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/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)