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
 

tests/unit/test_controllers.py

@@ -1,7 +1,7 @@
 """Tests for controller classes."""
 
 from pathlib import Path
-from unittest.mock import AsyncMock, MagicMock, patch
+from unittest.mock import patch
 
 import pytest
 
@@ -11,13 +11,11 @@ from clide.controllers.git import GitController
 from clide.controllers.jira import JiraController
 from clide.controllers.problems import ProblemsController
 from clide.controllers.todos import TodosController
-from clide.models.diff import ChangeType, DiffContent, DiffHunk, DiffLine
-from clide.models.editor import CursorPosition, FileBuffer
+from clide.models.diff import DiffContent, DiffHunk
+from clide.models.editor import FileBuffer
 from clide.models.git import ChangeStatus, GitBranch, GitChange, GitCommit, GitStatus
-from clide.models.problems import Problem, ProblemsSummary, Severity
-from clide.models.todos import TodoItem, TodosSummary, TodoType
-from clide.services.git_service import GitService
-from clide.services.process_service import CommandResult
+from clide.models.problems import Problem, Severity
+from clide.models.todos import TodoItem, TodoType
 
 
 class TestGitController:

tests/unit/test_models.py

@@ -6,12 +6,12 @@ import pytest
 from pydantic import ValidationError
 
 from clide.models.config import ClideSettings, KeybindingsConfig, PanelConfig
-from clide.models.diff import ChangeType, DiffContent, DiffHunk, DiffLine, DiffViewState
-from clide.models.editor import CursorPosition, EditorState, FileBuffer, Selection
-from clide.models.git import ChangeStatus, GitBranch, GitChange, GitCommit, GitGraph, GitStatus
-from clide.models.problems import Problem, ProblemsSummary, ProblemsState, Severity
+from clide.models.diff import ChangeType, DiffContent, DiffHunk, DiffLine
+from clide.models.editor import CursorPosition, EditorState, FileBuffer
+from clide.models.git import ChangeStatus, GitBranch, GitChange, GitCommit, GitStatus
+from clide.models.problems import Problem, ProblemsSummary, Severity
 from clide.models.theme import ThemeColors, ThemeDefinition, ThemeMetadata
-from clide.models.todos import TodoItem, TodosSummary, TodosState, TodoType
+from clide.models.todos import TodoItem, TodosSummary, TodoType
 
 
 class TestCursorPosition:

tests/unit/test_panels.py

@@ -1,12 +1,7 @@
 """Tests for panel widgets."""
 
 from pathlib import Path
-from unittest.mock import MagicMock, patch
 
-import pytest
-
-from clide.models.diff import DiffContent
-from clide.models.git import GitBranch, GitChange
 from clide.models.problems import Problem, Severity
 from clide.models.todos import TodoItem, TodoType
 

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

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