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>

CLAUDE.md

@@ -59,80 +59,20 @@ make build          # Build for current platform
 
 ```
 clide/
-├── src/clide/
+├── clide/                        # Package source
 │   ├── __init__.py
 │   ├── __main__.py
 │   ├── app.py                    # Main App, layout, keybindings
 │   ├── cli.py                    # Typer entry point
-│   │
 │   ├── controllers/              # Domain logic (no UI)
-│   │   ├── base.py               # BaseController ABC
-│   │   ├── git.py                # Git status, staging, branches
-│   │   ├── editor.py             # Open files, cursor state
-│   │   ├── diff.py               # Diff generation, accept/reject
-│   │   ├── problems.py           # Linter aggregation
-│   │   ├── todos.py              # TODO/FIXME scanning
-│   │   └── jira.py               # Jira CLI integration
-│   │
-│   ├── widgets/
+│   ├── widgets/                  # UI components
 │   │   ├── panels/               # Main layout containers
-│   │   │   ├── sidebar.py        # Left sidebar with tabs
-│   │   │   ├── workspace.py      # Editor/Diff/Terminal tabs
-│   │   │   ├── claude.py         # Claude interaction panel
-│   │   │   └── context.py        # Right context panel
-│   │   │
 │   │   └── components/           # Reusable UI pieces
-│   │       ├── files_view.py     # DirectoryTree wrapper
-│   │       ├── git_changes.py    # Staged/unstaged file list
-│   │       ├── git_graph.py      # Branch visualization
-│   │       ├── branch_status.py  # Current branch + popout
-│   │       ├── editor_pane.py    # TextArea with syntax
-│   │       ├── diff_pane.py      # Side-by-side/unified diff
-│   │       ├── terminal_pane.py  # PTY terminal
-│   │       ├── problems_view.py  # Linter errors list
-│   │       ├── todos_view.py     # TODO comments list
-│   │       └── jira_view.py      # Jira output display
-│   │
 │   ├── models/                   # Pydantic data models
-│   │   ├── config.py             # App settings (ClideSettings)
-│   │   ├── git.py                # GitStatus, GitChange, GitBranch
-│   │   ├── editor.py             # EditorState, FileBuffer
-│   │   ├── diff.py               # DiffContent, DiffHunk
-│   │   ├── problems.py           # Problem, Severity
-│   │   ├── todos.py              # TodoItem, TodoType
-│   │   └── theme.py              # ThemeColors, ThemeDefinition
-│   │
 │   ├── services/                 # Background task logic
-│   │   ├── process_service.py    # Generic subprocess mgmt
-│   │   ├── git_service.py        # Git command execution
-│   │   ├── file_service.py       # File I/O, language detection
-│   │   ├── linter_service.py     # Run linters, parse output
-│   │   └── todo_scanner.py       # Grep for TODOs
-│   │
 │   ├── themes/                   # Theme system
-│   │   ├── __init__.py
-│   │   ├── registry.py           # Theme registry, get_theme()
-│   │   ├── loader.py             # Load custom themes from .config
-│   │   └── builtin/              # 22 built-in themes
-│   │       ├── __init__.py       # Auto-register all themes
-│   │       ├── summer_night.py   # DEFAULT - Summer Night dark
-│   │       ├── summer_day.py     # Summer Day light
-│   │       ├── one_dark.py       # Atom One Dark
-│   │       ├── dracula.py        # Dracula theme
-│   │       ├── nord.py           # Nord color palette
-│   │       ├── gruvbox_dark.py   # Gruvbox dark
-│   │       ├── gruvbox_light.py  # Gruvbox light
-│   │       └── ...               # More themes
-│   │
 │   ├── extensions/               # Plugin system
-│   │   ├── hookspecs.py
-│   │   ├── manager.py
-│   │   └── builtin/
-│   │
-│   └── helpers/
-│       ├── async_utils.py
-│       ├── path_utils.py
-│       └── terminal_utils.py
+│   └── helpers/                  # Utility functions
 │
 ├── tests/
 │   ├── conftest.py

Makefile

@@ -43,7 +43,7 @@ test-single:
 	$(BIN)/pytest $(TEST) -v
 
 test-cov:
-	$(BIN)/pytest --cov=src/clide --cov-report=html --cov-report=term
+	$(BIN)/pytest --cov=clide/clide --cov-report=html --cov-report=term
 
 test-snapshots:
 	$(BIN)/pytest tests/snapshots/
@@ -52,14 +52,14 @@ test-snapshots-update:
 	$(BIN)/pytest tests/snapshots/ --snapshot-update
 
 typecheck:
-	$(BIN)/mypy src/
+	$(BIN)/mypy clide/
 
 lint:
-	$(BIN)/ruff check src/ tests/
+	$(BIN)/ruff check clide/ tests/
 
 format:
-	$(BIN)/ruff format src/ tests/
-	$(BIN)/ruff check --fix src/ tests/
+	$(BIN)/ruff format clide/ tests/
+	$(BIN)/ruff check --fix clide/ tests/
 
 build:
 	$(BIN)/pyinstaller clide.spec --clean
@@ -70,7 +70,7 @@ build-onefile:
 		--onefile \
 		--clean \
 		--noconfirm \
-		src/clide/__main__.py
+		clide/clide/__main__.py
 
 clean:
 	rm -rf $(VENV)
@@ -83,12 +83,12 @@ clean:
 # CI targets (for GitHub Actions)
 ci-lint:
 	pip install ruff mypy
-	ruff check src/ tests/
-	mypy src/
+	ruff check clide/ tests/
+	mypy clide/
 
 ci-test:
 	pip install -e ".[dev]"
-	pytest --cov=src/clide --cov-report=xml
+	pytest --cov=clide/clide --cov-report=xml
 
 ci-build:
 	pip install -e ".[build]"

clide/app.py

@@ -5,7 +5,7 @@ from typing import ClassVar
 
 from textual.app import App, ComposeResult
 from textual.binding import Binding
-from textual.containers import Container, Horizontal, Vertical
+from textual.containers import Horizontal, Vertical
 from textual.reactive import reactive
 from textual.widgets import Footer, Header
 
@@ -17,6 +17,7 @@ from clide.controllers.problems import ProblemsController
 from clide.controllers.todos import TodosController
 from clide.extensions.manager import ExtensionManager
 from clide.models.config import ClideSettings
+from clide.services.settings_service import SettingsService, get_settings_service
 from clide.themes.registry import get_all_themes, get_theme
 from clide.widgets.panels.claude import ClaudePanel
 from clide.widgets.panels.context import ContextPanel
@@ -151,6 +152,10 @@ class ClideApp(App[None]):
         self.settings = settings or ClideSettings()
         self._test_mode = test_mode
 
+        # User settings persistence
+        self._settings_service = get_settings_service()
+        self._user_settings = self._settings_service.load()
+
         # Extension manager
         self.extension_manager = ExtensionManager()
 
@@ -161,7 +166,7 @@ class ClideApp(App[None]):
         self.problems_controller = ProblemsController(self.workdir)
         self.todos_controller = TodosController(self.workdir)
         self.jira_controller = JiraController(
-            enabled=self.settings.jira_enabled,
+            enabled=self._user_settings.jira_enabled,
         )
 
         # Register themes
@@ -174,8 +179,28 @@ class ClideApp(App[None]):
             if theme_def:
                 self.register_theme(theme_def.to_textual_theme())
 
-        # Set initial theme
-        self.theme = self.settings.theme
+        # Set initial theme from user settings
+        self.theme = self._user_settings.theme
+
+    def set_theme(self, theme_name: str, *, save: bool = True) -> None:
+        """Set the application theme.
+
+        Args:
+            theme_name: Name of the theme to apply
+            save: Whether to persist the setting (default: True)
+        """
+        self.theme = theme_name
+        if save:
+            self._settings_service.set("theme", theme_name)
+
+    def save_user_settings(self) -> None:
+        """Save current user settings to disk."""
+        self._settings_service.update(
+            theme=self.theme,
+            compact_mode=self.compact_mode,
+            sidebar_visible=self.query_one(SidebarPanel).display,
+            context_visible=self.query_one(ContextPanel).display,
+        )
 
     def compose(self) -> ComposeResult:
         """Create the main layout."""
@@ -202,6 +227,9 @@ class ClideApp(App[None]):
 
     async def on_mount(self) -> None:
         """Initialize application on mount."""
+        # Apply saved user settings
+        self._apply_user_settings()
+
         # Load extensions
         self.extension_manager.load_extensions()
         await self.extension_manager.trigger_app_startup(self)
@@ -210,12 +238,24 @@ class ClideApp(App[None]):
         await self._refresh_git()
         await self._refresh_problems()
         await self._refresh_todos()
-        if self.settings.jira_enabled:
+        if self._user_settings.jira_enabled:
             await self._refresh_jira()
 
         # Focus Claude panel
         self.action_focus_claude()
 
+    def _apply_user_settings(self) -> None:
+        """Apply saved user settings on startup."""
+        # Panel visibility
+        sidebar = self.query_one(SidebarPanel)
+        sidebar.visible = self._user_settings.sidebar_visible
+
+        context = self.query_one(ContextPanel)
+        context.visible = self._user_settings.context_visible
+
+        # Compact mode
+        self.compact_mode = self._user_settings.compact_mode
+
     # Reactive watchers
     def watch_workspace_visible(self, visible: bool) -> None:
         """Update panels when workspace visibility changes."""
@@ -279,11 +319,13 @@ class ClideApp(App[None]):
         """Toggle sidebar visibility."""
         sidebar = self.query_one(SidebarPanel)
         sidebar.visible = not sidebar.visible
+        self._settings_service.set("sidebar_visible", sidebar.visible)
 
     def action_toggle_context(self) -> None:
         """Toggle context panel visibility."""
         context = self.query_one(ContextPanel)
         context.visible = not context.visible
+        self._settings_service.set("context_visible", context.visible)
 
     def action_toggle_terminal(self) -> None:
         """Toggle terminal (shows workspace with terminal tab)."""
@@ -297,6 +339,7 @@ class ClideApp(App[None]):
     def action_toggle_compact(self) -> None:
         """Toggle compact mode."""
         self.compact_mode = not self.compact_mode
+        self._settings_service.set("compact_mode", self.compact_mode)
 
     def action_toggle_fullscreen(self) -> None:
         """Toggle fullscreen for focused panel."""
@@ -364,7 +407,6 @@ class ClideApp(App[None]):
 
     def action_save_file(self) -> None:
         """Save current file."""
-        workspace = self.query_one(WorkspacePanel)
         # EditorPane handles save internally
         pass
 
@@ -378,10 +420,19 @@ class ClideApp(App[None]):
         # TODO: Implement quick open
         pass
 
-    def action_select_theme(self) -> None:
+    async def action_select_theme(self) -> None:
         """Open theme selector."""
-        # TODO: Implement theme selector via command palette
-        pass
+        from clide.themes.registry import get_all_themes
+
+        # Get all available themes
+        themes = get_all_themes()
+        theme_names = [t.name for t in themes]
+
+        # Use Textual's built-in selection if available, otherwise cycle
+        # For now, simple cycle through themes
+        current_idx = theme_names.index(self.theme) if self.theme in theme_names else 0
+        next_idx = (current_idx + 1) % len(theme_names)
+        self.set_theme(theme_names[next_idx])
 
     # Event handlers for panel messages
     async def on_sidebar_panel_file_selected(
@@ -439,14 +490,14 @@ class ClideApp(App[None]):
 
     async def on_context_panel_jira_refresh_requested(
         self,
-        event: ContextPanel.JiraRefreshRequested,
+        _event: ContextPanel.JiraRefreshRequested,
     ) -> None:
         """Handle Jira refresh request."""
         await self._refresh_jira()
 
     async def on_workspace_panel_file_saved(
         self,
-        event: WorkspacePanel.FileSaved,
+        _event: WorkspacePanel.FileSaved,
     ) -> None:
         """Handle file save - refresh problems and git."""
         await self._refresh_git()
@@ -493,7 +544,7 @@ class ClideApp(App[None]):
 
     def on_claude_panel_claude_started(
         self,
-        event: ClaudePanel.ClaudeStarted,
+        _event: ClaudePanel.ClaudeStarted,
     ) -> None:
         """Handle Claude Code started."""
         self.notify("Claude Code started", severity="information")

clide/cli.py

@@ -1,7 +1,7 @@
 """Typer CLI entry point for Clide."""
 
 from pathlib import Path
-from typing import Annotated, Optional
+from typing import Annotated
 
 import typer
 
@@ -25,12 +25,12 @@ def version_callback(value: bool) -> None:
 @app.callback(invoke_without_command=True)
 def main(
     ctx: typer.Context,
-    version: Annotated[
-        Optional[bool],
+    _version: Annotated[
+        bool | None,
         typer.Option("--version", "-v", callback=version_callback, is_eager=True),
     ] = None,
     workdir: Annotated[
-        Optional[Path],
+        Path | None,
         typer.Option("--workdir", "-w", help="Working directory to open"),
     ] = None,
 ) -> None:

clide/controllers/__init__.py

@@ -1,12 +1,12 @@
 """Domain controllers for Clide."""
 
-from clide.controllers.base import controller, ControllerMixin
-from clide.controllers.git import GitController
-from clide.controllers.editor import EditorController
+from clide.controllers.base import ControllerMixin, controller
 from clide.controllers.diff import DiffController
+from clide.controllers.editor import EditorController
+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.controllers.jira import JiraController
 
 __all__ = [
     "controller",

clide/controllers/base.py

@@ -1,17 +1,15 @@
 """Base controller utilities using decorator pattern."""
 
 from functools import wraps
-from typing import TYPE_CHECKING, Callable, TypeVar
+from typing import TYPE_CHECKING
 
 from textual.message import Message
 
 if TYPE_CHECKING:
     from textual.app import App
 
-T = TypeVar("T")
 
-
-def controller(cls: type[T]) -> type[T]:
+def controller[T](cls: type[T]) -> type[T]:
     """Decorator to add controller capabilities to a class.
 
     Adds:

clide/controllers/diff.py

@@ -186,17 +186,17 @@ class DiffController:
                 current_hunk_lines.append(DiffLine(
                     change_type=ChangeType.ADDED,
                     content=line[1:],
-                    new_line_num=new_start + len([l for l in current_hunk_lines if l.change_type != ChangeType.REMOVED]),
+                    new_line_num=new_start + len([ln for ln in current_hunk_lines if ln.change_type != ChangeType.REMOVED]),
                 ))
             elif line.startswith("-") and not line.startswith("---"):
                 current_hunk_lines.append(DiffLine(
                     change_type=ChangeType.REMOVED,
                     content=line[1:],
-                    old_line_num=old_start + len([l for l in current_hunk_lines if l.change_type != ChangeType.ADDED]),
+                    old_line_num=old_start + len([ln for ln in current_hunk_lines if ln.change_type != ChangeType.ADDED]),
                 ))
             elif line.startswith(" "):
-                old_num = old_start + len([l for l in current_hunk_lines if l.change_type != ChangeType.ADDED])
-                new_num = new_start + len([l for l in current_hunk_lines if l.change_type != ChangeType.REMOVED])
+                old_num = old_start + len([ln for ln in current_hunk_lines if ln.change_type != ChangeType.ADDED])
+                new_num = new_start + len([ln for ln in current_hunk_lines if ln.change_type != ChangeType.REMOVED])
                 current_hunk_lines.append(DiffLine(
                     change_type=ChangeType.CONTEXT,
                     content=line[1:],
@@ -232,7 +232,7 @@ class DiffController:
         """
         return await self.load_git_diff(path, staged)
 
-    async def accept_proposal(self, file_path: str) -> bool:
+    async def accept_proposal(self, _file_path: str) -> bool:
         """Accept a proposed change and apply it.
 
         Args:
@@ -249,7 +249,7 @@ class DiffController:
         self.clear()
         return True
 
-    async def reject_proposal(self, file_path: str) -> bool:
+    async def reject_proposal(self, _file_path: str) -> bool:
         """Reject a proposed change.
 
         Args:

clide/controllers/editor.py

@@ -6,7 +6,6 @@ from textual.message import Message
 
 from clide.controllers.base import controller
 from clide.models.editor import CursorPosition, EditorState, FileBuffer
-from clide.services.file_service import FileService
 
 
 @controller
@@ -131,11 +130,10 @@ class EditorController:
         self._state.buffers.remove(buffer)
 
         # Update active buffer
-        if self._state.active_buffer_index is not None:
-            if self._state.active_buffer_index >= len(self._state.buffers):
-                self._state.active_buffer_index = (
-                    len(self._state.buffers) - 1 if self._state.buffers else None
-                )
+        if self._state.active_buffer_index is not None and self._state.active_buffer_index >= len(self._state.buffers):
+            self._state.active_buffer_index = (
+                len(self._state.buffers) - 1 if self._state.buffers else None
+            )
 
         return True
 

clide/controllers/problems.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from textual.message import Message
 
 from clide.controllers.base import controller
-from clide.models.problems import Problem, ProblemsSummary, ProblemsState, Severity
+from clide.models.problems import Problem, ProblemsState, ProblemsSummary, Severity
 from clide.services.linter_service import LinterService
 
 

clide/controllers/todos.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from textual.message import Message
 
 from clide.controllers.base import controller
-from clide.models.todos import TodoItem, TodosSummary, TodosState, TodoType
+from clide.models.todos import TodoItem, TodosState, TodosSummary, TodoType
 from clide.services.todo_scanner import TodoScanner
 
 

clide/models/__init__.py

@@ -11,9 +11,9 @@ from clide.models.git import (
     GitGraph,
     GitStatus,
 )
-from clide.models.problems import Problem, ProblemsSummary, ProblemsState, Severity
+from clide.models.problems import Problem, ProblemsState, 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, TodosState, TodosSummary, TodoType
 
 __all__ = [
     # Config

clide/models/git.py

@@ -1,7 +1,6 @@
 """Git-related Pydantic models."""
 
 from enum import Enum
-from typing import Literal
 
 from pydantic import BaseModel, ConfigDict
 

clide/services/__init__.py

@@ -3,11 +3,15 @@
 from clide.services.git_service import GitService
 from clide.services.linter_service import LinterService
 from clide.services.process_service import ProcessService
+from clide.services.settings_service import SettingsService, UserSettings, get_settings_service
 from clide.services.todo_scanner import TodoScanner
 
 __all__ = [
     "GitService",
     "LinterService",
     "ProcessService",
+    "SettingsService",
     "TodoScanner",
+    "UserSettings",
+    "get_settings_service",
 ]

clide/services/process_service.py

@@ -65,7 +65,7 @@ class ProcessService:
                 stdout=stdout.decode("utf-8", errors="replace"),
                 stderr=stderr.decode("utf-8", errors="replace"),
             )
-        except asyncio.TimeoutError:
+        except TimeoutError:
             process.kill()
             return CommandResult(
                 returncode=-1,

clide/services/settings_service.py

@@ -0,0 +1,159 @@
+"""Settings persistence service for user preferences."""
+
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from typing import Any
+
+from pydantic import BaseModel
+
+
+class UserSettings(BaseModel):
+    """User settings that persist across sessions.
+
+    Stored in ~/.clide/settings.json
+    """
+
+    # Appearance
+    theme: str = "summer-night"
+
+    # Panel state
+    sidebar_visible: bool = True
+    context_visible: bool = True
+
+    # Window
+    compact_mode: bool = False
+
+    # Behavior
+    auto_save: bool = True
+    confirm_exit: bool = True
+
+    # Integrations
+    jira_enabled: bool = False
+
+
+class SettingsService:
+    """Service for loading and saving user settings.
+
+    Settings are stored in ~/.clide/settings.json
+    """
+
+    def __init__(self, settings_dir: Path | None = None) -> None:
+        """Initialize the settings service.
+
+        Args:
+            settings_dir: Override the settings directory (default: ~/.clide)
+        """
+        self._settings_dir = settings_dir or Path.home() / ".clide"
+        self._settings_file = self._settings_dir / "settings.json"
+        self._settings: UserSettings | None = None
+
+    @property
+    def settings_dir(self) -> Path:
+        """Get the settings directory path."""
+        return self._settings_dir
+
+    @property
+    def settings_file(self) -> Path:
+        """Get the settings file path."""
+        return self._settings_file
+
+    def load(self) -> UserSettings:
+        """Load settings from disk, creating defaults if needed.
+
+        Returns:
+            The loaded or default UserSettings
+        """
+        if self._settings is not None:
+            return self._settings
+
+        if self._settings_file.exists():
+            try:
+                data = json.loads(self._settings_file.read_text())
+                self._settings = UserSettings.model_validate(data)
+            except (json.JSONDecodeError, ValueError):
+                # Invalid JSON or schema, use defaults
+                self._settings = UserSettings()
+        else:
+            self._settings = UserSettings()
+
+        return self._settings
+
+    def save(self) -> None:
+        """Save current settings to disk."""
+        if self._settings is None:
+            return
+
+        # Ensure directory exists
+        self._settings_dir.mkdir(parents=True, exist_ok=True)
+
+        # Write settings as formatted JSON
+        data = self._settings.model_dump(mode="json")
+        self._settings_file.write_text(
+            json.dumps(data, indent=2, sort_keys=True) + "\n"
+        )
+
+    def get(self, key: str, default: Any = None) -> Any:
+        """Get a setting value.
+
+        Args:
+            key: The setting key (attribute name)
+            default: Default value if key doesn't exist
+
+        Returns:
+            The setting value or default
+        """
+        settings = self.load()
+        return getattr(settings, key, default)
+
+    def set(self, key: str, value: Any, *, save: bool = True) -> None:
+        """Set a setting value.
+
+        Args:
+            key: The setting key (attribute name)
+            value: The value to set
+            save: Whether to save immediately (default: True)
+        """
+        settings = self.load()
+        if hasattr(settings, key):
+            # Create new settings with updated value
+            data = settings.model_dump()
+            data[key] = value
+            self._settings = UserSettings.model_validate(data)
+
+            if save:
+                self.save()
+
+    def update(self, **kwargs: Any) -> None:
+        """Update multiple settings at once.
+
+        Args:
+            **kwargs: Key-value pairs to update
+        """
+        settings = self.load()
+        data = settings.model_dump()
+
+        for key, value in kwargs.items():
+            if hasattr(settings, key):
+                data[key] = value
+
+        self._settings = UserSettings.model_validate(data)
+        self.save()
+
+    def reset(self) -> None:
+        """Reset settings to defaults."""
+        self._settings = UserSettings()
+        self.save()
+
+
+# Global instance for convenience
+_settings_service: SettingsService | None = None
+
+
+def get_settings_service() -> SettingsService:
+    """Get the global settings service instance."""
+    global _settings_service
+    if _settings_service is None:
+        _settings_service = SettingsService()
+    return _settings_service

clide/themes/__init__.py

@@ -1,11 +1,11 @@
 """Theme system for Clide."""
 
 from clide.themes.registry import (
-    get_theme,
+    DEFAULT_THEME,
     get_all_themes,
+    get_theme,
     get_themes_by_category,
     register_theme,
-    DEFAULT_THEME,
 )
 
 __all__ = [

clide/themes/builtin/__init__.py

@@ -1,28 +1,28 @@
 """Built-in themes for Clide."""
 
 from clide.themes.builtin import (
-    summer_night,
-    summer_day,
-    one_dark,
-    one_dark_pro,
-    one_light,
+    all_hallows_eve,
+    christmas,
+    dark_autumn,
     dracula,
-    nord,
+    fall,
+    gamma,
     gruvbox_dark,
     gruvbox_light,
-    one_dark_teal,
-    gamma,
-    winter_is_coming,
-    monokai_winter,
-    fall,
-    dark_autumn,
-    all_hallows_eve,
-    halloween,
-    christmas,
-    santa_baby,
-    pro_hacker,
     hacker_style,
+    halloween,
     houston,
+    monokai_winter,
+    nord,
+    one_dark,
+    one_dark_pro,
+    one_dark_teal,
+    one_light,
+    pro_hacker,
+    santa_baby,
+    summer_day,
+    summer_night,
+    winter_is_coming,
 )
 
 __all__ = [

clide/themes/loader.py

@@ -1,8 +1,7 @@
 """Custom theme loader for user-defined themes."""
 
-from pathlib import Path
-
 import tomllib
+from pathlib import Path
 
 from clide.models.theme import ThemeColors, ThemeDefinition
 from clide.themes.registry import register_theme

clide/themes/registry.py

@@ -1,6 +1,5 @@
 """Theme registry for managing available themes."""
 
-from typing import Callable
 
 from clide.models.theme import ThemeDefinition, ThemeMetadata
 
@@ -71,28 +70,28 @@ def _load_builtin_themes() -> None:
     """Load all built-in themes."""
     # Import here to avoid circular imports
     from clide.themes.builtin import (
-        summer_night,
-        summer_day,
-        one_dark,
-        one_dark_pro,
-        one_light,
+        all_hallows_eve,
+        christmas,
+        dark_autumn,
         dracula,
-        nord,
+        fall,
+        gamma,
         gruvbox_dark,
         gruvbox_light,
-        one_dark_teal,
-        gamma,
-        winter_is_coming,
-        monokai_winter,
-        fall,
-        dark_autumn,
-        all_hallows_eve,
-        halloween,
-        christmas,
-        santa_baby,
-        pro_hacker,
         hacker_style,
+        halloween,
         houston,
+        monokai_winter,
+        nord,
+        one_dark,
+        one_dark_pro,
+        one_dark_teal,
+        one_light,
+        pro_hacker,
+        santa_baby,
+        summer_day,
+        summer_night,
+        winter_is_coming,
     )
 
     # Core themes

clide/widgets/components/branch_status.py

@@ -146,7 +146,7 @@ class BranchStatus(Vertical):
         """Handle click on status bar."""
         self.toggle_popout()
 
-    def on_button_pressed(self, event: Button.Pressed) -> None:
+    def on_button_pressed(self, _event: Button.Pressed) -> None:
         """Handle button presses."""
         if event.button.id == "btn-checkout":
             branch_list = self.query_one("#branch-list", ListView)

clide/widgets/components/diff_pane.py

@@ -5,7 +5,7 @@ from textual.containers import Horizontal, Vertical
 from textual.message import Message
 from textual.widgets import Button, RichLog, Static
 
-from clide.models.diff import ChangeType, DiffContent, DiffHunk
+from clide.models.diff import ChangeType, DiffContent
 
 
 class DiffPane(Vertical):
@@ -137,7 +137,7 @@ class DiffPane(Vertical):
         header = self.query_one(".diff-header", Static)
         header.update("No diff loaded")
 
-    def on_button_pressed(self, event: Button.Pressed) -> None:
+    def on_button_pressed(self, _event: Button.Pressed) -> None:
         """Handle button presses."""
         if not self._diff:
             return

clide/widgets/components/editor_pane.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from textual.app import ComposeResult
 from textual.containers import Vertical
 from textual.message import Message
-from textual.widgets import Label, Static, TextArea
+from textual.widgets import Static, TextArea
 
 from clide.models.editor import CursorPosition, FileBuffer
 
@@ -92,7 +92,7 @@ class EditorPane(Vertical):
             yield TextArea(id="editor-textarea", show_line_numbers=True)
             yield Static("", classes="editor-status", id="editor-status")
 
-    def load_buffer(self, buffer: FileBuffer) -> None:
+    def load_buffer(self, buffer: FileBuffer) -> None:  # noqa: ARG002
         """Load a file buffer into the editor."""
         self._buffer = buffer
 

clide/widgets/components/git_graph.py

@@ -1,9 +1,9 @@
 """Git graph visualization component."""
 
 from textual.app import ComposeResult
-from textual.message import Message
-from textual.widgets import RichLog, Static
 from textual.containers import Vertical
+from textual.message import Message
+from textual.widgets import RichLog
 
 from clide.models.git import GitCommit
 

clide/widgets/components/problems_view.py

@@ -3,11 +3,11 @@
 from pathlib import Path
 
 from textual.app import ComposeResult
-from textual.message import Message
-from textual.widgets import Label, ListItem, ListView, Static
 from textual.containers import Vertical
+from textual.message import Message
+from textual.widgets import ListItem, ListView, Static
 
-from clide.models.problems import Problem, Severity
+from clide.models.problems import Problem
 
 
 class ProblemItem(ListItem):

clide/widgets/components/todos_view.py

@@ -1,11 +1,10 @@
 """TODOs view component."""
 
-from pathlib import Path
 
 from textual.app import ComposeResult
-from textual.message import Message
-from textual.widgets import Label, ListItem, ListView, Static
 from textual.containers import Vertical
+from textual.message import Message
+from textual.widgets import ListItem, ListView, Static
 
 from clide.models.todos import TodoItem, TodoType
 

clide/widgets/panels/claude.py

@@ -9,6 +9,7 @@ import pty
 import shutil
 import struct
 import termios
+import time
 from pathlib import Path
 from typing import TYPE_CHECKING
 
@@ -49,6 +50,9 @@ class TerminalDisplay(Widget, can_focus=True):
         self._master_fd: int | None = None
         self._pid: int | None = None
         self._read_task: asyncio.Task | None = None
+        self._refresh_task: asyncio.Task | None = None
+        self._needs_refresh: bool = False
+        self._last_refresh: float = 0
 
     def on_resize(self, event) -> None:
         """Handle terminal resize."""
@@ -99,17 +103,35 @@ class TerminalDisplay(Widget, can_focus=True):
             # Start reading
             self._read_task = asyncio.create_task(self._read_output())
 
+    def _schedule_refresh(self) -> None:
+        """Schedule a throttled refresh to avoid glitching."""
+        self._needs_refresh = True
+        if self._refresh_task is None or self._refresh_task.done():
+            self._refresh_task = asyncio.create_task(self._throttled_refresh())
+
+    async def _throttled_refresh(self) -> None:
+        """Refresh at most every 16ms (~60fps) to avoid glitching."""
+        min_interval = 0.016  # ~60fps
+        while self._needs_refresh:
+            now = time.monotonic()
+            elapsed = now - self._last_refresh
+            if elapsed < min_interval:
+                await asyncio.sleep(min_interval - elapsed)
+            self._needs_refresh = False
+            self._last_refresh = time.monotonic()
+            self.refresh()
+            # Small delay to batch rapid updates
+            await asyncio.sleep(0.008)
+
     async def _read_output(self) -> None:
         """Read output from the PTY."""
         if self._master_fd is None:
             return
 
-        loop = asyncio.get_event_loop()
-
         while True:
             try:
                 # Wait for data to be available
-                await asyncio.sleep(0.01)
+                await asyncio.sleep(0.005)
 
                 try:
                     data = os.read(self._master_fd, 65536)
@@ -118,7 +140,7 @@ class TerminalDisplay(Widget, can_focus=True):
 
                     # Feed data to pyte
                     self._stream.feed(data.decode("utf-8", errors="replace"))
-                    self.refresh()
+                    self._schedule_refresh()
 
                 except BlockingIOError:
                     # No data available
@@ -136,6 +158,10 @@ class TerminalDisplay(Widget, can_focus=True):
             self._read_task.cancel()
             self._read_task = None
 
+        if self._refresh_task:
+            self._refresh_task.cancel()
+            self._refresh_task = None
+
         if self._master_fd is not None:
             try:
                 os.close(self._master_fd)

clide/widgets/panels/context.py

@@ -1,6 +1,5 @@
 """Context panel with Problems, TODOs, and Jira tabs."""
 
-from pathlib import Path
 
 from textual.app import ComposeResult
 from textual.containers import Horizontal, Vertical

clide/widgets/panels/sidebar.py

@@ -6,7 +6,7 @@ from textual.app import ComposeResult
 from textual.containers import Container, Vertical
 from textual.message import Message
 from textual.reactive import reactive
-from textual.widgets import Static, TabbedContent, TabPane
+from textual.widgets import TabbedContent, TabPane
 
 from clide.widgets.components.branch_status import BranchStatus
 from clide.widgets.components.files_view import FilesView
@@ -75,14 +75,13 @@ class SidebarPanel(Vertical):
         self.id = "panel-sidebar"
 
     def compose(self) -> ComposeResult:
-        with Container(classes="sidebar-content"):
-            with TabbedContent(id="sidebar-tabs"):
-                with TabPane("Files", id="sidebar-files"):
-                    yield FilesView(path=self._workdir)
-                with TabPane("Git", id="sidebar-git"):
-                    yield GitChangesView()
-                with TabPane("Tree", id="sidebar-tree"):
-                    yield GitGraphView()
+        with Container(classes="sidebar-content"), TabbedContent(id="sidebar-tabs"):
+            with TabPane("Files", id="sidebar-files"):
+                yield FilesView(path=self._workdir)
+            with TabPane("Git", id="sidebar-git"):
+                yield GitChangesView()
+            with TabPane("Tree", id="sidebar-tree"):
+                yield GitGraphView()
         yield BranchStatus(current_branch=self.current_branch)
 
     def watch_visible(self, visible: bool) -> None:

pyproject.toml

@@ -54,7 +54,7 @@ clide = "clide.cli:app"
 # example = "clide.extensions.builtin.example:ExampleExtension"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/clide"]
+packages = ["clide"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -75,7 +75,7 @@ exclude = ["tests", "dist", "build"]
 [tool.ruff]
 target-version = "py312"
 line-length = 100
-src = ["src", "tests"]
+src = ["clide", "tests"]
 
 [tool.ruff.lint]
 select = [
@@ -100,7 +100,7 @@ ignore = [
 known-first-party = ["clide"]
 
 [tool.coverage.run]
-source = ["src/clide"]
+source = ["clide"]
 branch = true
 
 [tool.coverage.report]

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