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/conftest.py

@@ -1,8 +1,7 @@
 """Shared pytest fixtures for Clide tests."""
 
+from collections.abc import AsyncGenerator, Generator
 from pathlib import Path
-from typing import AsyncGenerator, Generator
-from unittest.mock import MagicMock
 
 import pytest
 from textual.pilot import Pilot

tests/harnesses/app_harness.py

@@ -1,7 +1,6 @@
 """Full application test harness for Clide."""
 
 from pathlib import Path
-from typing import Optional
 
 from textual.pilot import Pilot
 
@@ -26,14 +25,14 @@ class AppHarness:
     def __init__(
         self,
         workdir: Path,
-        settings: Optional[ClideSettings] = None,
-        extension_manager: Optional[ExtensionManager] = None,
+        settings: ClideSettings | None = None,
+        extension_manager: ExtensionManager | None = None,
     ) -> None:
         self.workdir = workdir
         self.settings = settings or ClideSettings()
         self.extension_manager = extension_manager or ExtensionManager()
-        self._app: Optional[ClideApp] = None
-        self._pilot: Optional[Pilot] = None
+        self._app: ClideApp | None = None
+        self._pilot: Pilot | None = None
 
     async def start(self) -> tuple[ClideApp, Pilot]:
         """Start the application and return app and pilot for testing.

tests/harnesses/controller_harness.py

@@ -1,6 +1,6 @@
 """Controller isolation test harness for Clide."""
 
-from typing import TYPE_CHECKING, Any, Optional
+from typing import TYPE_CHECKING, Any
 from unittest.mock import AsyncMock, MagicMock
 
 from textual.message import Message
@@ -19,7 +19,7 @@ class MockApp:
     def _capture_message(self, message: Message) -> None:
         self.messages.append(message)
 
-    def get_messages(self, message_type: Optional[type] = None) -> list[Message]:
+    def get_messages(self, message_type: type | None = None) -> list[Message]:
         """Get captured messages, optionally filtered by type."""
         if message_type is None:
             return self.messages.copy()
@@ -46,7 +46,7 @@ class ControllerHarness:
 
     def __init__(self) -> None:
         self._mock_app = MockApp()
-        self._controllers: list["BaseController"] = []
+        self._controllers: list[BaseController] = []
         self._mocks: dict[str, Any] = {}
 
     @property
@@ -68,7 +68,7 @@ class ControllerHarness:
         for controller in self._controllers:
             await controller.shutdown()
 
-    def get_messages(self, message_type: Optional[type] = None) -> list[Message]:
+    def get_messages(self, message_type: type | None = None) -> list[Message]:
         """Get messages posted to the mock app."""
         return self._mock_app.get_messages(message_type)
 

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
 

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