.mock import MagicMock
 
-import pytest
-
-from clide.models.diff import ChangeType, DiffContent, DiffHunk, DiffLine
-from clide.models.editor import CursorPosition, FileBuffer
-from clide.models.git import ChangeStatus, GitBranch, GitChange, GitCommit
+from clide.models.diff import DiffContent
+from clide.models.editor import FileBuffer
+from clide.models.git import ChangeStatus, GitChange, GitCommit
 from clide.models.problems import Problem, Severity
 from clide.models.todos import TodoItem, TodoType