diff --git a/README.md b/README.md
index eda74ba7..74569d0c 100644
--- a/README.md
+++ b/README.md
@@ -4,53 +4,135 @@ A terminal-based IDE that wraps Claude Code CLI, putting AI-assisted development
 
 ## Why Clide?
 
-Claude Code is powerful, but switching between your terminal, editor, and project tools breaks your flow. Clide brings everything into one interface:
+Claude Code is powerful, but switching between terminal, editor, and project tools breaks your flow. Clide brings everything into one interface:
 
-- **Claude stays visible** — No more switching windows. Claude Code is always front and center.
-- **Context at a glance** — File tree, git status, problems, and TODOs in dedicated panels.
-- **Panels appear when needed** — Editor, diff viewer, and terminal stay hidden until you need them.
-- **Familiar keybindings** — VSCode-inspired shortcuts that don't interfere with your input.
+- **Claude stays visible** — Claude Code runs in the center panel, always accessible
+- **Context at a glance** — File tree, git status, problems, and TODOs in dedicated panels
+- **Panels appear when needed** — Editor, diff viewer, and terminal stay hidden until you need them
+- **Git integration** — Commit, stash, pull, and push via Claude with built-in skills
+- **22 themes** — From summer-night to dracula, with custom theme support
 
-## Layout
+## Screenshot
 
 ```
 ┌─────────────────┬─────────────────────────┬──────────────────┐
 │ Sidebar         │ Workspace               │ Context          │
 │                 │ [Editor][Diff][Terminal]│                  │
-│ [Files][Git]    │ (appears when needed)   │ [Problems][TODOs]│
-│ [Graph]         ├─────────────────────────┤ [Jira]           │
+│ [Files][Git]    │ (appears when needed)   │ [Jira][TODOs]    │
+│ [Tree]          ├─────────────────────────┤ [Problems]       │
 │                 │                         │                  │
 │                 │ Claude                  │                  │
 │                 │ (always visible)        │                  │
 │                 │                         │                  │
 ├─────────────────┤                         ├──────────────────┤
-│ ⎇ main ▾       │                         │ [⚠ 3][✓12][Jira]│
+│ ⎇ main ▾       │                         │                  │
+│ staged: 2      │                         │                  │
 └─────────────────┴─────────────────────────┴──────────────────┘
 ```
 
 ## Features
 
-**Left Sidebar**
-- File explorer with project tree
-- Git panel showing staged/unstaged changes
-- Visual branch graph
-- Quick branch switching
+### Left Sidebar
+- **Files** — Project file tree with syntax-aware icons
+- **Git** — Staged/unstaged changes with action buttons
+- **Tree** — Visual branch graph
+- **Branch status** — Current branch with quick switcher
 
-**Center Workspace**
-- Claude Code integration (primary focus)
-- Tabbed editor with syntax highlighting
-- Side-by-side diff viewer for proposed changes
-- Integrated terminal
+### Center
+- **Claude Code** — Full PTY terminal integration, always visible
+- **Editor** — Syntax highlighting via tree-sitter
+- **Diff** — Side-by-side diff viewer
+- **Terminal** — Command execution
 
-**Right Context Panel**
-- Problems view (linter errors/warnings)
-- TODOs extracted from codebase
-- Jira/Confluence integration
+### Right Context
+- **Jira** — Issue display via CLI integration
+- **TODOs** — Code comments and TODO.md items
+- **Problems** — Linter errors and warnings
 
-**Responsive Design**
-- Works on 13" laptops to widescreen monitors
-- Compact mode hides sidebars for focused work
-- Panels preserve state when hidden
+### Git Operations
+
+Click buttons in the Git panel to delegate operations to Claude:
+
+| Button | Skill | What Claude Does |
+|--------|-------|------------------|
+| Commit | `/commit` | Reviews changes, writes commit message |
+| Stash | `/stash` | Stashes working changes |
+| Pull | `/pull` | Pulls with rebase, helps resolve conflicts |
+| Push | `/push` | Pushes to remote, sets upstream if needed |
+
+Skills are installed automatically to your project's `.claude/skills/` directory.
+
+## Installation
+
+### Requirements
+
+- Python 3.12+
+- Git
+- Claude Code CLI (installed and authenticated)
+
+### Setup
+
+```bash
+git clone <repo-url>
+cd clide
+make setup
+make run
+```
+
+Or install directly:
+
+```bash
+pip install -e .
+clide
+```
+
+## Keybindings
+
+All shortcuts use `Alt` to avoid conflicts with Claude Code input.
+
+| Action | Binding |
+|--------|---------|
+| Toggle left sidebar | `Alt+B` |
+| Toggle right sidebar | `Alt+Shift+B` |
+| Toggle terminal | `` Alt+` `` |
+| Focus Claude | `Alt+1` |
+| Focus Editor | `Alt+2` |
+| Focus Terminal | `Alt+3` |
+| Toggle compact mode | `Alt+C` |
+| Select theme | `Alt+T` |
+| Quit | `Alt+Q` |
+
+## Themes
+
+22 built-in themes. Press `Alt+T` to switch.
+
+| Category | Themes |
+|----------|--------|
+| Core | summer-night (default), summer-day |
+| Popular | one-dark, one-dark-pro, one-light, dracula, nord, gruvbox-dark, gruvbox-light |
+| Seasonal | winter-is-coming, monokai-winter, fall, dark-autumn |
+| Special | all-hallows-eve, halloween, christmas, santa-baby |
+| Hacker | pro-hacker, hacker-style |
+
+Create custom themes in `~/.clide/themes/` as TOML files.
+
+## Configuration
+
+Settings stored in `~/.clide/settings.json`:
+
+```json
+{
+  "theme": "summer-night",
+  "compact_mode": false,
+  "jira_enabled": false
+}
+```
+
+Override with environment variables:
+
+```bash
+CLIDE_THEME=dracula clide
+```
 
 ## Tech Stack
 
@@ -61,37 +143,25 @@ Claude Code is powerful, but switching between your terminal, editor, and projec
 | CLI | Typer |
 | Data Validation | Pydantic v2 |
 | Extensions | Pluggy |
+| Syntax Highlighting | tree-sitter |
 
-## Getting Started
+## Development
 
 ```bash
-# Clone and setup
-git clone <repo-url>
-cd clide
-make setup
-
-# Run
-make run
+make setup      # Create venv, install deps
+make run        # Run application
+make test       # Run all tests
+make typecheck  # Run mypy
+make lint       # Run ruff
+make format     # Format code
 ```
 
-## Keybindings
-
-| Action | Binding |
-|--------|---------|
-| Toggle left sidebar | `Alt+B` |
-| Toggle right sidebar | `Alt+Shift+B` |
-| Toggle terminal | `` Alt+` `` |
-| Focus Claude | `Alt+1` |
-| Focus Editor | `Alt+2` |
-| Focus Terminal | `Alt+3` |
-| Command palette | `Alt+P` |
-| Quick open file | `Alt+O` |
-| Toggle compact mode | `Alt+C` |
-
 ## Documentation
 
-- [Full UI/UX Specification](docs/tui-ide-spec.md)
-- [Architecture Guide](docs/ARCHITECTURE.md)
+- [User Manual](docs/user-manual.md) — How to use Clide
+- [UI/UX Specification](docs/tui-ide-spec.md) — Design decisions
+- [Architecture](docs/ARCHITECTURE.md) — Technical overview
+- [Code Organization](docs/code-organization.md) — Project structure
 
 ## License
 
diff --git a/TODO.md b/TODO.md
index ccea40be..749eaff7 100644
--- a/TODO.md
+++ b/TODO.md
@@ -44,23 +44,23 @@ Long-term open items for Clide development.
 ### Git Integration
 - [ ] Stage/unstage files from Git tab
 - [ ] Discard changes context menu
-- [ ] Git graph visualization (Tree tab)
-- [ ] Branch popout with checkout/new branch actions
+- [x] Git graph visualization (Tree tab)
+- [x] Branch popout with checkout/new branch actions
 
 ## Context Panel (Right Sidebar)
 
 ### Problems View
 - [ ] Linter integration (ruff, eslint, etc.)
-- [ ] Click to navigate to file:line
-- [ ] Reactive problem count badge
+- [x] Click to navigate to file:line
+- [x] Reactive problem count badge
 
 ### TODOs View
-- [ ] Scan for TODO/FIXME/HACK/XXX comments
-- [ ] Click to navigate to file:line
-- [ ] Reactive count badge
+- [x] Scan for TODO/FIXME/HACK/XXX comments
+- [x] Click to navigate to file:line
+- [x] Reactive count badge
 
 ### Jira View
-- [ ] Render Jira CLI markdown output
+- [x] Render Jira CLI markdown output
 - [ ] Auto-refresh on panel focus
 - [ ] Configurable refresh interval
 
@@ -69,7 +69,7 @@ Long-term open items for Clide development.
 ### Responsiveness
 - [ ] CSS breakpoints for different terminal widths
 - [ ] Auto-hide sidebars on narrow terminals (<100 cols)
-- [ ] Compact mode toggle (`Alt+C`)
+- [x] Compact mode toggle (`Alt+C`)
 
 ### Fullscreen Mode
 - [ ] Any panel can go fullscreen (`F11`)
@@ -94,15 +94,15 @@ Long-term open items for Clide development.
 ## Plugin System
 
 - [ ] User-defined panels via pluggy
-- [ ] Custom integrations support
+- [x] Custom integrations support (hookspecs defined)
 - [ ] Extension API documentation
 
 ## Testing
 
-- [ ] Snapshot tests for all panels
-- [ ] Integration tests for panel communication
-- [ ] Unit tests for controllers
-- [ ] Unit tests for services
+- [x] Snapshot tests for all panels
+- [x] Integration tests for panel communication
+- [x] Unit tests for controllers
+- [x] Unit tests for services
 
 ## Documentation
 
diff --git a/clide/controllers/editor.py b/clide/controllers/editor.py
index c3e7e0db..dc11ea90 100644
--- a/clide/controllers/editor.py
+++ b/clide/controllers/editor.py
@@ -130,7 +130,9 @@ class EditorController:
         self._state.buffers.remove(buffer)
 
         # Update active buffer
-        if self._state.active_buffer_index is not None and self._state.active_buffer_index >= len(self._state.buffers):
+        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
             )
@@ -146,10 +148,7 @@ class EditorController:
         Returns:
             True if saved successfully
         """
-        if path:
-            buffer = self._state.get_buffer_by_path(path)
-        else:
-            buffer = self.active_buffer
+        buffer = self._state.get_buffer_by_path(path) if path else self.active_buffer
 
         if not buffer:
             return False
diff --git a/clide/services/claude_events.py b/clide/services/claude_events.py
index 10754c2e..68049419 100644
--- a/clide/services/claude_events.py
+++ b/clide/services/claude_events.py
@@ -7,13 +7,12 @@ from terminal output, enabling tight IDE integration.
 from __future__ import annotations
 
 import re
+from collections.abc import Callable
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Callable, Literal
 
 from textual.message import Message
 
-
 # Event Types
 # -----------
 
@@ -21,54 +20,63 @@ from textual.message import Message
 @dataclass
 class ClaudeEvent:
     """Base class for Claude Code events."""
+
     pass
 
 
 @dataclass
 class FileReadEvent(ClaudeEvent):
     """Emitted when Claude reads a file."""
+
     path: Path
 
 
 @dataclass
 class FileEditEvent(ClaudeEvent):
     """Emitted when Claude edits a file."""
+
     path: Path
 
 
 @dataclass
 class FileWriteEvent(ClaudeEvent):
     """Emitted when Claude creates/writes a file."""
+
     path: Path
 
 
 @dataclass
 class GlobEvent(ClaudeEvent):
     """Emitted when Claude searches for files."""
+
     pattern: str
 
 
 @dataclass
 class GrepEvent(ClaudeEvent):
     """Emitted when Claude searches file contents."""
+
     pattern: str
 
 
 @dataclass
 class ToolStartEvent(ClaudeEvent):
     """Emitted when Claude starts using a tool."""
+
     tool_name: str
 
 
 @dataclass
 class ToolEndEvent(ClaudeEvent):
     """Emitted when Claude finishes using a tool."""
+
     tool_name: str
 
 
 @dataclass
 class DiffProposedEvent(ClaudeEvent):
     """Emitted when Claude proposes a diff."""
+
     content: str
 
 
@@ -95,11 +103,9 @@ PATTERNS = {
     "tool_write": re.compile(r"● Write\(([^)]+)\)"),
     "tool_glob": re.compile(r"● Glob\(([^)]+)\)"),
     "tool_grep": re.compile(r"● Grep\(([^)]+)\)"),
-
     # Generic tool pattern
     "tool_start": re.compile(r"● (\w+)\("),
     "tool_end": re.compile(r"└─"),
-
     # Diff headers
     "diff_header": re.compile(r"^@@\s*-\d+(?:,\d+)?\s+\+\d+(?:,\d+)?\s*@@", re.MULTILINE),
     "diff_file": re.compile(r"^(?:---|\+\+\+)\s+([^\s]+)", re.MULTILINE),
diff --git a/clide/services/file_service.py b/clide/services/file_service.py
index 3e9399ca..610ddc2c 100644
--- a/clide/services/file_service.py
+++ b/clide/services/file_service.py
@@ -2,7 +2,6 @@
 
 from pathlib import Path
 
-
 # Language extension mapping for syntax highlighting
 # Maps file extensions to tree-sitter language identifiers
 LANGUAGE_MAP: dict[str, str] = {
diff --git a/clide/services/syntax_service.py b/clide/services/syntax_service.py
index 066911f7..f5f26d7e 100644
--- a/clide/services/syntax_service.py
+++ b/clide/services/syntax_service.py
@@ -8,10 +8,6 @@ registering additional languages.
 from __future__ import annotations
 
 import logging
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
-    pass
 
 logger = logging.getLogger(__name__)
 
diff --git a/clide/vendor/pyte/graphics.py b/clide/vendor/pyte/graphics.py
index beb93012..61bbc732 100644
--- a/clide/vendor/pyte/graphics.py
+++ b/clide/vendor/pyte/graphics.py
@@ -1,17 +1,17 @@
 """
-    pyte.graphics
-    ~~~~~~~~~~~~~
+pyte.graphics
+~~~~~~~~~~~~~
 
-    This module defines graphic-related constants, mostly taken from
-    :manpage:`console_codes(4)` and
-    http://pueblo.sourceforge.net/doc/manual/ansi_color_codes.html.
+This module defines graphic-related constants, mostly taken from
+:manpage:`console_codes(4)` and
+http://pueblo.sourceforge.net/doc/manual/ansi_color_codes.html.
 
-    :copyright: (c) 2011-2012 by Selectel.
-    :copyright: (c) 2012-2017 by pyte authors and contributors,
-                    see AUTHORS for details.
-    :license: LGPL, see LICENSE for more details.
+:copyright: (c) 2011-2012 by Selectel.
+:copyright: (c) 2012-2017 by pyte authors and contributors,
+                see AUTHORS for details.
+:license: LGPL, see LICENSE for more details.
 
-    Vendored for Clide with modifications for diagnostic logging.
+Vendored for Clide with modifications for diagnostic logging.
 """
 
 #: A mapping of ANSI text style codes to style names, "+" means the:
@@ -51,7 +51,7 @@ FG_ANSI = {
     35: "magenta",
     36: "cyan",
     37: "white",
-    39: "default"  # white.
+    39: "default",  # white.
 }
 
 #: An alias to :data:`~pyte.graphics.FG_ANSI` for compatibility.
@@ -67,7 +67,7 @@ FG_AIXTERM = {
     94: "brightblue",
     95: "brightmagenta",
     96: "brightcyan",
-    97: "brightwhite"
+    97: "brightwhite",
 }
 
 #: A mapping of ANSI background color codes to color names.
@@ -85,7 +85,7 @@ BG_ANSI = {
     45: "magenta",
     46: "cyan",
     47: "white",
-    49: "default"  # black.
+    49: "default",  # black.
 }
 
 #: An alias to :data:`~pyte.graphics.BG_ANSI` for compatibility.
@@ -101,7 +101,7 @@ BG_AIXTERM = {
     104: "brightblue",
     105: "bfightmagenta",
     106: "brightcyan",
-    107: "brightwhite"
+    107: "brightwhite",
 }
 
 #: SGR code for foreground in 256 or True color mode.
@@ -114,25 +114,25 @@ BG_256 = 48
 # The following code is part of the Pygments project (BSD licensed).
 _FG_BG_256 = [
     (0x00, 0x00, 0x00),  # 0
-    (0xcd, 0x00, 0x00),  # 1
-    (0x00, 0xcd, 0x00),  # 2
-    (0xcd, 0xcd, 0x00),  # 3
-    (0x00, 0x00, 0xee),  # 4
-    (0xcd, 0x00, 0xcd),  # 5
-    (0x00, 0xcd, 0xcd),  # 6
-    (0xe5, 0xe5, 0xe5),  # 7
-    (0x7f, 0x7f, 0x7f),  # 8
-    (0xff, 0x00, 0x00),  # 9
-    (0x00, 0xff, 0x00),  # 10
-    (0xff, 0xff, 0x00),  # 11
-    (0x5c, 0x5c, 0xff),  # 12
-    (0xff, 0x00, 0xff),  # 13
-    (0x00, 0xff, 0xff),  # 14
-    (0xff, 0xff, 0xff),  # 15
+    (0xCD, 0x00, 0x00),  # 1
+    (0x00, 0xCD, 0x00),  # 2
+    (0xCD, 0xCD, 0x00),  # 3
+    (0x00, 0x00, 0xEE),  # 4
+    (0xCD, 0x00, 0xCD),  # 5
+    (0x00, 0xCD, 0xCD),  # 6
+    (0xE5, 0xE5, 0xE5),  # 7
+    (0x7F, 0x7F, 0x7F),  # 8
+    (0xFF, 0x00, 0x00),  # 9
+    (0x00, 0xFF, 0x00),  # 10
+    (0xFF, 0xFF, 0x00),  # 11
+    (0x5C, 0x5C, 0xFF),  # 12
+    (0xFF, 0x00, 0xFF),  # 13
+    (0x00, 0xFF, 0xFF),  # 14
+    (0xFF, 0xFF, 0xFF),  # 15
 ]
 
 # colors 16..231: the 6x6x6 color cube
-valuerange = (0x00, 0x5f, 0x87, 0xaf, 0xd7, 0xff)
+valuerange = (0x00, 0x5F, 0x87, 0xAF, 0xD7, 0xFF)
 
 for i in range(216):
     r = valuerange[(i // 36) % 6]
@@ -145,4 +145,4 @@ for i in range(24):
     v = 8 + i * 10
     _FG_BG_256.append((v, v, v))
 
-FG_BG_256 = ["{0:02x}{1:02x}{2:02x}".format(r, g, b) for r, g, b in _FG_BG_256]
+FG_BG_256 = [f"{r:02x}{g:02x}{b:02x}" for r, g, b in _FG_BG_256]
diff --git a/clide/vendor/pyte/screens.py b/clide/vendor/pyte/screens.py
index 980f5f92..2db9c1fb 100644
--- a/clide/vendor/pyte/screens.py
+++ b/clide/vendor/pyte/screens.py
@@ -1,16 +1,17 @@
 """
-    pyte.screens
-    ~~~~~~~~~~~~
+pyte.screens
+~~~~~~~~~~~~
 
-    This module provides classes for terminal screens.
+This module provides classes for terminal screens.
 
-    :copyright: (c) 2011-2012 by Selectel.
-    :copyright: (c) 2012-2017 by pyte authors and contributors,
-                    see AUTHORS for details.
-    :license: LGPL, see LICENSE for more details.
+:copyright: (c) 2011-2012 by Selectel.
+:copyright: (c) 2012-2017 by pyte authors and contributors,
+                see AUTHORS for details.
+:license: LGPL, see LICENSE for more details.
 
-    Vendored for Clide with modifications for diagnostic logging.
+Vendored for Clide with modifications for diagnostic logging.
 """
+
 from __future__ import annotations
 
 import copy
@@ -20,18 +21,22 @@ import os
 import sys
 import unicodedata
 import warnings
-from collections import deque, defaultdict
+from collections import defaultdict, deque
+from collections.abc import Callable, Generator, Sequence
 from functools import lru_cache
-from typing import Any, Callable, DefaultDict, Dict, Generator, List, NamedTuple, Optional, Set, Sequence, TextIO, TypeVar
+from typing import (
+    Any,
+    NamedTuple,
+    TextIO,
+    TypeVar,
+)
 
 from wcwidth import wcwidth as _wcwidth  # type: ignore[import]
 
-from . import (
-    charsets as cs,
-    control as ctrl,
-    graphics as g,
-    modes as mo
-)
+from . import charsets as cs
+from . import control as ctrl
+from . import graphics as g
+from . import modes as mo
 from .streams import Stream
 
 wcwidth: Callable[[str], int] = lru_cache(maxsize=4096)(_wcwidth)
@@ -40,10 +45,10 @@ KT = TypeVar("KT")
 VT = TypeVar("VT")
 
 # Clide diagnostic logging support
-_debug_logger: Optional[Callable[[str], None]] = None
+_debug_logger: Callable[[str], None] | None = None
 
 
-def set_debug_logger(logger: Optional[Callable[[str], None]]) -> None:
+def set_debug_logger(logger: Callable[[str], None] | None) -> None:
     """Set a debug logger function for diagnostic output."""
     global _debug_logger
     _debug_logger = logger
@@ -57,12 +62,14 @@ def _log_debug(message: str) -> None:
 
 class Margins(NamedTuple):
     """A container for screen's scroll margins."""
+
     top: int
     bottom: int
 
 
 class Savepoint(NamedTuple):
     """A container for savepoint, created on :data:`~pyte.escape.DECSC`."""
+
     cursor: Cursor
     g0_charset: str
     g1_charset: str
@@ -73,6 +80,7 @@ class Savepoint(NamedTuple):
 
 class Char(NamedTuple):
     """A single styled on-screen character."""
+
     data: str
     fg: str = "default"
     bg: str = "default"
@@ -86,6 +94,7 @@ class Char(NamedTuple):
 
 class Cursor:
     """Screen cursor."""
+
     __slots__ = ("x", "y", "attrs", "hidden")
 
     def __init__(self, x: int, y: int, attrs: Char = Char(" ")) -> None:
@@ -95,8 +104,9 @@ class Cursor:
         self.hidden = False
 
 
-class StaticDefaultDict(Dict[KT, VT]):
+class StaticDefaultDict(dict[KT, VT]):
     """A dict with a static default value."""
+
     def __init__(self, default: VT) -> None:
         self.default = default
 
@@ -117,22 +127,24 @@ class Screen:
         return Char(data=" ", fg="default", bg="default", reverse=reverse)
 
     def __init__(self, columns: int, lines: int) -> None:
-        self.savepoints: List[Savepoint] = []
+        self.savepoints: list[Savepoint] = []
         self.columns = columns
         self.lines = lines
-        self.buffer: Dict[int, StaticDefaultDict[int, Char]] = defaultdict(lambda: StaticDefaultDict[int, Char](self.default_char))
-        self.dirty: Set[int] = set()
+        self.buffer: dict[int, StaticDefaultDict[int, Char]] = defaultdict(
+            lambda: StaticDefaultDict[int, Char](self.default_char)
+        )
+        self.dirty: set[int] = set()
         self.reset()
         self.mode = _DEFAULT_MODE.copy()
-        self.margins: Optional[Margins] = None
+        self.margins: Margins | None = None
 
     def __repr__(self) -> str:
-        return ("{0}({1}, {2})".format(self.__class__.__name__,
-                                       self.columns, self.lines))
+        return f"{self.__class__.__name__}({self.columns}, {self.lines})"
 
     @property
-    def display(self) -> List[str]:
+    def display(self) -> list[str]:
         """A list of screen lines as unicode strings."""
+
         def render(line: StaticDefaultDict[int, Char]) -> Generator[str, None, None]:
             is_wide_char = False
             for x in range(self.columns):
@@ -167,9 +179,9 @@ class Screen:
         self.cursor = Cursor(0, 0)
         self.cursor_position()
 
-        self.saved_columns: Optional[int] = None
+        self.saved_columns: int | None = None
 
-    def resize(self, lines: Optional[int] = None, columns: Optional[int] = None) -> None:
+    def resize(self, lines: int | None = None, columns: int | None = None) -> None:
         """Resize the screen to the given size."""
         lines = lines or self.lines
         columns = columns or self.columns
@@ -195,7 +207,7 @@ class Screen:
         self.lines, self.columns = lines, columns
         self.set_margins()
 
-    def set_margins(self, top: Optional[int] = None, bottom: Optional[int] = None) -> None:
+    def set_margins(self, top: int | None = None, bottom: int | None = None) -> None:
         """Select top and bottom margins for the scrolling region."""
         if (top is None or top == 0) and bottom is None:
             self.margins = None
@@ -293,8 +305,7 @@ class Screen:
 
     def draw(self, data: str) -> None:
         """Display decoded characters at the current cursor position."""
-        data = data.translate(
-            self.g1_charset if self.charset else self.g0_charset)
+        data = data.translate(self.g1_charset if self.charset else self.g0_charset)
 
         for char in data:
             char_width = wcwidth(char)
@@ -303,7 +314,9 @@ class Screen:
             if _debug_logger is not None and char_width > 0:
                 code = ord(char)
                 if code > 127 or code < 32:
-                    _log_debug(f"[DRAW] char={char!r} code=U+{code:04X} width={char_width} pos=({self.cursor.x},{self.cursor.y})")
+                    _log_debug(
+                        f"[DRAW] char={char!r} code=U+{code:04X} width={char_width} pos=({self.cursor.x},{self.cursor.y})"
+                    )
 
             if self.cursor.x == self.columns:
                 if mo.DECAWM in self.mode:
@@ -331,7 +344,9 @@ class Screen:
                 elif self.cursor.y:
                     last = self.buffer[self.cursor.y - 1][self.columns - 1]
                     normalized = unicodedata.normalize("NFC", last.data + char)
-                    self.buffer[self.cursor.y - 1][self.columns - 1] = last._replace(data=normalized)
+                    self.buffer[self.cursor.y - 1][self.columns - 1] = last._replace(
+                        data=normalized
+                    )
             else:
                 break
 
@@ -396,12 +411,16 @@ class Screen:
 
     def save_cursor(self) -> None:
         """Push the current cursor position onto the stack."""
-        self.savepoints.append(Savepoint(copy.copy(self.cursor),
-                                         self.g0_charset,
-                                         self.g1_charset,
-                                         self.charset,
-                                         mo.DECOM in self.mode,
-                                         mo.DECAWM in self.mode))
+        self.savepoints.append(
+            Savepoint(
+                copy.copy(self.cursor),
+                self.g0_charset,
+                self.g1_charset,
+                self.charset,
+                mo.DECOM in self.mode,
+                mo.DECAWM in self.mode,
+            )
+        )
 
     def restore_cursor(self) -> None:
         """Set the current cursor position to whatever cursor is on top of the stack."""
@@ -421,7 +440,7 @@ class Screen:
             self.reset_mode(mo.DECOM)
             self.cursor_position()
 
-    def insert_lines(self, count: Optional[int] = None) -> None:
+    def insert_lines(self, count: int | None = None) -> None:
         """Insert the indicated # of lines at line with cursor."""
         count = count or 1
         top, bottom = self.margins or Margins(0, self.lines - 1)
@@ -433,7 +452,7 @@ class Screen:
                 self.buffer.pop(y, None)
             self.carriage_return()
 
-    def delete_lines(self, count: Optional[int] = None) -> None:
+    def delete_lines(self, count: int | None = None) -> None:
         """Delete the indicated # of lines."""
         count = count or 1
         top, bottom = self.margins or Margins(0, self.lines - 1)
@@ -447,7 +466,7 @@ class Screen:
                     self.buffer.pop(y, None)
             self.carriage_return()
 
-    def insert_characters(self, count: Optional[int] = None) -> None:
+    def insert_characters(self, count: int | None = None) -> None:
         """Insert the indicated # of blank characters at the cursor position."""
         self.dirty.add(self.cursor.y)
         count = count or 1
@@ -457,7 +476,7 @@ class Screen:
                 line[x + count] = line[x]
             line.pop(x, None)
 
-    def delete_characters(self, count: Optional[int] = None) -> None:
+    def delete_characters(self, count: int | None = None) -> None:
         """Delete the indicated # of characters."""
         self.dirty.add(self.cursor.y)
         count = count or 1
@@ -468,7 +487,7 @@ class Screen:
             else:
                 line.pop(x, None)
 
-    def erase_characters(self, count: Optional[int] = None) -> None:
+    def erase_characters(self, count: int | None = None) -> None:
         """Erase the indicated # of characters."""
         self.dirty.add(self.cursor.y)
         count = count or 1
@@ -525,7 +544,7 @@ class Screen:
         """Ensure the cursor is within horizontal screen bounds."""
         self.cursor.x = min(max(0, self.cursor.x), self.columns - 1)
 
-    def ensure_vbounds(self, use_margins: Optional[bool] = None) -> None:
+    def ensure_vbounds(self, use_margins: bool | None = None) -> None:
         """Ensure the cursor is within vertical screen bounds."""
         if (use_margins or mo.DECOM in self.mode) and self.margins is not None:
             top, bottom = self.margins
@@ -533,39 +552,39 @@ class Screen:
             top, bottom = 0, self.lines - 1
         self.cursor.y = min(max(top, self.cursor.y), bottom)
 
-    def cursor_up(self, count: Optional[int] = None) -> None:
+    def cursor_up(self, count: int | None = None) -> None:
         """Move cursor up the indicated # of lines."""
         top, _bottom = self.margins or Margins(0, self.lines - 1)
         self.cursor.y = max(self.cursor.y - (count or 1), top)
 
-    def cursor_up1(self, count: Optional[int] = None) -> None:
+    def cursor_up1(self, count: int | None = None) -> None:
         """Move cursor up the indicated # of lines to column 1."""
         self.cursor_up(count)
         self.carriage_return()
 
-    def cursor_down(self, count: Optional[int] = None) -> None:
+    def cursor_down(self, count: int | None = None) -> None:
         """Move cursor down the indicated # of lines."""
         _top, bottom = self.margins or Margins(0, self.lines - 1)
         self.cursor.y = min(self.cursor.y + (count or 1), bottom)
 
-    def cursor_down1(self, count: Optional[int] = None) -> None:
+    def cursor_down1(self, count: int | None = None) -> None:
         """Move cursor down the indicated # of lines to column 1."""
         self.cursor_down(count)
         self.carriage_return()
 
-    def cursor_back(self, count: Optional[int] = None) -> None:
+    def cursor_back(self, count: int | None = None) -> None:
         """Move cursor left the indicated # of columns."""
         if self.cursor.x == self.columns:
             self.cursor.x -= 1
         self.cursor.x -= count or 1
         self.ensure_hbounds()
 
-    def cursor_forward(self, count: Optional[int] = None) -> None:
+    def cursor_forward(self, count: int | None = None) -> None:
         """Move cursor right the indicated # of columns."""
         self.cursor.x += count or 1
         self.ensure_hbounds()
 
-    def cursor_position(self, line: Optional[int] = None, column: Optional[int] = None) -> None:
+    def cursor_position(self, line: int | None = None, column: int | None = None) -> None:
         """Set the cursor to a specific line and column."""
         column = (column or 1) - 1
         line = (line or 1) - 1
@@ -580,12 +599,12 @@ class Screen:
         self.ensure_hbounds()
         self.ensure_vbounds()
 
-    def cursor_to_column(self, column: Optional[int] = None) -> None:
+    def cursor_to_column(self, column: int | None = None) -> None:
         """Move cursor to a specific column in the current line."""
         self.cursor.x = (column or 1) - 1
         self.ensure_hbounds()
 
-    def cursor_to_line(self, line: Optional[int] = None) -> None:
+    def cursor_to_line(self, line: int | None = None) -> None:
         """Move cursor to a specific line in the current column."""
         self.cursor.y = (line or 1) - 1
         if mo.DECOM in self.mode:
@@ -608,7 +627,7 @@ class Screen:
         """Set display attributes."""
         replace = {}
 
-        if not attrs or attrs == (0, ):
+        if not attrs or attrs == (0,):
             self.cursor.attrs = self.default_char
             return
 
@@ -637,8 +656,9 @@ class Screen:
                         m = attrs_list.pop()
                         replace[key] = g.FG_BG_256[m]
                     elif n == 2:
-                        replace[key] = "{0:02x}{1:02x}{2:02x}".format(
-                            attrs_list.pop(), attrs_list.pop(), attrs_list.pop())
+                        replace[key] = (
+                            f"{attrs_list.pop():02x}{attrs_list.pop():02x}{attrs_list.pop():02x}"
+                        )
                 except IndexError:
                     pass
 
@@ -659,7 +679,7 @@ class Screen:
             if mo.DECOM in self.mode:
                 assert self.margins is not None
                 y -= self.margins.top
-            self.write_process_input(ctrl.CSI + "{0};{1}R".format(y, x))
+            self.write_process_input(ctrl.CSI + f"{y};{x}R")
 
     def write_process_input(self, data: str) -> None:
         """Write data to the process running inside the terminal."""
@@ -673,10 +693,13 @@ class Screen:
 
 class DiffScreen(Screen):
     """A screen subclass, which maintains a set of dirty lines. Deprecated."""
+
     def __init__(self, *args: Any, **kwargs: Any) -> None:
         warnings.warn(
             "The functionality of ``DiffScreen` has been merged into "
-            "``Screen`` and will be removed in 0.8.0.", DeprecationWarning)
+            "``Screen`` and will be removed in 0.8.0.",
+            DeprecationWarning,
+        )
         super(DiffScreen, self).__init__(*args, **kwargs)
 
 
@@ -694,12 +717,10 @@ class HistoryScreen(Screen):
     _wrapped = set(Stream.events)
     _wrapped.update(["next_page", "prev_page"])
 
-    def __init__(self, columns: int, lines: int, history: int = 100, ratio: float = .5) -> None:
-        self.history = History(deque(maxlen=history),
-                               deque(maxlen=history),
-                               float(ratio),
-                               history,
-                               history)
+    def __init__(self, columns: int, lines: int, history: int = 100, ratio: float = 0.5) -> None:
+        self.history = History(
+            deque(maxlen=history), deque(maxlen=history), float(ratio), history, history
+        )
         super(HistoryScreen, self).__init__(columns, lines)
 
     def _make_wrapper(self, event: str, handler: Callable[..., Any]) -> Callable[..., Any]:
@@ -708,6 +729,7 @@ class HistoryScreen(Screen):
             result = handler(*args, **kwargs)
             self.after_event(event)
             return result
+
         return inner
 
     def __getattribute__(self, attr: str) -> Callable[..., Any]:
@@ -732,8 +754,7 @@ class HistoryScreen(Screen):
                         line.pop(x)
 
         self.cursor.hidden = not (
-            self.history.position == self.history.size and
-            mo.DECTCEM in self.mode
+            self.history.position == self.history.size and mo.DECTCEM in self.mode
         )
 
     def _reset_history(self) -> None:
@@ -769,12 +790,11 @@ class HistoryScreen(Screen):
     def prev_page(self) -> None:
         """Move the screen page up through the history buffer."""
         if self.history.position > self.lines and self.history.top:
-            mid = min(len(self.history.top),
-                      int(math.ceil(self.lines * self.history.ratio)))
+            mid = min(len(self.history.top), int(math.ceil(self.lines * self.history.ratio)))
 
             self.history.bottom.extendleft(
-                self.buffer[y]
-                for y in range(self.lines - 1, self.lines - mid - 1, -1))
+                self.buffer[y] for y in range(self.lines - 1, self.lines - mid - 1, -1)
+            )
             self.history = self.history._replace(position=self.history.position - mid)
 
             for y in range(self.lines - 1, mid - 1, -1):
@@ -787,8 +807,7 @@ class HistoryScreen(Screen):
     def next_page(self) -> None:
         """Move the screen page down through the history buffer."""
         if self.history.position < self.history.size and self.history.bottom:
-            mid = min(len(self.history.bottom),
-                      int(math.ceil(self.lines * self.history.ratio)))
+            mid = min(len(self.history.bottom), int(math.ceil(self.lines * self.history.ratio)))
 
             self.history.top.extend(self.buffer[y] for y in range(mid))
             self.history = self.history._replace(position=self.history.position + mid)
@@ -803,6 +822,7 @@ class HistoryScreen(Screen):
 
 class DebugEvent(NamedTuple):
     """Event dispatched to DebugScreen."""
+
     name: str
     args: Any
     kwargs: Any
@@ -830,6 +850,7 @@ class DebugScreen:
         def wrapper(*args: Any, **kwargs: Any) -> None:
             self.to.write(str(DebugEvent(attr, args, kwargs)))
             self.to.write(str(os.linesep))
+
         return wrapper
 
     def __getattribute__(self, attr: str) -> Callable[..., None]:
diff --git a/clide/vendor/pyte/streams.py b/clide/vendor/pyte/streams.py
index 11d857c7..1a720691 100644
--- a/clide/vendor/pyte/streams.py
+++ b/clide/vendor/pyte/streams.py
@@ -1,25 +1,26 @@
 """
-    pyte.streams
-    ~~~~~~~~~~~~
+pyte.streams
+~~~~~~~~~~~~
 
-    This module provides three stream implementations with different
-    features; for starters, here's a quick example of how streams are
-    typically used:
+This module provides three stream implementations with different
+features; for starters, here's a quick example of how streams are
+typically used:
 
-    >>> import pyte
-    >>> screen = pyte.Screen(80, 24)
-    >>> stream = pyte.Stream(screen)
-    >>> stream.feed("\x1b[5B")  # Move the cursor down 5 rows.
-    >>> screen.cursor.y
-    5
+>>> import pyte
+>>> screen = pyte.Screen(80, 24)
+>>> stream = pyte.Stream(screen)
+>>> stream.feed("\x1b[5B")  # Move the cursor down 5 rows.
+>>> screen.cursor.y
+5
 
-    :copyright: (c) 2011-2012 by Selectel.
-    :copyright: (c) 2012-2017 by pyte authors and contributors,
-                    see AUTHORS for details.
-    :license: LGPL, see LICENSE for more details.
+:copyright: (c) 2011-2012 by Selectel.
+:copyright: (c) 2012-2017 by pyte authors and contributors,
+                see AUTHORS for details.
+:license: LGPL, see LICENSE for more details.
 
-    Vendored for Clide with modifications for diagnostic logging.
+Vendored for Clide with modifications for diagnostic logging.
 """
+
 from __future__ import annotations
 
 import codecs
@@ -27,21 +28,22 @@ import itertools
 import re
 import warnings
 from collections import defaultdict
-from collections.abc import Mapping
-from typing import Any, Callable, Dict, Generator, Optional, TYPE_CHECKING
+from collections.abc import Callable, Generator, Mapping
+from typing import TYPE_CHECKING, Any
 
-from . import control as ctrl, escape as esc
+from . import control as ctrl
+from . import escape as esc
 
 if TYPE_CHECKING:
     from .screens import Screen
 
 
 # Clide diagnostic logging support
-_debug_logger: Optional[Callable[[str], None]] = None
-_event_callback: Optional[Callable[[str], None]] = None
+_debug_logger: Callable[[str], None] | None = None
+_event_callback: Callable[[str], None] | None = None
 
 
-def set_debug_logger(logger: Optional[Callable[[str], None]]) -> None:
+def set_debug_logger(logger: Callable[[str], None] | None) -> None:
     """Set a debug logger function for diagnostic output.
 
     Args:
@@ -51,7 +53,7 @@ def set_debug_logger(logger: Optional[Callable[[str], None]]) -> None:
     _debug_logger = logger
 
 
-def set_event_callback(callback: Optional[Callable[[str], None]]) -> None:
+def set_event_callback(callback: Callable[[str], None] | None) -> None:
     """Set an event callback for raw terminal data.
 
     This callback is invoked with the raw data before parsing.
@@ -70,7 +72,7 @@ def _log_debug(message: str) -> None:
         _debug_logger(message)
 
 
-ParserGenerator = Generator[Optional[bool], str, None]
+ParserGenerator = Generator[bool | None, str, None]
 
 
 class Stream:
@@ -158,30 +160,35 @@ class Stream:
         esc.SGR: "select_graphic_rendition",
         esc.DSR: "report_device_status",
         esc.DECSTBM: "set_margins",
-        esc.HPA: "cursor_to_column"
+        esc.HPA: "cursor_to_column",
     }
 
     #: A set of all events dispatched by the stream.
-    events = frozenset(itertools.chain(
-        basic.values(), escape.values(), sharp.values(), csi.values(),
-        ["define_charset"],
-        ["set_icon_name", "set_title"],  # OSC.
-        ["draw", "debug"]))
+    events = frozenset(
+        itertools.chain(
+            basic.values(),
+            escape.values(),
+            sharp.values(),
+            csi.values(),
+            ["define_charset"],
+            ["set_icon_name", "set_title"],  # OSC.
+            ["draw", "debug"],
+        )
+    )
 
     #: A regular expression pattern matching everything what can be
     #: considered plain text.
     _special = set([ctrl.ESC, ctrl.CSI_C1, ctrl.NUL, ctrl.DEL, ctrl.OSC_C1])
     _special.update(basic)
-    _text_pattern = re.compile(
-        "[^" + "".join(map(re.escape, _special)) + "]+")
+    _text_pattern = re.compile("[^" + "".join(map(re.escape, _special)) + "]+")
     del _special
 
-    def __init__(self, screen: Optional[Screen] = None, strict: bool = True) -> None:
-        self.listener: Optional[Screen] = None
+    def __init__(self, screen: Screen | None = None, strict: bool = True) -> None:
+        self.listener: Screen | None = None
         self.strict = strict
         self.use_utf8: bool = True
 
-        self._taking_plain_text: Optional[bool] = None
+        self._taking_plain_text: bool | None = None
 
         if screen is not None:
             self.attach(screen)
@@ -192,18 +199,20 @@ class Stream:
         :param pyte.screens.Screen screen: a screen to attach to.
         """
         if self.listener is not None:
-            warnings.warn("As of version 0.6.0 the listener queue is "
-                          "restricted to a single element. Existing "
-                          "listener {0} will be replaced."
-                          .format(self.listener), DeprecationWarning)
+            warnings.warn(
+                "As of version 0.6.0 the listener queue is "
+                "restricted to a single element. Existing "
+                f"listener {self.listener} will be replaced.",
+                DeprecationWarning,
+            )
 
         if self.strict:
             for event in self.events:
                 if not hasattr(screen, event):
-                    raise TypeError("{0} is missing {1}".format(screen, event))
+                    raise TypeError(f"{screen} is missing {event}")
 
         self.listener = screen
-        self._parser: Optional[ParserGenerator] = None
+        self._parser: ParserGenerator | None = None
         self._initialize_parser()
 
     def detach(self, screen: Screen) -> None:
@@ -230,7 +239,7 @@ class Stream:
         # Clide: Debug log incoming data
         if _debug_logger is not None:
             # Log escape sequences in a readable format
-            escaped = data.encode('unicode_escape').decode('ascii')
+            escaped = data.encode("unicode_escape").decode("ascii")
             if len(escaped) > 200:
                 escaped = escaped[:200] + "..."
             _log_debug(f"[STREAM] feed: {escaped}")
@@ -254,12 +263,12 @@ class Stream:
                 else:
                     taking_plain_text = False
             else:
-                taking_plain_text = send(data[offset:offset + 1])
+                taking_plain_text = send(data[offset : offset + 1])
                 offset += 1
 
         self._taking_plain_text = taking_plain_text
 
-    def _send_to_parser(self, data: str) -> Optional[bool]:
+    def _send_to_parser(self, data: str) -> bool | None:
         try:
             assert self._parser is not None
             return self._parser.send(data)
@@ -294,25 +303,28 @@ class Stream:
         SP_OR_GT = ctrl.SP + ">"
         NUL_OR_DEL = ctrl.NUL + ctrl.DEL
         CAN_OR_SUB = ctrl.CAN + ctrl.SUB
-        ALLOWED_IN_CSI = "".join([ctrl.BEL, ctrl.BS, ctrl.HT, ctrl.LF,
-                                  ctrl.VT, ctrl.FF, ctrl.CR])
+        ALLOWED_IN_CSI = "".join([ctrl.BEL, ctrl.BS, ctrl.HT, ctrl.LF, ctrl.VT, ctrl.FF, ctrl.CR])
         OSC_TERMINATORS = set([ctrl.ST_C0, ctrl.ST_C1, ctrl.BEL])
 
-        def create_dispatcher(mapping: Mapping[str, str]) -> Dict[str, Callable[..., None]]:
-            d = defaultdict(lambda: debug, dict(
-                (event, getattr(listener, attr))
-                for event, attr in mapping.items()))
+        def create_dispatcher(mapping: Mapping[str, str]) -> dict[str, Callable[..., None]]:
+            d = defaultdict(
+                lambda: debug,
+                dict((event, getattr(listener, attr)) for event, attr in mapping.items()),
+            )
 
             # Clide: Wrap dispatchers with debug logging
             if _debug_logger is not None:
                 original_d = dict(d)
                 for event, attr in mapping.items():
                     original_handler = original_d.get(event, debug)
+
                     def make_wrapper(e: str, a: str, h: Callable[..., None]) -> Callable[..., None]:
                         def wrapper(*args: Any, **kwargs: Any) -> None:
                             _log_debug(f"[DISPATCH] {a}({args}, {kwargs})")
                             return h(*args, **kwargs)
+
                         return wrapper
+
                     d[event] = make_wrapper(event, attr, original_handler)
 
             return d
@@ -360,7 +372,7 @@ class Stream:
                         listener.define_charset(code, mode=char)
                     else:
                         escape_dispatch[char]()
-                    continue    # Don't go to CSI.
+                    continue  # Don't go to CSI.
 
             if char in basic:
                 # Ignore shifts in UTF-8 mode. See
@@ -485,6 +497,7 @@ class ByteStream(Stream):
        Assume the input to :meth:`~pyte.streams.ByteStream.feed` is encoded
        using UTF-8. Defaults to ``True``.
     """
+
     def __init__(self, *args: Any, **kwargs: Any):
         super(ByteStream, self).__init__(*args, **kwargs)
 
diff --git a/clide/widgets/components/action_bar.py b/clide/widgets/components/action_bar.py
index 5e135aaa..597a3e92 100644
--- a/clide/widgets/components/action_bar.py
+++ b/clide/widgets/components/action_bar.py
@@ -2,14 +2,13 @@
 
 from __future__ import annotations
 
+from collections.abc import Callable
 from dataclasses import dataclass
-from typing import Callable
 
 from textual.app import ComposeResult
 from textual.containers import Horizontal
 from textual.message import Message
 from textual.reactive import reactive
-from textual.widget import Widget
 from textual.widgets import Button, Static
 
 
diff --git a/clide/widgets/components/diff_pane.py b/clide/widgets/components/diff_pane.py
index a7ebcb54..b9ce4af5 100644
--- a/clide/widgets/components/diff_pane.py
+++ b/clide/widgets/components/diff_pane.py
@@ -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
diff --git a/clide/widgets/panels/workspace.py b/clide/widgets/panels/workspace.py
index 6356e682..281d2b05 100644
--- a/clide/widgets/panels/workspace.py
+++ b/clide/widgets/panels/workspace.py
@@ -6,10 +6,10 @@ from textual.app import ComposeResult
 from textual.containers import Horizontal, Vertical
 from textual.message import Message
 from textual.reactive import reactive
-from textual.widgets import ContentSwitcher, Tab, TabPane, Tabs
+from textual.widgets import ContentSwitcher, Tab, Tabs
 
 from clide.models.diff import DiffContent
-from clide.widgets.components.action_bar import ActionBar, ActionButton, STANDARD_BUTTONS
+from clide.widgets.components.action_bar import ActionBar, ActionButton
 from clide.widgets.components.diff_pane import DiffPane
 from clide.widgets.components.editor_pane import EditorPane
 from clide.widgets.components.terminal_pane import TerminalPane
@@ -104,6 +104,7 @@ class WorkspacePanel(Vertical):
 
     class CloseRequested(Message):
         """Emitted when workspace should be hidden."""
+
         pass
 
     # Reactive state - persisted when hidden
@@ -114,10 +115,12 @@ class WorkspacePanel(Vertical):
     # Messages for app-level actions
     class MaximizeRequested(Message):
         """Emitted when workspace should be maximized."""
+
         pass
 
     class RestoreRequested(Message):
         """Emitted when workspace should be restored from maximized."""
+
         pass
 
     def __init__(
@@ -163,43 +166,53 @@ class WorkspacePanel(Vertical):
 
         # Register standard buttons using simple ASCII icons
         # Save button (for editor)
-        self._action_bar.register_button(ActionButton(
-            id="save",
-            icon="[S]",
-            tooltip="Save",
-        ))
+        self._action_bar.register_button(
+            ActionButton(
+                id="save",
+                icon="[S]",
+                tooltip="Save",
+            )
+        )
 
         # Add separator
         self._action_bar.add_separator()
 
         # Close button
-        self._action_bar.register_button(ActionButton(
-            id="close",
-            icon="x",
-            tooltip="Close",
-        ))
+        self._action_bar.register_button(
+            ActionButton(
+                id="close",
+                icon="x",
+                tooltip="Close",
+            )
+        )
 
         # Minimize button
-        self._action_bar.register_button(ActionButton(
-            id="minimize",
-            icon="_",
-            tooltip="Minimize",
-        ))
+        self._action_bar.register_button(
+            ActionButton(
+                id="minimize",
+                icon="_",
+                tooltip="Minimize",
+            )
+        )
 
         # Maximize button
-        self._action_bar.register_button(ActionButton(
-            id="maximize",
-            icon="^",
-            tooltip="Maximize",
-        ))
+        self._action_bar.register_button(
+            ActionButton(
+                id="maximize",
+                icon="^",
+                tooltip="Maximize",
+            )
+        )
 
         # Restore button (hidden by default)
-        self._action_bar.register_button(ActionButton(
-            id="restore",
-            icon="v",
-            tooltip="Restore",
-            visible=False,
-        ))
+        self._action_bar.register_button(
+            ActionButton(
+                id="restore",
+                icon="v",
+                tooltip="Restore",
+                visible=False,
+            )
+        )
 
         # Update button visibility based on current tab
         self._update_action_bar_for_tab(self.active_tab)
diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
index d72e86d4..0f3d7aca 100644
--- a/docs/ARCHITECTURE.md
+++ b/docs/ARCHITECTURE.md
@@ -1,11 +1,11 @@
-# Clide Architecture Documentation
+# Clide Architecture
 
-Comprehensive documentation of architecture patterns, best practices, and implementation guidelines.
+Technical documentation covering Clide's architecture, the frameworks it builds on, and implementation patterns.
 
 ## Table of Contents
 
+- [Application Architecture](#application-architecture)
 - [Textual TUI Framework](#textual-tui-framework)
-- [Typer CLI Framework](#typer-cli-framework)
 - [Pydantic Data Validation](#pydantic-data-validation)
 - [Extension System](#extension-system)
 - [Testing Strategy](#testing-strategy)
@@ -13,199 +13,238 @@ Comprehensive documentation of architecture patterns, best practices, and implem
 
 ---
 
+## Application Architecture
+
+Clide follows a layered architecture with clear separation between UI, business logic, and data.
+
+### Layer Overview
+
+```
+┌─────────────────────────────────────────────────────────┐
+│                    ClideApp (app.py)                    │
+│         Main application, layout, keybindings           │
+├─────────────────────────────────────────────────────────┤
+│                      Widgets Layer                       │
+│  ┌─────────────┐  ┌─────────────┐  ┌─────────────┐     │
+│  │   Panels    │  │ Components  │  │   Themes    │     │
+│  │  (layout)   │  │ (reusable)  │  │  (styling)  │     │
+│  └─────────────┘  └─────────────┘  └─────────────┘     │
+├─────────────────────────────────────────────────────────┤
+│                    Controllers Layer                     │
+│         Business logic, state management                 │
+├─────────────────────────────────────────────────────────┤
+│                     Services Layer                       │
+│      Git, files, scanning, settings, skills              │
+├─────────────────────────────────────────────────────────┤
+│                      Models Layer                        │
+│           Pydantic data structures                       │
+└─────────────────────────────────────────────────────────┘
+```
+
+### Data Flow
+
+```
+User Action (click, keypress)
+         │
+         ▼
+    Widget Event
+         │
+         ▼
+  Message Bubbles Up
+         │
+         ▼
+   App Event Handler
+         │
+         ▼
+  Controller Method
+         │
+         ▼
+   Service Call
+         │
+         ▼
+  Return Data/Status
+         │
+         ▼
+   Update UI State
+         │
+         ▼
+ Reactive UI Update
+```
+
+### Key Patterns
+
+**Message-based communication** — Widgets emit messages that bubble up. Parent widgets or the app handle messages and coordinate responses.
+
+**Reactive properties** — UI state uses Textual's `reactive` type. Changes automatically trigger `watch_*` methods.
+
+**Background workers** — Long operations use `@work(thread=True)` to avoid blocking the UI.
+
+**State preservation** — Hiding panels uses `display: none`, never destroying widgets. All state persists.
+
+For detailed code organization, see [Code Organization](code-organization.md).
+
+---
+
 ## Textual TUI Framework
 
-Textual models TUIs as a reactive tree of widgets, similar to React's component tree but grid-based on character cells.
+Textual provides the foundation for Clide's terminal UI.
 
-### Key Concepts
+### Core Concepts
 
-**Widgets and Containers**
-- Widgets are the building blocks of the UI
-- Containers are widgets that hold other widgets
-- Default layout stacks widgets vertically from top of screen
+**Widgets** — Building blocks of the UI. Everything visible is a widget.
 
-**Reactive Programming**
-- State changes trigger automatic UI updates
-- No manual refresh loops needed
-- Use reactive attributes for state management
+**Containers** — Widgets that hold other widgets (Vertical, Horizontal, Container).
 
-**Event-Driven Model**
-- Define callbacks for key presses, mouse clicks, timer ticks
-- Actions are functions callable via keystroke or text link
+**Reactive Programming** — State changes trigger automatic UI updates.
 
-### Best Practices
+**CSS Styling** — Layout and appearance defined in CSS, similar to web development.
 
-1. **Use Immutable Objects**
-   - Prefer tuples, NamedTuples, or frozen dataclasses
-   - Easier to reason about, cache, and test
-   - Enables side-effect-free code
+### Layout System
 
-2. **Separate Styles**
-   - Keep CSS in `.tcss` files, not inline
-   - Python code stays clean and focused on logic
+Clide uses CSS Grid for the main layout:
 
-3. **Async-First**
-   - Textual is async under the hood
-   - Use `async`/`await` for I/O operations
-   - Can integrate with async libraries if needed
-
-### Layout Management
-
-```python
-# Grid layout example
-CSS = """
+```css
 Screen {
     layout: grid;
     grid-size: 3 1;
-    grid-columns: 1fr 2fr 1fr;
+    grid-columns: 20% 1fr 25%;
 }
-"""
+```
+
+Panels use percentage widths with minimum sizes:
+
+```css
+#panel-sidebar {
+    width: 20%;
+    min-width: 25;
+}
+```
+
+### Widget Lifecycle
+
+```python
+class MyWidget(Widget):
+    def __init__(self):
+        super().__init__()
+        # Initialize instance variables
+
+    def compose(self) -> ComposeResult:
+        # Yield child widgets
+        yield Label("Hello")
+
+    def on_mount(self) -> None:
+        # Called after widget is added to DOM
+        # Safe to query other widgets here
+
+    def on_unmount(self) -> None:
+        # Cleanup when removed
+```
+
+### Event Handling
+
+Events bubble up through the widget tree:
+
+```python
+# Define a message
+class FileSelected(Message):
+    def __init__(self, path: Path):
+        self.path = path
+        super().__init__()
+
+# Emit the message
+self.post_message(self.FileSelected(path))
+
+# Handle in parent (naming convention: on_<widget>_<message>)
+def on_files_view_file_selected(self, event: FilesView.FileSelected):
+    self.open_file(event.path)
+```
+
+### Background Tasks
+
+Use `@work` for operations that shouldn't block the UI:
+
+```python
+from textual import work
+
+@work(thread=True)
+def fetch_data(self) -> dict:
+    """Runs in thread pool."""
+    result = expensive_operation()
+    return result
+
+def on_worker_state_changed(self, event: Worker.StateChanged) -> None:
+    if event.state == WorkerState.SUCCESS:
+        self.update_ui(event.worker.result)
 ```
 
 ### References
 
 - [Textual Documentation](https://textual.textualize.io/)
-- [Textual Tutorial](https://textual.textualize.io/tutorial/)
-- [Real Python Textual Guide](https://realpython.com/python-textual/)
-- [Textual GitHub](https://github.com/Textualize/textual)
-
----
-
-## Typer CLI Framework
-
-Typer is built on Click with Python type hints for automatic argument parsing.
-
-### Project Structure Pattern
-
-```
-app/
-├── __init__.py
-├── main.py          # Root Typer app
-├── commands/        # Subcommand modules
-│   ├── users.py
-│   └── tasks.py
-└── helpers/         # Shared utilities
-    └── validate.py
-```
-
-### Best Practices
-
-1. **Organize Commands**
-   - Use `add_typer()` to group commands
-   - Avoid giant files with dozens of commands
-   - Each command function should orchestrate, not contain all logic
-
-2. **Entry Point Support**
-   - Add `__main__.py` for `python -m` support
-   - Define entry points in pyproject.toml for CLI scripts
-
-3. **Standard Exit Codes**
-   - `0` for success
-   - Non-zero for errors
-   - Crucial for CI/CD integration
-
-4. **Type Hints for Validation**
-   - Use Enum for dropdown-style restrictions
-   - Type hints provide editor autocompletion
-
-### Subcommand Example
-
-```python
-# commands/users.py
-import typer
-
-app = typer.Typer()
-
-@app.command()
-def create(name: str):
-    """Create a new user."""
-    ...
-
-# main.py
-from commands import users
-
-main_app = typer.Typer()
-main_app.add_typer(users.app, name="users")
-```
-
-### References
-
-- [Typer Documentation](https://typer.tiangolo.com/)
-- [Typer Subcommands](https://typer.tiangolo.com/tutorial/subcommands/)
-- [Building a Package](https://typer.tiangolo.com/tutorial/package/)
+- [Textual Widgets](https://textual.textualize.io/widgets/)
+- [Textual CSS](https://textual.textualize.io/guide/CSS/)
 
 ---
 
 ## Pydantic Data Validation
 
-Pydantic v2 with strict mode ensures type safety and validation.
+All data models use Pydantic v2 with strict mode.
 
-### Strict Mode Configuration
+### Model Configuration
 
 ```python
 from pydantic import BaseModel, ConfigDict
 
-class MyModel(BaseModel):
+class GitChange(BaseModel):
     model_config = ConfigDict(strict=True, frozen=True)
-    name: str
-    count: int  # Will reject "123" string
+
+    path: str
+    status: Literal["added", "modified", "deleted"]
+    staged: bool
 ```
 
+**strict=True** — No type coercion. `"123"` won't become `123`.
+
+**frozen=True** — Immutable instances. Enables hashing for use as dict keys.
+
 ### Settings Management
 
-Settings have moved to `pydantic-settings` package:
+Application settings use `pydantic-settings`:
 
 ```python
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
-class AppSettings(BaseSettings):
+class ClideSettings(BaseSettings):
     model_config = SettingsConfigDict(
-        env_prefix="APP_",
+        env_prefix="CLIDE_",
         env_file=".env",
-        env_nested_delimiter="__",
     )
 
-    database_url: str
-    debug: bool = False
+    theme: str = "summer-night"
+    jira_enabled: bool = False
 ```
 
-### Best Practices
-
-1. **Use `frozen=True` for Immutability**
-   - Prevents accidental mutation
-   - Enables hashing for use as dict keys
-
-2. **Explicit Strict Types**
-   - `StrictInt`, `StrictStr` for field-level strictness
-   - Or use `model_config` for model-wide strictness
-
-3. **Validation vs Parsing**
-   - Strict mode rejects type coercion
-   - JSON parsing allows some conversion (ISO8601 → datetime)
+Settings load from (in priority order):
+1. Environment variables (`CLIDE_THEME=dracula`)
+2. `.env` file
+3. Default values
 
 ### References
 
-- [Pydantic v2 Documentation](https://docs.pydantic.dev/latest/)
+- [Pydantic Documentation](https://docs.pydantic.dev/latest/)
 - [Pydantic Settings](https://docs.pydantic.dev/latest/concepts/pydantic_settings/)
-- [Pydantic Configuration](https://docs.pydantic.dev/latest/api/config/)
-- [Migration Guide](https://docs.pydantic.dev/latest/migration/)
 
 ---
 
 ## Extension System
 
-The plugin system uses Pluggy for hook-based extensibility.
+Clide uses Pluggy for hook-based extensibility.
 
-### Pluggy Concepts
+### Hook Specifications
 
-1. **Hook Specifications** - Define the interface extensions implement
-2. **Hook Implementations** - Extension code implementing hooks
-3. **Plugin Manager** - Discovers and calls implementations
-
-### Architecture
+Hooks define extension points:
 
 ```python
-# hookspecs.py - Define hooks
+# clide/extensions/hookspecs.py
 import pluggy
 
 hookspec = pluggy.HookspecMarker("clide")
@@ -213,18 +252,36 @@ hookimpl = pluggy.HookimplMarker("clide")
 
 class ClideHookSpec:
     @hookspec
-    def register_panel(self) -> dict: ...
+    def clide_startup(self, app: App) -> None:
+        """Called when the app starts."""
+
+    @hookspec
+    def clide_on_file_changed(self, event: FileEvent) -> None:
+        """Called when a file changes."""
+```
+
+### Implementing Hooks
+
+Extensions implement hooks with the `@hookimpl` decorator:
+
+```python
+from clide.extensions import hookimpl
 
-# extension.py - Implement hooks
 class MyExtension:
     @hookimpl
-    def register_panel(self) -> dict:
-        return {"name": "custom", "widget": CustomWidget}
+    def clide_startup(self, app: App) -> None:
+        app.notify("Extension loaded!")
+
+    @hookimpl
+    def clide_on_file_changed(self, event: FileEvent) -> None:
+        if event.path.suffix == ".py":
+            # React to Python file changes
+            pass
 ```
 
 ### Distribution
 
-Extensions can be distributed as packages using entry points:
+Extensions can be packaged and distributed via entry points:
 
 ```toml
 # pyproject.toml of extension package
@@ -232,55 +289,73 @@ Extensions can be distributed as packages using entry points:
 my_extension = "my_package:MyExtension"
 ```
 
-### Hook Execution Order
+### Available Hooks
 
-- Multiple implementations called in LIFO (Last In, First Out) order
-- Use `hookimpl(tryfirst=True)` or `hookimpl(trylast=True)` for ordering
-
-### Alternatives
-
-- **Stevedore** - Better for driver/extension patterns, uses entry points
-- Choose Pluggy for hook-based systems (like pytest uses)
+| Hook | When Called |
+|------|-------------|
+| `clide_startup` | App initialization |
+| `clide_shutdown` | App cleanup |
+| `clide_on_file_changed` | File created/modified/deleted |
+| `clide_on_file_saved` | File saved in editor |
 
 ### References
 
 - [Pluggy Documentation](https://pluggy.readthedocs.io/)
-- [Stevedore Documentation](https://docs.openstack.org/stevedore/latest/)
-- [Creating Plugins with Stevedore](https://docs.openstack.org/stevedore/latest/user/tutorial/creating_plugins.html)
 
 ---
 
 ## Testing Strategy
 
-### pytest-asyncio
+### Test Organization
 
-Configure auto mode for automatic async test discovery:
+```
+tests/
+├── unit/           # Isolated component tests
+├── integration/    # Component interaction tests
+└── snapshots/      # Visual regression tests
+```
+
+### Async Testing
+
+Configure pytest-asyncio in auto mode:
 
 ```toml
-# pyproject.toml
 [tool.pytest.ini_options]
 asyncio_mode = "auto"
 ```
 
-### Async Test Patterns
+Tests can be async without decorators:
 
 ```python
-import pytest
-
-# Auto mode - no decorator needed
 async def test_async_operation():
     result = await some_async_function()
     assert result == expected
-
-# Async fixtures
-@pytest.fixture
-async def database_connection():
-    conn = await create_connection()
-    yield conn
-    await conn.close()
 ```
 
-### Async Mocking
+### Snapshot Testing
+
+Visual regression testing with pytest-textual-snapshot:
+
+```python
+def test_layout(snap_compare):
+    assert snap_compare(ClideApp(), terminal_size=(120, 40))
+
+def test_with_interaction(snap_compare):
+    async def setup(pilot):
+        await pilot.press("tab", "enter")
+
+    assert snap_compare(ClideApp(), run_before=setup)
+```
+
+Update snapshots after intentional changes:
+
+```bash
+pytest tests/snapshots/ --snapshot-update
+```
+
+### Mocking
+
+Use `AsyncMock` for async dependencies:
 
 ```python
 from unittest.mock import AsyncMock
@@ -291,73 +366,43 @@ async def test_with_mock():
     assert result["status"] == "ok"
 ```
 
-### Snapshot Testing
-
-Visual regression with pytest-textual-snapshot:
-
-```python
-def test_layout(snap_compare):
-    assert snap_compare("app.py", terminal_size=(120, 40))
-
-def test_with_interaction(snap_compare):
-    async def setup(pilot):
-        await pilot.press("tab", "enter")
-
-    assert snap_compare("app.py", run_before=setup)
-```
-
-Update snapshots after intentional changes:
-```bash
-pytest tests/snapshots/ --snapshot-update
-```
-
-### Test Harness Pattern
-
-Harnesses provide isolated test environments:
-
-```python
-class AppHarness:
-    async def start(self) -> tuple[App, Pilot]:
-        """Start app with mocked dependencies."""
-
-    async def stop(self) -> None:
-        """Clean shutdown."""
-```
-
-### Best Practices
-
-1. **Always use `@pytest.mark.asyncio`** (or auto mode)
-2. **Use async fixtures** for async setup/teardown
-3. **Mock external services** - don't hit real APIs
-4. **Choose appropriate fixture scopes** for performance
-5. **Avoid blocking the event loop** in async tests
-
 ### References
 
-- [pytest-asyncio Documentation](https://pytest-asyncio.readthedocs.io/en/latest/)
+- [pytest-asyncio](https://pytest-asyncio.readthedocs.io/)
 - [pytest-textual-snapshot](https://github.com/Textualize/pytest-textual-snapshot)
 - [Textual Testing Guide](https://textual.textualize.io/guide/testing/)
-- [pytest Fixtures](https://docs.pytest.org/en/stable/how-to/fixtures.html)
 
 ---
 
 ## Build and Distribution
 
-### PyInstaller Limitations
+### Development
 
-**Critical: PyInstaller cannot cross-compile.**
-- Build on the target OS
-- Use CI/CD for multi-platform builds
+```bash
+make setup      # Create venv, install deps
+make run        # Run application
+make test       # Run all tests
+make typecheck  # Run mypy
+make lint       # Run ruff
+make format     # Format code
+```
 
-### CI/CD Multi-Platform Build
+### PyInstaller
 
-Use Gitea Actions (or compatible CI) for multi-platform builds:
+Build standalone executables:
+
+```bash
+pip install -e ".[build]"
+pyinstaller clide.spec --clean
+```
+
+**Important**: PyInstaller cannot cross-compile. Build on each target platform.
+
+### CI/CD
+
+Multi-platform builds via Gitea Actions:
 
 ```yaml
-# .gitea/workflows/build.yml
-name: Build
-on: [push, tag]
-
 jobs:
   build-linux:
     runs-on: ubuntu-latest
@@ -371,45 +416,17 @@ jobs:
 
   build-macos:
     runs-on: macos-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - run: pip install -e ".[build]"
-      - run: pyinstaller clide.spec --clean
-
-  build-windows:
-    runs-on: windows-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - run: pip install -e ".[build]"
-      - run: pyinstaller clide.spec --clean
+    # ... same steps
 ```
 
-### Optimization Tips
+### Optimization
 
-1. **Use `--onefile`** for single executable
-2. **Apply `--strip`** to reduce binary size
-3. **Use UPX compression** (460 MB → ~130 MB possible)
-4. **Exclude unused modules** with `--exclude-module`
-5. **Lazy imports** for large libraries
-
-### Platform-Specific Output
-
-- **Windows**: `.exe` or MSIX installer
-- **macOS**: `.app` bundle in `.dmg`
-- **Linux**: AppImage or native package
-
-### Linux Compatibility
-
-Build on the oldest target distro version. Newer systems may produce incompatible binaries.
+- Use `--onefile` for single executable
+- Apply `--strip` to reduce size
+- Use UPX compression for further reduction
+- Exclude unused modules with `--exclude-module`
 
 ### References
 
 - [PyInstaller Documentation](https://pyinstaller.org/)
-- [Building the Bootloader](https://pyinstaller.org/en/latest/bootloader-building.html)
 - [Gitea Actions](https://docs.gitea.com/usage/actions/overview)
diff --git a/docs/code-organization.md b/docs/code-organization.md
new file mode 100644
index 00000000..0578f75c
--- /dev/null
+++ b/docs/code-organization.md
@@ -0,0 +1,342 @@
+# Code Organization
+
+Clide follows a layered architecture separating UI components from business logic, enabling testability and maintainability.
+
+## Directory Structure
+
+```
+clide/
+├── app.py                    # Main application, layout, keybindings
+├── cli.py                    # Typer entry point
+├── models/                   # Pydantic data models
+├── services/                 # Background services and utilities
+├── controllers/              # Business logic (no UI)
+├── widgets/
+│   ├── panels/               # Main layout containers
+│   └── components/           # Reusable UI pieces
+├── themes/                   # Theme definitions and registry
+├── extensions/               # Plugin system (hookspecs, manager)
+├── templates/                # Bundled templates (skills, etc.)
+└── vendor/                   # Vendored dependencies (pyte)
+```
+
+## Layers
+
+### Models (`clide/models/`)
+
+Pure data structures using Pydantic with strict mode. Models are immutable and contain no business logic.
+
+```python
+from pydantic import BaseModel, ConfigDict
+
+class GitChange(BaseModel):
+    model_config = ConfigDict(strict=True, frozen=True)
+
+    path: str
+    status: Literal["added", "modified", "deleted", "untracked", "renamed"]
+    staged: bool
+```
+
+**Key models:**
+- `git.py` — Git-related types (GitBranch, GitCommit, GitChange, GitStatus)
+- `config.py` — Application settings (ClideSettings, PanelConfig)
+- `problems.py` — Linter output (Problem, Severity)
+- `todos.py` — TODO items (TodoItem, ProjectTodoItem, TodoType)
+
+### Services (`clide/services/`)
+
+Stateless utilities that perform work without UI interaction. Services may be async or use background threads.
+
+```python
+class GitService:
+    """Git operations via subprocess."""
+
+    def __init__(self, workdir: Path):
+        self._workdir = workdir
+
+    async def get_status(self) -> GitStatus:
+        """Get current repository status."""
+        ...
+
+    async def get_branches(self) -> list[GitBranch]:
+        """List all branches."""
+        ...
+```
+
+**Key services:**
+- `git_service.py` — Git CLI operations
+- `file_service.py` — File read/write operations
+- `todo_scanner.py` — Scans codebase for TODO/FIXME comments
+- `settings_service.py` — User settings persistence
+- `skill_installer.py` — Claude Code skill management
+- `file_watcher.py` — File system change monitoring
+- `syntax_service.py` — Tree-sitter syntax highlighting
+
+### Controllers (`clide/controllers/`)
+
+Bridge between services and UI. Controllers contain business logic, manage state, and emit Textual messages. Controllers have no direct UI rendering.
+
+```python
+from clide.controllers.base import controller
+
+@controller
+class GitController:
+    """Manages git state and operations."""
+
+    def __init__(self, workdir: Path):
+        self._service = GitService(workdir)
+        self._status: GitStatus | None = None
+
+    async def refresh_status(self) -> GitStatus:
+        """Refresh and cache git status."""
+        self._status = await self._service.get_status()
+        return self._status
+
+    def stage_file(self, path: str) -> None:
+        """Stage a file for commit."""
+        ...
+```
+
+**Key controllers:**
+- `git.py` — Git operations, skill integration
+- `editor.py` — File editing state
+- `diff.py` — Diff viewing and management
+- `problems.py` — Linter integration
+- `todos.py` — TODO tracking
+- `jira.py` — Jira CLI integration
+
+### Widgets (`clide/widgets/`)
+
+UI components split into panels (layout containers) and components (reusable pieces).
+
+#### Panels (`clide/widgets/panels/`)
+
+Top-level layout containers that compose the application UI.
+
+```python
+class SidebarPanel(Vertical):
+    """Left sidebar with Files, Git, and Tree tabs."""
+
+    class FileSelected(Message):
+        """Emitted when a file is selected."""
+        def __init__(self, path: Path):
+            self.path = path
+            super().__init__()
+
+    def compose(self) -> ComposeResult:
+        with TabbedContent():
+            with TabPane("Files"):
+                yield FilesView(path=self._workdir)
+            with TabPane("Git"):
+                yield GitChangesView()
+            with TabPane("Tree"):
+                yield GitGraphView()
+        yield BranchStatus()
+```
+
+**Panels:**
+- `sidebar.py` — Left sidebar (files, git, graph)
+- `context.py` — Right sidebar (problems, todos, jira)
+- `workspace.py` — Center workspace (editor, diff, terminal)
+- `claude.py` — Claude Code terminal integration
+
+#### Components (`clide/widgets/components/`)
+
+Reusable UI pieces composed into panels.
+
+**File browsing:**
+- `files_view.py` — Project file tree
+- `file_entry.py` — Single file/directory entry
+
+**Git:**
+- `git_changes.py` — Staged/unstaged file lists
+- `git_graph.py` — Visual branch graph
+- `branch_status.py` — Branch indicator with popout selector
+
+**Context:**
+- `problems_view.py` — Linter problems list
+- `todos_view.py` — TODO/FIXME list with sub-tabs
+- `jira_view.py` — Jira issue display
+
+**Editor:**
+- `editor_pane.py` — Code editor with syntax highlighting
+- `diff_pane.py` — Side-by-side diff viewer
+- `terminal_pane.py` — Command execution terminal
+
+## Communication Patterns
+
+### Message Flow
+
+Components communicate via Textual's message system. Messages bubble up through the widget tree.
+
+```
+Component emits message
+        │
+        ▼
+Parent panel receives and may re-emit
+        │
+        ▼
+App handles and coordinates response
+        │
+        ▼
+App calls controller methods
+        │
+        ▼
+Controller updates state, may emit messages
+        │
+        ▼
+UI updates reactively
+```
+
+**Example: File selection**
+
+```python
+# In FilesView (component)
+class FileSelected(Message):
+    def __init__(self, path: Path):
+        self.path = path
+        super().__init__()
+
+def on_tree_node_selected(self, event):
+    if event.node.data.is_file:
+        self.post_message(self.FileSelected(event.node.data.path))
+
+# In SidebarPanel (panel)
+def on_files_view_file_selected(self, event: FilesView.FileSelected):
+    # Re-emit for app to handle
+    self.post_message(self.FileSelected(event.path))
+
+# In ClideApp (app)
+def on_sidebar_panel_file_selected(self, event: SidebarPanel.FileSelected):
+    self.editor_controller.open_file(event.path)
+    self.show_workspace("editor")
+```
+
+### Reactive Properties
+
+State that affects UI uses Textual's reactive system:
+
+```python
+class ClideApp(App):
+    # Reactive state
+    workspace_visible: reactive[bool] = reactive(False)
+    problem_count: reactive[int] = reactive(0)
+    current_branch: reactive[str] = reactive("main")
+
+    def watch_workspace_visible(self, visible: bool) -> None:
+        """React to workspace visibility changes."""
+        workspace = self.query_one("#panel-workspace")
+        workspace.display = visible
+
+        claude = self.query_one("#panel-claude")
+        claude.styles.height = "40%" if visible else "100%"
+```
+
+### Background Tasks
+
+Long-running operations use the `@work` decorator to avoid blocking the UI:
+
+```python
+from textual import work
+
+class ClideApp(App):
+    @work(thread=True)
+    def refresh_git_status(self) -> None:
+        """Refresh git status in background."""
+        status = self.git_controller.get_status_sync()
+        self.call_from_thread(self._update_git_ui, status)
+
+    def _update_git_ui(self, status: GitStatus) -> None:
+        """Update UI with git status (runs on main thread)."""
+        sidebar = self.query_one(SidebarPanel)
+        sidebar.update_git_status(status.staged, status.unstaged)
+```
+
+## Extension System
+
+Clide uses Pluggy for extensibility. Extensions implement hooks defined in `hookspecs.py`.
+
+```python
+# clide/extensions/hookspecs.py
+class ClideHookSpec:
+    @hookspec
+    def clide_startup(self, app: App) -> None:
+        """Called when app starts."""
+
+    @hookspec
+    def clide_on_file_changed(self, event: FileEvent) -> None:
+        """Called when a file changes."""
+
+# User extension
+class MyExtension:
+    @hookimpl
+    def clide_on_file_changed(self, event: FileEvent) -> None:
+        if event.path.suffix == ".py":
+            # Custom logic for Python files
+            ...
+```
+
+**Available hooks:**
+- `clide_startup` — App initialization
+- `clide_shutdown` — App cleanup
+- `clide_on_file_changed` — File system changes
+- `clide_on_file_saved` — File saved in editor
+
+## Skills System
+
+Clide integrates with Claude Code skills for git operations. Skills are installed to the project's `.claude/skills/` directory.
+
+```python
+# clide/services/skill_installer.py
+class SkillInstaller:
+    def install(self, skill_name: str, scope: Literal["user", "project"] = "project"):
+        """Install a skill from bundled templates."""
+        template_dir = TEMPLATES_DIR / skill_name
+        target_dir = self.project_skills_dir / skill_name
+        shutil.copytree(template_dir, target_dir)
+```
+
+**Bundled skills** (`clide/templates/skills/`):
+- `commit` — Git commit workflow
+- `stash` — Git stash operations
+- `pull` — Git pull with rebase
+- `push` — Git push to remote
+- `branch` — Branch management
+
+When a git action button is clicked, Clide ensures the skill is installed before sending the command to Claude.
+
+## Testing
+
+Tests mirror the source structure:
+
+```
+tests/
+├── unit/
+│   ├── test_models.py
+│   ├── test_services.py
+│   ├── test_controllers.py
+│   ├── test_widgets.py
+│   └── test_app.py
+├── integration/
+│   └── test_files_view.py
+└── snapshots/
+    └── test_app_snapshots.py
+```
+
+**Unit tests** verify individual components in isolation.
+**Integration tests** verify component interactions.
+**Snapshot tests** catch visual regressions using pytest-textual-snapshot.
+
+## Configuration
+
+### Application Settings
+
+`ClideSettings` in `clide/models/config.py` defines app configuration loaded from environment or `.config/settings.toml`.
+
+### User Settings
+
+`UserSettings` persisted to `~/.clide/settings.json` stores user preferences:
+- Theme selection
+- Panel visibility defaults
+- Compact mode preference
+- Jira integration settings
diff --git a/docs/tui-ide-spec.md b/docs/tui-ide-spec.md
index 6985bf20..54af80d5 100644
--- a/docs/tui-ide-spec.md
+++ b/docs/tui-ide-spec.md
@@ -1,14 +1,14 @@
 # TUI IDE Specification
 
-A terminal-based IDE built with Textual, designed to wrap Claude Code and integrate project management tooling (Jira/Confluence via CLI).
+Design specification for Clide's terminal user interface. This document describes the layout, interactions, and design decisions.
 
 ## Design Principles
 
-- **Claude-centric**: Claude Code is the primary workspace, always visible
-- **Contextual panels**: Editor/Diff/Terminal appear only when needed
-- **VSCode-familiar**: Keybindings and interaction patterns follow VSCode conventions
-- **Responsive**: Works on 13" laptop and widescreen monitors
-- **No vim magic**: Standard keyboard navigation, no modal editing
+- **Claude-centric** — Claude Code is the primary workspace, always visible
+- **Contextual panels** — Editor/Diff/Terminal appear only when needed
+- **Alt-key shortcuts** — Keybindings use Alt to avoid conflicts with Claude Code input
+- **Responsive** — Works on 13" laptops to widescreen monitors
+- **State preservation** — Hiding panels preserves all state (never destroy widgets)
 
 ---
 
@@ -19,112 +19,105 @@ A terminal-based IDE built with Textual, designed to wrap Claude Code and integr
 ```
 ┌─────────────────┬─────────────────────────┬──────────────────┐
 │ panel-sidebar   │ panel-workspace (60%)   │ panel-context    │
-│                 │ [Editor][Diff][Terminal]│                  │
-│ [Files][Git]    │ (hidden when inactive)  │ (content area)   │
-│ [Tree]          ├─────────────────────────┤                  │
-│                 │                         │                  │
-│ (content area)  │ panel-claude            │                  │
-│                 │ (40% when workspace     │                  │
+│ 20%             │ [Editor][Diff][Terminal]│ 25%              │
+│                 │ (hidden when inactive)  │                  │
+│ [Files][Git]    ├─────────────────────────┤ [Jira][TODOs]    │
+│ [Tree]          │                         │ [Problems]       │
+│                 │ panel-claude            │                  │
+│ (content area)  │ (40% when workspace     │ (content area)   │
 │                 │  visible, else 100%)    │                  │
 ├─────────────────┤                         ├──────────────────┤
-│ branch-status   │                         │[⚠ 3][✓12][Jira] │
-│ ⎇ main ▾       │                         │ context-tabs     │
+│ branch-status   │                         │                  │
+│ ⎇ main ▾       │                         │                  │
+│ staged: 2      │                         │                  │
 └─────────────────┴─────────────────────────┴──────────────────┘
 ```
 
-### Panel Definitions
+### Panel IDs
 
 ```python
 PANELS = {
     # Left sidebar
     "sidebar": "panel-sidebar",
-    "sidebar-files": "panel-sidebar-files",
-    "sidebar-git": "panel-sidebar-git", 
-    "sidebar-tree": "panel-sidebar-tree",
-    "branch-status": "panel-branch-status",
-    
+
     # Center
     "claude": "panel-claude",
     "workspace": "panel-workspace",
-    "editor": "panel-editor",
-    "diff": "panel-diff",
-    "terminal": "panel-terminal",
-    
+
     # Right context
     "context": "panel-context",
-    "context-jira": "panel-context-jira",
-    "context-problems": "panel-context-problems",
-    "context-todos": "panel-context-todos",
 }
 ```
 
 ---
 
-## Left Sidebar (`panel-sidebar`)
+## Left Sidebar
 
 ### Tabs
 
-| Tab | Content | Widget |
-|-----|---------|--------|
-| Files | Project file tree | `DirectoryTree` |
-| Git | Staged/Unstaged changes | `GitChangesView` (custom) |
-| Tree | Merge/branch graph | `GitGraphView` (custom) |
+| Tab | Content | Purpose |
+|-----|---------|---------|
+| Files | Project file tree | Navigate and open files |
+| Git | Staged/Unstaged changes | Review and manage changes |
+| Tree | Branch graph | Visualize git history |
 
-### Git Tab Details
+### Git Tab
 
-Two collapsible sections:
-- **Staged**: Files in index, ready to commit
-- **Unstaged**: Modified/untracked files
+Two collapsible sections showing staged and unstaged changes.
 
-Each file item shows:
-- Status icon: `+` added, `~` modified, `-` deleted, `?` untracked, `→` renamed
-- File path (relative)
+**File status indicators:**
+- `+` Added
+- `~` Modified
+- `-` Deleted
+- `?` Untracked
+- `→` Renamed
 
-**Interactions:**
-- Click file → opens in Editor panel
-- Double-click or keybind → stage/unstage file
-- Right-click or keybind → show context menu (discard, diff, etc.)
+**Action buttons:**
+- **Commit** — Delegate to Claude with `/commit` skill
+- **Stash** — Delegate to Claude with `/stash` skill
+- **Pull** — Delegate to Claude with `/pull` skill
+- **Push** — Delegate to Claude with `/push` skill
 
-### Tree Tab Details
+### Tree Tab
 
-Renders `git log --graph --oneline --decorate --all` with visual styling.
+Visual git graph using box-drawing characters:
 
-**Polish item**: Consider custom rendering with box-drawing characters for a cleaner look:
 ```
-●──┬── main: Latest commit message
-│  ●── feature: Feature work
-●──┴── Merge branch 'feature'
-◆───── Tagged release v1.0
+● main: Latest commit message
+│
+├─● feature: Feature work
+│
+●─┴ Merge branch 'feature'
+◆ Tagged release v1.0
 ```
 
-Use canvas or rich text with:
-```python
-GRAPH_CHARS = {
-    'commit': '●',
-    'merge': '◆',
-    'line': '│',
-    'branch': '├──',
-    'join': '┴──',
-}
-```
+**Symbols:**
+- `●` Regular commit
+- `◆` Merge commit
+- `│` Branch line
+- `├` Branch point
+- `┴` Merge point
 
 ### Branch Status Bar
 
-Fixed at bottom of sidebar. Shows current branch with popout toggle.
+Fixed at bottom of sidebar. Shows current branch and git stats.
+
+```
+┌─────────────────────────────────┐
+│ ⎇ main ▾    staged: 2 unstaged: 5│
+└─────────────────────────────────┘
+```
+
+Click to expand branch selector:
 
 ```
 ┌─────────────────┐
-│ ⎇ main ▾       │  ← Click or keybind to expand
-└─────────────────┘
-        │
-        ▼ (popout overlay)
-┌─────────────────┐
 │ Recent branches │
-│ ○ main         │
+│ ● main         │
 │ ○ feature/xyz  │
 │ ○ develop      │
 ├─────────────────┤
-│ [Checkout] [New]│
+│[Checkout] [New] │
 └─────────────────┘
 ```
 
@@ -132,232 +125,162 @@ Fixed at bottom of sidebar. Shows current branch with popout toggle.
 
 ## Center Column
 
-### Claude Panel (`panel-claude`)
+### Claude Panel
 
-The primary workspace. Displays Claude Code interaction.
+The primary workspace. Always visible.
 
-**Default state**: 100% height of center column
-**With workspace**: 40% height (bottom)
+**Default state:** 100% height of center column
+**With workspace:** 40% height (bottom)
 
 **Content:**
-- Streaming markdown responses (use `Markdown` or `RichLog` widget)
-- Visual distinction between:
-  - Claude's responses
-  - Tool calls / file operations
-  - User input
-- Input area at bottom
+- Full PTY terminal running Claude Code CLI
+- Scrollback history (1000 lines)
+- Input at bottom
 
-### Workspace Panel (`panel-workspace`)
+### Workspace Panel
 
-Tabbed container for Editor, Diff, and Terminal. **Hidden by default.**
+Tabbed container for Editor, Diff, and Terminal. Hidden by default.
 
-**Important**: Hiding is not closing. All panels retain state when hidden:
-- Editor: Open files, cursor position, scroll position, unsaved changes
+**Visibility principle:** Hiding is not closing. All panels retain state:
+- Editor: Open file, cursor position, scroll, unsaved changes
 - Diff: Current diff content, scroll position
-- Terminal: Active session, command history, output buffer
-
-Use `display: none` for visibility, never destroy/recreate widgets.
+- Terminal: Command history, output buffer
 
 **Visibility triggers:**
 
 | Trigger | Result |
 |---------|--------|
-| Click file in sidebar | Show workspace, focus Editor tab |
-| Claude proposes changes | Show workspace, focus Diff tab |
-| User presses `` Ctrl+` `` | Show workspace, focus Terminal tab |
-| User runs command | Show workspace, focus Terminal tab |
-| Close all tabs / Escape | Hide workspace, Claude reclaims space |
-
-**Height**: 60% of center column when visible
+| Click file in sidebar | Show workspace, focus Editor |
+| Click problem/TODO | Show workspace, focus Editor at line |
+| Press `` Alt+` `` | Show workspace, focus Terminal |
+| Close all content | Hide workspace, Claude reclaims space |
 
 #### Editor Tab
 
-- `TextArea` widget with syntax highlighting
-- Language detection from file extension
-- Theme: Follow terminal theme or user preference
+Code editor with:
+- Syntax highlighting (tree-sitter based)
+- Line numbers
+- Current line highlighting
 
 #### Diff Tab
 
-- Side-by-side or unified diff view
-- Syntax highlighting for changed content
-- Accept/Reject buttons for Claude-proposed changes
+Side-by-side diff viewer for:
+- Git changes (staged and unstaged)
+- Claude-proposed edits
 
 #### Terminal Tab
 
-- Proper PTY integration for full terminal emulation
-- Or simpler command runner with output display (decide based on complexity)
+Command execution terminal:
 - Working directory tied to project root
+- Output preserved when panel hidden
 
 ---
 
-## Right Sidebar (`panel-context`)
+## Right Context Panel
 
-### Content Area
+### Tabs
 
-Switches based on selected bottom tab. Shows one of:
-- Jira view (default)
-- Problems view
-- TODOs view
+| Tab | Badge | Content |
+|-----|-------|---------|
+| Jira | — | Jira issue display |
+| TODOs | Count | TODO/FIXME from code and TODO.md |
+| Problems | Count | Linter errors and warnings |
 
-### Bottom Tab Bar (`context-tabs`)
+Tab badges update reactively as counts change.
 
-```
-┌──────────────────┐
-│ [⚠ 3][✓12][Jira]│
-└──────────────────┘
-```
+### Jira Tab
 
-Tabs show inline counts that update reactively.
+Displays Jira issues via CLI integration. Manual refresh button.
 
-| Tab | Icon | Content |
-|-----|------|---------|
-| Problems | ⚠ | Linter errors, warnings (count badge) |
-| TODOs | ✓ | TODO/FIXME comments from codebase (count badge) |
-| Jira | Jira | Output from your CLI tool (default) |
+### TODOs Tab
 
-### Jira View
+Two sub-tabs:
 
-Renders markdown output from your CLI tool. Refreshes on:
-- Panel focus
-- Manual refresh keybind
-- Configurable interval
+**Project tab:** Items from `TODO.md` (checkbox format)
+**Comments tab:** TODO/FIXME/HACK/XXX comments in code
 
-### Problems View
+Click any item to jump to source location.
 
-Aggregates from linters (eslint, ruff, etc.). Shows:
+### Problems Tab
+
+Linter output showing:
 - File path
 - Line number
-- Severity icon
+- Severity (error/warning)
 - Message
 
-Click → opens file in Editor at that line.
-
-### TODOs View
-
-Grep results for `TODO`, `FIXME`, `HACK`, `XXX`. Shows:
-- File path
-- Line number  
-- Comment text
-
-Click → opens file in Editor at that line.
+Click to navigate to source.
 
 ---
 
 ## Responsiveness
 
-### CSS Breakpoints
+### CSS Strategy
 
 ```css
-/* Widescreen (default) */
+/* Default layout */
 #panel-sidebar { width: 20%; min-width: 25; }
 #panel-context { width: 25%; min-width: 30; }
 #panel-claude { width: 1fr; }
-
-/* Medium terminals */
-@media (width < 120) {
-    #panel-sidebar { width: 18%; }
-    #panel-context { width: 22%; }
-}
-
-/* Narrow terminals (laptop, split screen) */
-@media (width < 100) {
-    #panel-sidebar { display: none; }
-    #panel-context { width: 25%; }
-}
-
-@media (width < 80) {
-    #panel-context { display: none; }
-    #panel-claude { width: 100%; }
-}
 ```
 
 ### Compact Mode
 
-Toggle with `Ctrl+Shift+C`. Hides both sidebars, maximizes Claude + workspace.
+Toggle with `Alt+C`. Hides both sidebars:
 
 ```css
 .compact #panel-sidebar { display: none; }
 .compact #panel-context { display: none; }
 ```
 
-### Fullscreen Mode
-
-Any panel can go fullscreen with `F11` (when focused). Press `Escape` to exit.
-
-```css
-.fullscreen {
-    dock: top;
-    width: 100%;
-    height: 100%;
-    layer: fullscreen;
-}
-```
+All panel state preserved when hidden.
 
 ---
 
 ## Keybindings
 
-Following VSCode conventions where possible.
+All shortcuts use `Alt` modifier to avoid conflicts with Claude Code input.
 
-### Global
+### Panel Navigation
 
 | Action | Binding |
 |--------|---------|
-| Command palette | `Ctrl+Shift+P` |
-| Quick open file | `Ctrl+P` |
-| Toggle left sidebar | `Ctrl+B` |
-| Toggle right sidebar | `Ctrl+Shift+B` |
-| Toggle terminal | `` Ctrl+` `` |
-| Toggle compact mode | `Ctrl+Shift+C` |
-| Fullscreen focused panel | `F11` |
-| Exit fullscreen | `Escape` |
+| Toggle left sidebar | `Alt+B` |
+| Toggle right sidebar | `Alt+Shift+B` |
+| Toggle terminal | `` Alt+` `` |
+| Focus Claude | `Alt+1` |
+| Focus Editor | `Alt+2` |
+| Focus Terminal | `Alt+3` |
+| Toggle compact mode | `Alt+C` |
 
-### Navigation
+### Application
 
 | Action | Binding |
 |--------|---------|
-| Focus Claude panel | `Ctrl+1` |
-| Focus Editor | `Ctrl+2` |
-| Focus Terminal | `Ctrl+3` |
-| Focus sidebar | `Ctrl+0` |
-| Next tab (in tabbed panels) | `Ctrl+Tab` |
-| Previous tab | `Ctrl+Shift+Tab` |
-| Close current tab/editor | `Ctrl+W` |
+| Command palette | `Alt+P` |
+| Quick open file | `Alt+O` |
+| Select theme | `Alt+T` |
+| Quit | `Alt+Q` |
 
 ### Git
 
 | Action | Binding |
 |--------|---------|
-| Open Git panel | `Ctrl+Shift+G` |
-| Stage file | `Ctrl+Enter` (in git view) |
-| Unstage file | `Ctrl+Backspace` (in git view) |
-
-### Search & Problems
-
-| Action | Binding |
-|--------|---------|
-| Find in file | `Ctrl+F` |
-| Find in project | `Ctrl+Shift+F` |
-| Go to problems | `Ctrl+Shift+M` |
-| Next problem | `F8` |
-| Previous problem | `Shift+F8` |
+| Open Git panel | `Alt+G` |
 
 ### Editor
 
 | Action | Binding |
 |--------|---------|
-| Save | `Ctrl+S` |
-| Undo | `Ctrl+Z` |
-| Redo | `Ctrl+Shift+Z` |
-| Go to line | `Ctrl+G` |
+| Save | `Alt+S` |
+| Go to line | `Alt+L` |
+| Go to problems | `Alt+M` |
 
 ---
 
 ## Panel Communication
 
-Panels should feel connected, like a normal IDE.
-
-### File Navigation
+### File Navigation Flow
 
 ```
 Sidebar file click
@@ -372,7 +295,7 @@ Editor tab focused
 File loaded in Editor
 ```
 
-### Problems/TODOs Navigation
+### Problem/TODO Navigation Flow
 
 ```
 Click problem/todo item
@@ -387,117 +310,57 @@ Editor tab focused
 File opened at specific line
        │
        ▼
-Line highlighted/scrolled into view
+Line scrolled into view
 ```
 
-### Claude Diff Flow
+### Git Action Flow
 
 ```
-Claude proposes file changes
+Click git action button (Commit, Stash, etc.)
        │
        ▼
-Workspace appears
+Ensure skill installed (async, with notification)
        │
        ▼
-Diff tab focused
+Send /command to Claude
        │
        ▼
-Changes displayed with Accept/Reject
-       │
-       ├─► Accept: Apply changes, optionally close diff
-       │
-       └─► Reject: Discard, close diff
-```
-
-### Git File Actions
-
-```
-Click file in Git tab
-       │
-       ▼
-Workspace appears
-       │
-       ▼
-Diff tab shows unstaged changes
-       │
-       ▼
-Stage/unstage from diff view
+Claude executes git workflow
 ```
 
 ---
 
-## Implementation Notes
+## State Management
 
-### Recommended Textual Widgets
-
-| Component | Widget |
-|-----------|--------|
-| File browser | `DirectoryTree` |
-| Claude output | `Markdown` or `RichLog` (for streaming) |
-| Editor | `TextArea` (syntax highlighting built-in) |
-| Tabbed panels | `TabbedContent`, `TabPane` |
-| Panel switching | `ContentSwitcher` |
-| Problems/TODOs list | `ListView` with `ListItem` |
-| Git graph | `RichLog` or custom canvas widget |
-| Command palette | `CommandPalette` (built-in) |
-
-### Background Tasks
-
-Use Textual's `@work` decorator for:
-- Git status refresh
-- Linter execution  
-- TODO scanning
-- Jira CLI calls
+### Reactive Properties
 
 ```python
-@work(thread=True)
-def refresh_git_status(self) -> None:
-    result = subprocess.run(["git", "status", "--porcelain"], ...)
-    self.call_from_thread(self.update_git_view, result.stdout)
-```
-
-### State Management
-
-**Core principle**: Hiding is not closing. All panels persist state when hidden.
-
-```python
-class IDEApp(App):
-    current_file: reactive[str | None] = reactive(None)
+class ClideApp(App):
     workspace_visible: reactive[bool] = reactive(False)
     problem_count: reactive[int] = reactive(0)
     todo_count: reactive[int] = reactive(0)
+    current_branch: reactive[str] = reactive("main")
     compact_mode: reactive[bool] = reactive(False)
 ```
 
-**Panel visibility pattern** — toggle `display`, don't destroy:
-
-```python
-def toggle_workspace(self, visible: bool) -> None:
-    workspace = self.query_one("#panel-workspace")
-    workspace.display = visible  # Retains all child state
-    
-    # Adjust Claude panel height
-    claude = self.query_one("#panel-claude")
-    claude.styles.height = "40%" if visible else "100%"
-```
-
-**State to preserve per panel:**
+### State Preservation
 
 | Panel | Preserved State |
 |-------|-----------------|
-| Editor | Open files, cursor positions, scroll, unsaved changes, undo history |
-| Diff | Current diff content, scroll position, accept/reject state |
-| Terminal | PTY session, command history, output buffer, working directory |
-| Sidebar tabs | Scroll position, expanded/collapsed sections, selection |
-| Context tabs | Scroll position, selected item |
-| Git views | Expanded sections, selected files |
+| Editor | Open file, cursor, scroll, unsaved changes |
+| Diff | Current diff, scroll position |
+| Terminal | Session, history, output buffer |
+| Sidebar tabs | Scroll, expanded sections, selection |
+| Context tabs | Scroll, selected item |
 
 ---
 
-## Future Considerations
+## Themes
 
-- **Session persistence**: Remember open files, panel sizes, last git state
-- **Multiple projects**: Workspace switcher
-- **Claude history**: Browse past conversations
-- **Custom themes**: User-selectable color schemes
-- **Plugin system**: User-defined panels/integrations
\ No newline at end of file
+22 built-in themes with custom theme support.
+
+**Default:** summer-night (dark theme)
+
+Theme selection persists in user settings (`~/.clide/settings.json`).
+
+Custom themes can be added to `~/.clide/themes/` as TOML files.
diff --git a/docs/user-manual.md b/docs/user-manual.md
new file mode 100644
index 00000000..d3fb35fd
--- /dev/null
+++ b/docs/user-manual.md
@@ -0,0 +1,398 @@
+# Clide User Manual
+
+Clide is a terminal-based IDE that puts Claude Code at the center of your development workflow. This manual covers installation, daily usage, and customization.
+
+## Installation
+
+### Requirements
+
+- Python 3.12 or later
+- Git
+- Claude Code CLI installed and authenticated
+
+### Setup
+
+```bash
+# Clone the repository
+git clone <repo-url>
+cd clide
+
+# Install dependencies and create virtual environment
+make setup
+
+# Run Clide
+make run
+```
+
+Or install directly:
+
+```bash
+pip install -e .
+clide
+```
+
+### First Run
+
+On first launch, Clide creates a configuration directory at `~/.clide/` for user settings. Project-specific settings are stored in `.clide/` within your project.
+
+## Interface Overview
+
+```
+┌─────────────────┬─────────────────────────┬──────────────────┐
+│ Sidebar         │ Workspace               │ Context          │
+│                 │ [Editor][Diff][Terminal]│                  │
+│ [Files][Git]    │ (appears when needed)   │ [Jira][TODOs]    │
+│ [Tree]          ├─────────────────────────┤ [Problems]       │
+│                 │                         │                  │
+│                 │ Claude                  │                  │
+│                 │ (always visible)        │                  │
+│                 │                         │                  │
+├─────────────────┤                         ├──────────────────┤
+│ ⎇ main ▾       │                         │                  │
+│ staged: 2      │                         │                  │
+└─────────────────┴─────────────────────────┴──────────────────┘
+```
+
+### Panels
+
+**Left Sidebar** — File browser, git changes, and branch graph
+
+**Center** — Claude Code (always visible) and workspace panels (editor, diff, terminal) that appear when needed
+
+**Right Context** — Jira integration, TODO list, and problems from linters
+
+## Keyboard Shortcuts
+
+All shortcuts use `Alt` as the modifier to avoid conflicts with Claude Code input.
+
+### Panel Navigation
+
+| Action | Shortcut |
+|--------|----------|
+| Toggle left sidebar | `Alt+B` |
+| Toggle right sidebar | `Alt+Shift+B` |
+| Toggle terminal | `` Alt+` `` |
+| Focus Claude | `Alt+1` |
+| Focus Editor | `Alt+2` |
+| Focus Terminal | `Alt+3` |
+| Toggle compact mode | `Alt+C` |
+
+### File Operations
+
+| Action | Shortcut |
+|--------|----------|
+| Quick open file | `Alt+O` |
+| Save file | `Alt+S` |
+| Go to line | `Alt+L` |
+
+### Git Operations
+
+| Action | Shortcut |
+|--------|----------|
+| Open Git panel | `Alt+G` |
+| Open Problems panel | `Alt+M` |
+
+### Application
+
+| Action | Shortcut |
+|--------|----------|
+| Command palette | `Alt+P` |
+| Select theme | `Alt+T` |
+| Quit | `Alt+Q` |
+
+## Working with Claude
+
+Claude Code runs in the center panel and is always visible. Type your prompts directly and Claude will respond with code suggestions, explanations, and file operations.
+
+### Git Integration
+
+The sidebar includes buttons for common git operations that delegate to Claude:
+
+- **Commit** — Claude reviews staged changes and creates a well-formatted commit
+- **Stash** — Claude stashes your working changes
+- **Pull** — Claude pulls with rebase and helps resolve conflicts
+- **Push** — Claude pushes to remote, setting upstream if needed
+
+On first use, Clide installs the corresponding skill to your project's `.claude/skills/` directory. These skills guide Claude through each operation following best practices.
+
+### Branch Status
+
+The branch status bar at the bottom of the sidebar shows:
+
+- Current branch name
+- Staged and unstaged file counts
+
+Click the branch name to open the branch selector:
+
+```
+┌─────────────────┐
+│ Recent branches │
+│ ● main         │
+│ ○ feature/xyz  │
+│ ○ develop      │
+├─────────────────┤
+│[Checkout] [New] │
+└─────────────────┘
+```
+
+## Left Sidebar
+
+### Files Tab
+
+Browse your project structure. Click a file to open it in the editor.
+
+- Directories expand/collapse on click
+- Hidden files (starting with `.`) are shown but dimmed
+- Noisy directories (`.git`, `__pycache__`, `node_modules`) are filtered
+
+### Git Tab
+
+View staged and unstaged changes:
+
+```
+Staged (2)
+  + src/new_file.py
+  ~ src/modified.py
+
+Unstaged (3)
+  ~ README.md
+  ? untracked.txt
+  - deleted.py
+```
+
+**Status indicators:**
+- `+` Added
+- `~` Modified
+- `-` Deleted
+- `?` Untracked
+- `→` Renamed
+
+Click a file to view its diff. Use the action buttons to commit, stash, pull, or push via Claude.
+
+### Tree Tab
+
+Visual git graph showing branch history:
+
+```
+● main: Latest commit message
+│
+├─● feature: Feature work
+│
+●─┴ Merge branch 'feature'
+```
+
+**Commit types:**
+- `●` Regular commit
+- `◆` Merge commit
+
+## Right Context Panel
+
+### Jira Tab
+
+Displays Jira issues when configured. Click the refresh button to update.
+
+Configure Jira integration in settings:
+
+```json
+{
+  "jira_enabled": true,
+  "jira_cli_path": "jira"
+}
+```
+
+### TODOs Tab
+
+Scans your codebase for TODO comments and project tasks.
+
+**Sub-tabs:**
+
+- **Project** — Items from `TODO.md` (checkbox format)
+- **Comments** — TODO/FIXME/HACK/XXX comments in code
+
+Click an item to jump to that location in the editor.
+
+**Supported comment markers:**
+- `TODO` — Tasks to complete
+- `FIXME` — Bugs to fix
+- `HACK` — Temporary solutions
+- `XXX` — Dangerous or problematic code
+- `NOTE` — Important notes
+- `BUG` — Known bugs
+
+### Problems Tab
+
+Displays linter errors and warnings. Click a problem to jump to the source location.
+
+## Workspace Panels
+
+The workspace appears when you need to view or edit files. It contains three tabs:
+
+### Editor
+
+Full-featured code editor with:
+
+- Syntax highlighting (Python, JavaScript, TypeScript, HTML, CSS, JSON, YAML, Markdown, and more)
+- Line numbers
+- Current line highlighting
+
+### Diff
+
+Side-by-side diff viewer for reviewing changes. Used when:
+
+- Viewing git changes
+- Reviewing Claude's proposed edits
+
+### Terminal
+
+Command-line terminal for running commands. Output is preserved when the panel is hidden.
+
+## Themes
+
+Clide includes 22 built-in themes. Press `Alt+T` to open the theme selector.
+
+**Theme categories:**
+
+| Category | Themes |
+|----------|--------|
+| Core | summer-night (default), summer-day |
+| Popular | one-dark, one-dark-pro, one-light, dracula, nord, gruvbox-dark, gruvbox-light |
+| Seasonal | winter-is-coming, monokai-winter, fall, dark-autumn |
+| Halloween | all-hallows-eve, halloween |
+| Christmas | christmas, santa-baby |
+| Hacker | pro-hacker, hacker-style |
+| Other | gamma, one-dark-teal, houston |
+
+Your theme choice is saved and persists across sessions.
+
+### Custom Themes
+
+Create custom themes in `~/.clide/themes/`:
+
+```toml
+# ~/.clide/themes/my-theme.toml
+name = "my-theme"
+display_name = "My Custom Theme"
+dark = true
+
+[colors]
+primary = "#007acc"
+secondary = "#3c3c3c"
+accent = "#0e639c"
+background = "#1e1e1e"
+surface = "#252526"
+panel = "#2d2d30"
+foreground = "#d4d4d4"
+success = "#4ec9b0"
+warning = "#dcdcaa"
+error = "#f44747"
+```
+
+## Configuration
+
+### User Settings
+
+Settings are stored in `~/.clide/settings.json`:
+
+```json
+{
+  "theme": "summer-night",
+  "compact_mode": false,
+  "jira_enabled": false,
+  "jira_cli_path": "jira"
+}
+```
+
+### Project Settings
+
+Project-specific settings in `.clide/`:
+
+```
+.clide/
+├── settings.json     # Project overrides
+└── skills/           # Installed Claude skills
+    ├── commit/
+    ├── stash/
+    └── ...
+```
+
+### Environment Variables
+
+Override settings with environment variables prefixed with `CLIDE_`:
+
+```bash
+CLIDE_THEME=dracula clide
+```
+
+## Compact Mode
+
+Press `Alt+C` to toggle compact mode, which hides both sidebars for focused work. All panel state is preserved—nothing is lost when hiding panels.
+
+## Project TODOs
+
+Clide integrates with a `TODO.md` file in your project root. Format:
+
+```markdown
+# TODO
+
+## Features
+
+- [ ] Implement user authentication
+- [ ] Add search functionality
+- [x] Set up database connection
+
+## Bugs
+
+- [ ] Fix login redirect
+```
+
+Items appear in the TODOs panel, grouped by section. Click to jump to that line. Check off items directly in the file.
+
+If no `TODO.md` exists, click "Create TODO.md" in the TODOs panel to generate a template.
+
+## Tips
+
+### Efficient Navigation
+
+1. Use `Alt+1/2/3` to quickly switch between Claude, Editor, and Terminal
+2. Click items in Problems or TODOs to jump directly to source
+3. Use compact mode (`Alt+C`) when you need more space for Claude
+
+### Git Workflow
+
+1. Make changes to your code
+2. Review changes in the Git tab
+3. Click "Commit" to have Claude create a well-formatted commit
+4. Use "Push" when ready to share
+
+### Working with Claude
+
+- Claude sees your project context automatically
+- Use the git action buttons for consistent commit messages
+- Click files in the sidebar to show Claude what you're working on
+
+## Troubleshooting
+
+### Claude Code not starting
+
+Ensure Claude Code CLI is installed and authenticated:
+
+```bash
+claude --version
+claude auth status
+```
+
+### Theme not applying
+
+Check that the theme name in settings matches exactly. Theme names are case-sensitive.
+
+### Skills not working
+
+Skills are installed to `.claude/skills/` in your project. If a skill fails:
+
+1. Check that the skill folder exists
+2. Verify `SKILL.md` is present
+3. Try removing and re-triggering the action
+
+### Panels not updating
+
+Try refreshing with the relevant shortcut or clicking the refresh button. File changes should update automatically via file watching.
diff --git a/pyproject.toml b/pyproject.toml
index 7f63c392..13539e98 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -80,6 +80,7 @@ asyncio_default_fixture_loop_scope = "function"
 addopts = [
     "-v",
     "--tb=short",
+    "--snapshot-report=logs/snapshot_report.html",
 ]
 
 [tool.mypy]
@@ -93,6 +94,7 @@ exclude = ["tests", "dist", "build"]
 target-version = "py312"
 line-length = 100
 src = ["clide", "tests"]
+exclude = ["clide/vendor"]
 
 [tool.ruff.lint]
 select = [
@@ -116,6 +118,8 @@ ignore = [
     "SIM105", # contextlib.suppress (try-except-pass is clearer in context)
     "SIM115", # context handler for files (sometimes not applicable)
     "PTH123", # Path.open() vs open() (not always cleaner)
+    "TCH002", # move third-party imports to TYPE_CHECKING (clutters code)
+    "TCH003", # move stdlib imports to TYPE_CHECKING (clutters code)
 ]
 
 [tool.ruff.lint.isort]
diff --git a/tests/snapshots/__snapshots__/test_app_snapshots/test_initial_layout.svg b/tests/snapshots/__snapshots__/test_app_snapshots/test_initial_layout.svg
index fb3f0e79..6af352f6 100644
--- a/tests/snapshots/__snapshots__/test_app_snapshots/test_initial_layout.svg
+++ b/tests/snapshots/__snapshots__/test_app_snapshots/test_initial_layout.svg
@@ -180,10 +180,10 @@
             </g>
 
     <g transform="translate(9, 41)" clip-path="url(#terminal-clip-terminal)">
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