Add TODO.md integration to TODOs panel

- Parse TODO.md markdown checkboxes and display in collapsible section
- Add ProjectTodoItem model for TODO.md items with section/subsection support
- Swap context panel tab order to: Jira, TODOs, Problems
- Add "Create TODO.md" button when file doesn't exist with template
- Click project TODO items to navigate to TODO.md at that line
- Add header to TODO.md explaining Clide integration format
- Add pre-commit config with ruff linting and formatting
- Update ruff ignore rules for Textual patterns

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+# Pre-commit configuration for Clide
+# See https://pre-commit.com for more information
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.0
+    hooks:
+      # Run the linter
+      - id: ruff
+        args: [--fix]
+      # Run the formatter
+      - id: ruff-format

TODO.md

@@ -1,5 +1,18 @@
 # TODO
 
+<!--
+  Clide Integration: This file is parsed by Clide's TODO panel.
+
+  Format:
+  - Use ## for sections and ### for subsections
+  - Use markdown checkboxes: - [ ] for open items, - [x] for completed
+  - Items appear in the TODOs panel grouped by section
+  - Click an item in Clide to jump to this file at that line
+
+  For AI agents: Add new items under the appropriate section using the
+  checkbox format. Mark items as done with [x] when completed.
+-->
+
 Long-term open items for Clide development.
 
 ## Core Features

clide/app.py

@@ -19,13 +19,13 @@ from clide.extensions.manager import ExtensionManager
 from clide.models.config import ClideSettings
 from clide.services.claude_events import (
     ClaudeEvent,
-    FileReadEvent,
     FileEditEvent,
+    FileReadEvent,
     FileWriteEvent,
     setup_event_parsing,
 )
 from clide.services.file_watcher import FileEvent, FileEventMessage, setup_file_watching
-from clide.services.settings_service import SettingsService, get_settings_service
+from clide.services.settings_service import get_settings_service
 from clide.services.syntax_service import register_languages
 from clide.themes.registry import get_all_themes, get_theme
 from clide.widgets.panels.claude import ClaudePanel
@@ -242,6 +242,7 @@ class ClideApp(App[None]):
             # Right context panel
             yield ContextPanel(
                 jira_enabled=self.settings.jira_enabled,
+                project_path=self.workdir,
             )
 
         yield Footer()
@@ -293,6 +294,7 @@ class ClideApp(App[None]):
         thread-safe, but we create the Message on the main thread to avoid any
         potential Textual threading issues.
         """
+
         def post_file_event():
             self.post_message(FileEventMessage(event))
 
@@ -353,9 +355,7 @@ class ClideApp(App[None]):
                 pass
 
             # Trigger extension hook
-            self.extension_manager.trigger_claude_event(
-                "file_read", {"path": str(event.path)}
-            )
+            self.extension_manager.trigger_claude_event("file_read", {"path": str(event.path)})
 
         elif isinstance(event, FileEditEvent):
             # Claude edited a file - notify user
@@ -363,9 +363,7 @@ class ClideApp(App[None]):
             self.notify(f"Claude edited: {event.path.name}", severity="information")
 
             # Trigger extension hook
-            self.extension_manager.trigger_claude_event(
-                "file_edit", {"path": str(event.path)}
-            )
+            self.extension_manager.trigger_claude_event("file_edit", {"path": str(event.path)})
 
         elif isinstance(event, FileWriteEvent):
             # Claude created/wrote a file - notify user
@@ -374,9 +372,7 @@ class ClideApp(App[None]):
             self.notify(f"Claude wrote: {event.path.name}", severity="information")
 
             # Trigger extension hook
-            self.extension_manager.trigger_claude_event(
-                "file_write", {"path": str(event.path)}
-            )
+            self.extension_manager.trigger_claude_event("file_write", {"path": str(event.path)})
 
     def _apply_user_settings(self) -> None:
         """Apply saved user settings on startup."""
@@ -438,9 +434,9 @@ class ClideApp(App[None]):
 
     async def _refresh_todos(self) -> None:
         """Refresh TODOs."""
-        todos = await self.todos_controller.scan()
+        code_todos, project_todos = await self.todos_controller.scan()
         context = self.query_one(ContextPanel)
-        context.update_todos(todos)
+        context.update_todos(code_todos, project_todos)
 
     async def _refresh_jira(self) -> None:
         """Refresh Jira content."""
@@ -643,6 +639,31 @@ class ClideApp(App[None]):
         workspace = self.query_one(WorkspacePanel)
         workspace.open_file(item.file_path, line=item.line)
 
+    async def on_context_panel_project_todo_clicked(
+        self,
+        event: ContextPanel.ProjectTodoClicked,
+    ) -> None:
+        """Handle project TODO click - open TODO.md at line."""
+        item = event.item
+        todo_path = self.workdir / "TODO.md"
+        if todo_path.exists():
+            self.workspace_visible = True
+            workspace = self.query_one(WorkspacePanel)
+            workspace.open_file(todo_path, line=item.line)
+
+    async def on_context_panel_todo_md_created(
+        self,
+        event: ContextPanel.TodoMdCreated,
+    ) -> None:
+        """Handle TODO.md creation - refresh TODOs and open file."""
+        # Refresh TODOs to pick up the new file
+        await self._refresh_todos()
+        # Open the new file in editor
+        self.workspace_visible = True
+        workspace = self.query_one(WorkspacePanel)
+        workspace.open_file(event.path)
+        self.notify("Created TODO.md")
+
     async def on_context_panel_jira_refresh_requested(
         self,
         _event: ContextPanel.JiraRefreshRequested,
@@ -749,3 +770,22 @@ class ClideApp(App[None]):
     ) -> None:
         """Handle workspace close request."""
         self.workspace_visible = False
+
+    def on_sidebar_panel_claude_command_requested(
+        self,
+        event: SidebarPanel.ClaudeCommandRequested,
+    ) -> None:
+        """Handle Claude command request from git panel.
+
+        Sends skill commands (e.g., /commit) to Claude terminal.
+        Ensures the git-workflow skill is installed before sending.
+        """
+        # Ensure skill is available
+        self.git_controller._ensure_git_skill()
+
+        # Send command to Claude terminal
+        claude = self.query_one(ClaudePanel)
+        claude.send_input(event.command)
+
+        # Focus Claude panel so user can see the response
+        self.action_focus_claude()

clide/controllers/todos.py

@@ -5,7 +5,13 @@ from pathlib import Path
 from textual.message import Message
 
 from clide.controllers.base import controller
-from clide.models.todos import TodoItem, TodosState, TodosSummary, TodoType
+from clide.models.todos import (
+    ProjectTodoItem,
+    TodoItem,
+    TodosState,
+    TodosSummary,
+    TodoType,
+)
 from clide.services.todo_scanner import TodoScanner
 
 
@@ -16,8 +22,14 @@ class TodosController:
     class TodosUpdated(Message):
         """Emitted when TODOs list is updated."""
 
-        def __init__(self, items: list[TodoItem], summary: TodosSummary) -> None:
+        def __init__(
+            self,
+            items: list[TodoItem],
+            project_items: list[ProjectTodoItem],
+            summary: TodosSummary,
+        ) -> None:
             self.items = items
+            self.project_items = project_items
             self.summary = summary
             super().__init__()
 
@@ -39,9 +51,14 @@ class TodosController:
 
     @property
     def items(self) -> list[TodoItem]:
-        """Get list of TODO items."""
+        """Get list of code TODO items."""
         return self._state.items
 
+    @property
+    def project_items(self) -> list[ProjectTodoItem]:
+        """Get list of project TODO items from TODO.md."""
+        return self._state.project_items
+
     @property
     def summary(self) -> TodosSummary:
         """Get TODOs summary."""
@@ -49,21 +66,29 @@ class TodosController:
 
     @property
     def total_count(self) -> int:
-        """Get total TODO count."""
+        """Get total code TODO count."""
         return self._state.summary.total
 
-    async def refresh(self) -> tuple[list[TodoItem], TodosSummary]:
+    @property
+    def project_count(self) -> int:
+        """Get total project TODO count."""
+        return self._state.summary.project_total
+
+    async def refresh(
+        self,
+    ) -> tuple[list[TodoItem], list[ProjectTodoItem], TodosSummary]:
         """Refresh TODOs from project.
 
         Returns:
-            Tuple of (items, summary)
+            Tuple of (code items, project items, summary)
         """
-        items, summary = await self._scanner.scan()
+        items, project_items, summary = await self._scanner.scan()
 
         self._state.items = items
+        self._state.project_items = project_items
         self._state.summary = summary
 
-        return items, summary
+        return items, project_items, summary
 
     def filter_by_type(self, todo_type: TodoType | None) -> list[TodoItem]:
         """Filter TODOs by type.
@@ -128,11 +153,11 @@ class TodosController:
             grouped[item.file_path].append(item)
         return grouped
 
-    async def scan(self) -> list[TodoItem]:
+    async def scan(self) -> tuple[list[TodoItem], list[ProjectTodoItem]]:
         """Scan for TODOs and return items.
 
         Returns:
-            List of TODO items
+            Tuple of (code items, project items)
         """
-        items, _ = await self.refresh()
-        return items
+        items, project_items, _ = await self.refresh()
+        return items, project_items

clide/models/todos.py

@@ -19,6 +19,30 @@ class TodoType(str, Enum):
     REVIEW = "REVIEW"
 
 
+class ProjectTodoItem(BaseModel):
+    """A TODO item from TODO.md file."""
+
+    model_config = ConfigDict(strict=True, frozen=True)
+
+    text: str
+    section: str  # Top-level section (## heading)
+    subsection: str | None = None  # Optional subsection (### heading)
+    line: int  # Line number in TODO.md
+    checked: bool = False  # Whether the checkbox is checked
+
+    @property
+    def category(self) -> str:
+        """Get full category path."""
+        if self.subsection:
+            return f"{self.section} › {self.subsection}"
+        return self.section
+
+    @property
+    def icon(self) -> str:
+        """Icon for display."""
+        return "☑" if self.checked else "☐"
+
+
 class TodoItem(BaseModel):
     """A single TODO comment found in code."""
 
@@ -61,12 +85,19 @@ class TodosSummary(BaseModel):
     fixme_count: int = 0
     hack_count: int = 0
     other_count: int = 0
+    project_todo_count: int = 0  # Count from TODO.md
+    project_done_count: int = 0  # Checked items in TODO.md
 
     @property
     def total(self) -> int:
-        """Total number of TODOs."""
+        """Total number of code TODOs."""
         return self.todo_count + self.fixme_count + self.hack_count + self.other_count
 
+    @property
+    def project_total(self) -> int:
+        """Total number of project TODOs."""
+        return self.project_todo_count + self.project_done_count
+
     @property
     def display_text(self) -> str:
         """Text for tab badge."""
@@ -79,10 +110,12 @@ class TodosState(BaseModel):
     model_config = ConfigDict(strict=True)
 
     items: list[TodoItem] = []
+    project_items: list[ProjectTodoItem] = []  # Items from TODO.md
     summary: TodosSummary = TodosSummary()
     filter_type: TodoType | None = None
     selected_index: int | None = None
     group_by_file: bool = True
+    show_completed_project_todos: bool = False  # Toggle for checked items
 
     def items_for_file(self, path: Path) -> list[TodoItem]:
         """Get TODO items for a specific file."""
@@ -91,3 +124,15 @@ class TodosState(BaseModel):
     def items_by_type(self, todo_type: TodoType) -> list[TodoItem]:
         """Get TODO items of a specific type."""
         return [item for item in self.items if item.todo_type == todo_type]
+
+    def project_items_by_section(self, section: str) -> list[ProjectTodoItem]:
+        """Get project TODO items for a specific section."""
+        return [item for item in self.project_items if item.section == section]
+
+    def get_project_sections(self) -> list[str]:
+        """Get unique sections from project TODOs."""
+        sections: list[str] = []
+        for item in self.project_items:
+            if item.section not in sections:
+                sections.append(item.section)
+        return sections

clide/services/todo_scanner.py

@@ -3,7 +3,7 @@
 import re
 from pathlib import Path
 
-from clide.models.todos import TodoItem, TodosSummary, TodoType
+from clide.models.todos import ProjectTodoItem, TodoItem, TodosSummary, TodoType
 from clide.services.process_service import ProcessService
 
 
@@ -16,33 +16,66 @@ class TodoScanner:
         re.IGNORECASE,
     )
 
+    # Pattern to match markdown checkboxes: - [ ] or - [x]
+    CHECKBOX_PATTERN = re.compile(r"^(\s*)-\s*\[([ xX])\]\s*(.+)$")
+
     # File extensions to scan
     SCAN_EXTENSIONS = {
-        ".py", ".js", ".ts", ".jsx", ".tsx", ".java", ".c", ".cpp", ".h",
-        ".go", ".rs", ".rb", ".php", ".css", ".scss", ".html", ".vue",
-        ".svelte", ".md", ".sh", ".bash", ".yaml", ".yml", ".toml",
+        ".py",
+        ".js",
+        ".ts",
+        ".jsx",
+        ".tsx",
+        ".java",
+        ".c",
+        ".cpp",
+        ".h",
+        ".go",
+        ".rs",
+        ".rb",
+        ".php",
+        ".css",
+        ".scss",
+        ".html",
+        ".vue",
+        ".svelte",
+        ".md",
+        ".sh",
+        ".bash",
+        ".yaml",
+        ".yml",
+        ".toml",
     }
 
     def __init__(self, project_path: Path) -> None:
         self.project_path = project_path
         self._process = ProcessService(cwd=project_path)
 
-    async def scan(self) -> tuple[list[TodoItem], TodosSummary]:
-        """Scan project for TODO comments.
+    async def scan(
+        self,
+    ) -> tuple[list[TodoItem], list[ProjectTodoItem], TodosSummary]:
+        """Scan project for TODO comments and TODO.md items.
 
         Returns:
-            Tuple of (todo items, summary)
+            Tuple of (code todo items, project todo items, summary)
         """
         items: list[TodoItem] = []
 
         # Use ripgrep if available for speed
         result = await self._process.run(
-            "rg", "--line-number", "--no-heading",
-            "-e", r"\b(TODO|FIXME|HACK|XXX|NOTE|BUG|OPTIMIZE|REVIEW)\b",
-            "--type-add", "code:*.py",
-            "--type-add", "code:*.js",
-            "--type-add", "code:*.ts",
-            "--type", "code",
+            "rg",
+            "--line-number",
+            "--no-heading",
+            "-e",
+            r"\b(TODO|FIXME|HACK|XXX|NOTE|BUG|OPTIMIZE|REVIEW)\b",
+            "--type-add",
+            "code:*.py",
+            "--type-add",
+            "code:*.js",
+            "--type-add",
+            "code:*.ts",
+            "--type",
+            "code",
             ".",
         )
 
@@ -52,20 +85,76 @@ class TodoScanner:
             # Fallback to Python-based scanning
             items = await self._scan_with_python()
 
+        # Parse TODO.md if it exists
+        project_items = self._parse_todo_md()
+
         # Create summary
         todo_count = sum(1 for i in items if i.todo_type == TodoType.TODO)
         fixme_count = sum(1 for i in items if i.todo_type == TodoType.FIXME)
         hack_count = sum(1 for i in items if i.todo_type == TodoType.HACK)
         other_count = len(items) - todo_count - fixme_count - hack_count
+        project_todo_count = sum(1 for i in project_items if not i.checked)
+        project_done_count = sum(1 for i in project_items if i.checked)
 
         summary = TodosSummary(
             todo_count=todo_count,
             fixme_count=fixme_count,
             hack_count=hack_count,
             other_count=other_count,
+            project_todo_count=project_todo_count,
+            project_done_count=project_done_count,
         )
 
-        return items, summary
+        return items, project_items, summary
+
+    def _parse_todo_md(self) -> list[ProjectTodoItem]:
+        """Parse TODO.md file for checkbox items.
+
+        Returns:
+            List of project TODO items
+        """
+        todo_md_path = self.project_path / "TODO.md"
+        if not todo_md_path.exists():
+            return []
+
+        items: list[ProjectTodoItem] = []
+        current_section = "General"
+        current_subsection: str | None = None
+
+        try:
+            content = todo_md_path.read_text(encoding="utf-8")
+            for line_num, line in enumerate(content.split("\n"), 1):
+                # Check for section headers (## Section)
+                if line.startswith("## "):
+                    current_section = line[3:].strip()
+                    current_subsection = None
+                    continue
+
+                # Check for subsection headers (### Subsection)
+                if line.startswith("### "):
+                    current_subsection = line[4:].strip()
+                    continue
+
+                # Check for checkbox items
+                match = self.CHECKBOX_PATTERN.match(line)
+                if match:
+                    checkbox_state = match.group(2)
+                    text = match.group(3).strip()
+                    checked = checkbox_state.lower() == "x"
+
+                    items.append(
+                        ProjectTodoItem(
+                            text=text,
+                            section=current_section,
+                            subsection=current_subsection,
+                            line=line_num,
+                            checked=checked,
+                        )
+                    )
+        except (OSError, UnicodeDecodeError):
+            pass
+
+        return items
 
     def _parse_ripgrep_output(self, output: str) -> list[TodoItem]:
         """Parse ripgrep output into TodoItems."""
@@ -99,14 +188,16 @@ class TodoScanner:
                 except ValueError:
                     todo_type = TodoType.TODO
 
-                items.append(TodoItem(
-                    file_path=file_path,
-                    line=line_num,
-                    column=content.find(todo_type_str) + 1,
-                    todo_type=todo_type,
-                    text=todo_text,
-                    context_line=content.strip(),
-                ))
+                items.append(
+                    TodoItem(
+                        file_path=file_path,
+                        line=line_num,
+                        column=content.find(todo_type_str) + 1,
+                        todo_type=todo_type,
+                        text=todo_text,
+                        context_line=content.strip(),
+                    )
+                )
 
         return items
 
@@ -137,14 +228,16 @@ class TodoScanner:
                             except ValueError:
                                 todo_type = TodoType.TODO
 
-                            items.append(TodoItem(
-                                file_path=file_path.relative_to(self.project_path),
-                                line=line_num,
-                                column=line.find(todo_type_str) + 1,
-                                todo_type=todo_type,
-                                text=todo_text,
-                                context_line=line.strip(),
-                            ))
+                            items.append(
+                                TodoItem(
+                                    file_path=file_path.relative_to(self.project_path),
+                                    line=line_num,
+                                    column=line.find(todo_type_str) + 1,
+                                    todo_type=todo_type,
+                                    text=todo_text,
+                                    context_line=line.strip(),
+                                )
+                            )
                 except (OSError, UnicodeDecodeError):
                     continue
 

clide/vendor/pyte/__init__.py

@@ -1,37 +1,39 @@
 """
-    pyte
-    ~~~~
+pyte
+~~~~
 
-    `pyte` implements a mix of VT100, VT220 and VT520 specification,
-    and aims to support most of the `TERM=linux` functionality.
+`pyte` implements a mix of VT100, VT220 and VT520 specification,
+and aims to support most of the `TERM=linux` functionality.
 
-    :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.
 """
 
 __all__ = (
-    "Screen", "DiffScreen", "HistoryScreen", "DebugScreen",
-    "Stream", "ByteStream",
+    "Screen",
+    "DiffScreen",
+    "HistoryScreen",
+    "DebugScreen",
+    "Stream",
+    "ByteStream",
     # Clide additions
-    "set_debug_logger", "set_event_callback",
+    "set_debug_logger",
+    "get_debug_logger",
+    "set_event_callback",
 )
 
 import io
-from typing import Union
-
-from .screens import Screen, DiffScreen, HistoryScreen, DebugScreen
-from .screens import set_debug_logger as _set_screen_logger
-from .streams import Stream, ByteStream
-from .streams import set_debug_logger as _set_stream_logger
-from .streams import set_event_callback
 
 # Re-export submodules for compatibility
-from . import modes
 from . import screens
+from .screens import DebugScreen, DiffScreen, HistoryScreen, Screen
+from .screens import set_debug_logger as _set_screen_logger
+from .streams import ByteStream, Stream, set_event_callback
+from .streams import set_debug_logger as _set_stream_logger
 
 
 def set_debug_logger(logger):
@@ -44,8 +46,18 @@ def set_debug_logger(logger):
     _set_screen_logger(logger)
 
 
+def get_debug_logger():
+    """Get the current debug logger (if set).
+
+    Returns:
+        The current debug logger callable, or None if not set.
+    """
+    return screens._debug_logger
+
+
 if __debug__:
-    def dis(chars: Union[bytes, str]) -> None:
+
+    def dis(chars: bytes | str) -> None:
         """A :func:`dis.dis` for terminals."""
         if isinstance(chars, str):
             chars = chars.encode("utf-8")

clide/widgets/components/todos_view.py

@@ -1,20 +1,54 @@
 """TODOs view component."""
 
+from pathlib import Path
 
 from textual.app import ComposeResult
 from textual.containers import Vertical
 from textual.message import Message
-from textual.widgets import ListItem, ListView, Static
+from textual.widgets import Button, Collapsible, ListItem, ListView, Static
 
-from clide.models.todos import TodoItem, TodoType
+from clide.models.todos import ProjectTodoItem, TodoItem, TodoType
+
+# Template for new TODO.md files
+TODO_MD_TEMPLATE = """# TODO
+
+<!--
+  Clide Integration: This file is parsed by Clide's TODO panel.
+
+  Format:
+  - Use ## for sections and ### for subsections
+  - Use markdown checkboxes: - [ ] for open items, - [x] for completed
+  - Items appear in the TODOs panel grouped by section
+  - Click an item in Clide to jump to this file at that line
+
+  For AI agents: Add new items under the appropriate section using the
+  checkbox format. Mark items as done with [x] when completed.
+-->
+
+Project TODO items.
+
+## Features
+
+- [ ] Add your first feature here
+- [ ] Another feature to implement
+
+## Bugs
+
+- [ ] Bug to fix
+
+## Documentation
+
+- [ ] Documentation to write
+"""
 
 
 class TodoListItem(ListItem):
-    """A single TODO item."""
+    """A single code TODO item."""
 
     def __init__(self, item: TodoItem) -> None:
         super().__init__()
         self.item = item
+        self.is_project_item = False
 
     def compose(self) -> ComposeResult:
         icon = self.item.type_icon
@@ -28,8 +62,27 @@ class TodoListItem(ListItem):
         )
 
 
+class ProjectTodoListItem(ListItem):
+    """A single project TODO item from TODO.md."""
+
+    def __init__(self, item: ProjectTodoItem) -> None:
+        super().__init__()
+        self.item = item
+        self.is_project_item = True
+
+    def compose(self) -> ComposeResult:
+        icon = self.item.icon
+        checked_style = "dim strike" if self.item.checked else ""
+        category = f"[dim]{self.item.category}[/] " if self.item.subsection else ""
+
+        yield Static(
+            f"[project]{icon}[/] {category}" f"[{checked_style}]{self.item.text}[/]",
+            markup=True,
+        )
+
+
 class TodosView(Vertical):
-    """View for TODO/FIXME comments."""
+    """View for TODO/FIXME comments and project TODOs."""
 
     DEFAULT_CSS = """
     TodosView {
@@ -42,8 +95,31 @@ class TodosView(Vertical):
         padding: 0 1;
     }
 
+    TodosView .section-header {
+        height: 1;
+        background: $panel;
+        padding: 0 1;
+        color: $text-muted;
+    }
+
     TodosView ListView {
+        height: auto;
+        max-height: 50%;
+    }
+
+    TodosView #code-todos-list {
         height: 1fr;
+        max-height: none;
+    }
+
+    TodosView Collapsible {
+        padding: 0;
+        border: none;
+    }
+
+    TodosView CollapsibleTitle {
+        background: $panel;
+        padding: 0 1;
     }
 
     TodosView .todo { color: $primary; }
@@ -52,59 +128,215 @@ class TodosView(Vertical):
     TodosView .xxx { color: $error; }
     TodosView .note { color: $secondary; }
     TodosView .bug { color: $error; }
+    TodosView .project { color: $accent; }
 
     TodosView .empty-message {
         padding: 2;
         text-align: center;
         color: $success;
     }
+
+    TodosView .create-todo-section {
+        height: auto;
+        padding: 1 2;
+        align: center middle;
+    }
+
+    TodosView .create-todo-message {
+        text-align: center;
+        color: $text-muted;
+        margin-bottom: 1;
+    }
+
+    TodosView #create-todo-btn {
+        width: auto;
+    }
     """
 
     class TodoClicked(Message):
-        """Emitted when a TODO is clicked."""
+        """Emitted when a code TODO is clicked."""
 
         def __init__(self, item: TodoItem) -> None:
             self.item = item
             super().__init__()
 
-    def __init__(self, items: list[TodoItem] | None = None, **kwargs) -> None:
+    class ProjectTodoClicked(Message):
+        """Emitted when a project TODO is clicked."""
+
+        def __init__(self, item: ProjectTodoItem) -> None:
+            self.item = item
+            super().__init__()
+
+    class CreateTodoMdRequested(Message):
+        """Emitted when user wants to create a TODO.md file."""
+
+        pass
+
+    class TodoMdCreated(Message):
+        """Emitted when TODO.md has been created."""
+
+        def __init__(self, path: Path) -> None:
+            self.path = path
+            super().__init__()
+
+    def __init__(
+        self,
+        items: list[TodoItem] | None = None,
+        project_items: list[ProjectTodoItem] | None = None,
+        project_path: Path | None = None,
+        **kwargs,
+    ) -> None:
         super().__init__(**kwargs)
         self._items = items or []
+        self._project_items = project_items or []
+        self._project_path = project_path or Path.cwd()
+        self._has_todo_md = (self._project_path / "TODO.md").exists()
 
     def compose(self) -> ComposeResult:
-        count = len(self._items)
-        yield Static(f"TODOs ({count})", classes="todos-header", id="todos-header")
+        total = len(self._items) + len(self._project_items)
+        yield Static(f"TODOs ({total})", classes="todos-header", id="todos-header")
 
-        if self._items:
-            yield ListView(
-                *[TodoListItem(item) for item in self._items],
-                id="todos-list",
+        # Create TODO.md section (shown when file doesn't exist)
+        with Vertical(classes="create-todo-section", id="create-todo-section"):
+            yield Static(
+                "No TODO.md found in project",
+                classes="create-todo-message",
             )
-        else:
-            yield Static("No TODOs found ✓", classes="empty-message")
+            yield Button("Create TODO.md", id="create-todo-btn", variant="primary")
 
-    def update_items(self, items: list[TodoItem]) -> None:
-        """Update the TODOs list."""
-        self._items = items
+        # Project TODOs section (collapsible)
+        with Collapsible(title="Project TODOs", id="project-todos-section"):
+            yield ListView(id="project-todos-list")
 
-        # Update header
-        header = self.query_one("#todos-header", Static)
-        header.update(f"TODOs ({len(items)})")
+        # Code TODOs section
+        yield Static("Code TODOs", classes="section-header", id="code-todos-header")
+        yield ListView(id="code-todos-list")
 
-        # Update list
+        yield Static("No TODOs found", classes="empty-message", id="todos-empty")
+
+    def on_mount(self) -> None:
+        """Initialize the lists with items."""
+        self._refresh_lists()
+
+    def _refresh_lists(self) -> None:
+        """Refresh both list views with current items."""
         try:
-            todos_list = self.query_one("#todos-list", ListView)
-            todos_list.clear()
-            for item in items:
-                todos_list.append(TodoListItem(item))
+            create_section = self.query_one("#create-todo-section", Vertical)
+            project_section = self.query_one("#project-todos-section", Collapsible)
+            project_list = self.query_one("#project-todos-list", ListView)
+            code_header = self.query_one("#code-todos-header", Static)
+            code_list = self.query_one("#code-todos-list", ListView)
+            empty_msg = self.query_one("#todos-empty", Static)
+
+            # Clear both lists
+            project_list.clear()
+            code_list.clear()
+
+            # Check if TODO.md exists
+            self._has_todo_md = (self._project_path / "TODO.md").exists()
+
+            has_items = False
+
+            # Show create button if no TODO.md and no project items
+            if not self._has_todo_md and not self._project_items:
+                create_section.display = True
+                project_section.display = False
+            else:
+                create_section.display = False
+
+                # Populate project TODOs
+                if self._project_items:
+                    has_items = True
+                    # Group by section
+                    sections: dict[str, list[ProjectTodoItem]] = {}
+                    for item in self._project_items:
+                        if item.section not in sections:
+                            sections[item.section] = []
+                        sections[item.section].append(item)
+
+                    # Add items (flat list, grouped display can be added later)
+                    for item in self._project_items:
+                        if not item.checked:  # Only show unchecked by default
+                            project_list.append(ProjectTodoListItem(item))
+
+                    unchecked = sum(1 for i in self._project_items if not i.checked)
+                    project_section.title = f"Project TODOs ({unchecked})"
+                    project_section.display = True
+                else:
+                    project_section.display = False
+
+            # Populate code TODOs
+            if self._items:
+                has_items = True
+                for item in self._items:
+                    code_list.append(TodoListItem(item))
+                code_header.update(f"Code TODOs ({len(self._items)})")
+                code_header.display = True
+                code_list.display = True
+            else:
+                code_header.display = False
+                code_list.display = False
+
+            # Show empty message only if no items at all and TODO.md exists
+            empty_msg.display = not has_items and self._has_todo_md
+
         except Exception:
             pass
 
+    def update_items(
+        self,
+        items: list[TodoItem],
+        project_items: list[ProjectTodoItem] | None = None,
+    ) -> None:
+        """Update both TODO lists."""
+        self._items = items
+        self._project_items = project_items or []
+
+        # Update header with total count
+        try:
+            unchecked_project = sum(1 for p in self._project_items if not p.checked)
+            total = len(items) + unchecked_project
+            header = self.query_one("#todos-header", Static)
+            header.update(f"TODOs ({total})")
+        except Exception:
+            pass
+
+        # Refresh the lists
+        self._refresh_lists()
+
     def filter_by_type(self, todo_type: TodoType) -> list[TodoItem]:
-        """Filter by TODO type."""
+        """Filter code TODOs by type."""
         return [i for i in self._items if i.todo_type == todo_type]
 
     def on_list_view_selected(self, event: ListView.Selected) -> None:
         """Handle item selection."""
         if isinstance(event.item, TodoListItem):
             self.post_message(self.TodoClicked(event.item.item))
+        elif isinstance(event.item, ProjectTodoListItem):
+            self.post_message(self.ProjectTodoClicked(event.item.item))
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Handle button presses."""
+        if event.button.id == "create-todo-btn":
+            self._create_todo_md()
+
+    def _create_todo_md(self) -> None:
+        """Create a new TODO.md file with template."""
+        todo_path = self._project_path / "TODO.md"
+        if todo_path.exists():
+            return
+
+        try:
+            todo_path.write_text(TODO_MD_TEMPLATE)
+            self._has_todo_md = True
+            self.post_message(self.TodoMdCreated(todo_path))
+            # Notify app to refresh TODOs
+            self.post_message(self.CreateTodoMdRequested())
+        except OSError as e:
+            self.app.notify(f"Failed to create TODO.md: {e}", severity="error")
+
+    def set_project_path(self, path: Path) -> None:
+        """Update the project path."""
+        self._project_path = path
+        self._has_todo_md = (path / "TODO.md").exists()
+        self._refresh_lists()

clide/widgets/panels/claude.py

@@ -22,9 +22,10 @@ from textual.reactive import reactive
 from textual.strip import Strip
 from textual.widget import Widget
 
+from clide.services.settings_service import get_settings_service
+
 # Use vendored pyte with diagnostic logging support
 from clide.vendor import pyte
-from clide.services.settings_service import get_settings_service
 
 if TYPE_CHECKING:
     from textual.app import ComposeResult
@@ -46,6 +47,7 @@ def _setup_terminal_debug_logging() -> None:
     def debug_logger(message: str) -> None:
         """Log debug message with timestamp."""
         import datetime
+
         timestamp = datetime.datetime.now().isoformat()
         log_file.write(f"[{timestamp}] {message}\n")
         log_file.flush()
@@ -153,6 +155,7 @@ class TerminalDisplay(Widget, can_focus=True):
             # Send SIGWINCH to notify the child process of resize
             if self._pid is not None:
                 import signal
+
                 try:
                     os.kill(self._pid, signal.SIGWINCH)
                 except OSError:
@@ -231,11 +234,11 @@ class TerminalDisplay(Widget, can_focus=True):
     # Kitty keyboard protocol, bracketed paste mode queries, etc.
     _UNSUPPORTED_ESCAPES = re.compile(
         r"\x1b\[[\=\>\<][0-9;]*[a-zA-Z]"  # Kitty keyboard protocol (=, >, or < prefix)
-        r"|\x1b\[\?[0-9;]*u"              # Kitty keyboard query
-        r"|\x1b\[\?[0-9;]*c"              # Device attributes query
-        r"|\x1b\[>[0-9;]*c"               # Secondary device attributes
+        r"|\x1b\[\?[0-9;]*u"  # Kitty keyboard query
+        r"|\x1b\[\?[0-9;]*c"  # Device attributes query
+        r"|\x1b\[>[0-9;]*c"  # Secondary device attributes
         r"|\x1b\]\d+;[^\x07\x1b]*(?:\x07|\x1b\\)"  # OSC sequences (title, etc.)
-        r"|\x1b\[\?2026[hl]"              # Synchronized update mode (not used by pyte)
+        r"|\x1b\[\?2026[hl]"  # Synchronized update mode (not used by pyte)
     )
 
     def _filter_unsupported_escapes(self, data: str) -> str:
@@ -417,7 +420,11 @@ class TerminalDisplay(Widget, can_focus=True):
         screen_rows = self._rows
 
         # Widget display dimensions (what we need to output)
-        output_width = self.size.width if self.size.width > 0 else screen_cols + self.PADDING_LEFT + self.PADDING_RIGHT
+        output_width = (
+            self.size.width
+            if self.size.width > 0
+            else screen_cols + self.PADDING_LEFT + self.PADDING_RIGHT
+        )
 
         if y >= screen_rows:
             return Strip.blank(output_width)
@@ -436,7 +443,7 @@ class TerminalDisplay(Widget, can_focus=True):
         cols_to_render = min(screen_cols, output_width - self.PADDING_LEFT - self.PADDING_RIGHT)
 
         # Debug logging for render pipeline
-        debug_logger = getattr(pyte, '_debug_logger', None)
+        debug_logger = pyte.get_debug_logger()
         log_this_line = False
 
         for x in range(cols_to_render):
@@ -450,16 +457,15 @@ class TerminalDisplay(Widget, can_focus=True):
                 if 0x2500 <= code <= 0x257F:
                     log_this_line = True
                     if debug_logger:
-                        debug_logger(f"RENDER y={y} x={x}: box-drawing U+{code:04X} char='{char_data}'")
+                        debug_logger(
+                            f"RENDER y={y} x={x}: box-drawing U+{code:04X} char='{char_data}'"
+                        )
 
             # Handle characters that may not render correctly
             if len(char_data) == 1:
                 code = ord(char_data)
                 # Control characters (except space)
-                if code < 32 and code != 0:
-                    char_data = " "
-                # DEL and C1 control characters
-                elif 127 <= code <= 159:
+                if code < 32 and code != 0 or 127 <= code <= 159:
                     char_data = " "
                 # Braille patterns (U+2800-U+28FF) - used for spinners
                 # Replace with simple ASCII spinner chars or spaces
@@ -510,7 +516,7 @@ class TerminalDisplay(Widget, can_focus=True):
         # Debug: log segments if we had box-drawing chars
         if log_this_line and debug_logger:
             for i, seg in enumerate(segments[:10]):  # First 10 segments
-                seg_text = seg.text if hasattr(seg, 'text') else str(seg)
+                seg_text = seg.text if hasattr(seg, "text") else str(seg)
                 if len(seg_text) <= 5:
                     debug_logger(f"RENDER y={y} seg[{i}]: '{seg_text}' (repr: {repr(seg_text)})")
 
@@ -665,6 +671,7 @@ class ClaudePanel(Vertical):
 
     class ClaudeStarted(Message):
         """Emitted when Claude Code process starts."""
+
         pass
 
     # Reactive state

clide/widgets/panels/context.py

@@ -1,5 +1,6 @@
-"""Context panel with Problems, TODOs, and Jira tabs."""
+"""Context panel with Jira, TODOs, and Problems tabs."""
 
+from pathlib import Path
 
 from textual.app import ComposeResult
 from textual.containers import Horizontal, Vertical
@@ -8,14 +9,14 @@ from textual.reactive import reactive
 from textual.widgets import Static, TabbedContent, TabPane
 
 from clide.models.problems import Problem
-from clide.models.todos import TodoItem
+from clide.models.todos import ProjectTodoItem, TodoItem
 from clide.widgets.components.jira_view import JiraView
 from clide.widgets.components.problems_view import ProblemsView
 from clide.widgets.components.todos_view import TodosView
 
 
 class ContextPanel(Vertical):
-    """Right context panel with Problems, TODOs, and Jira integration."""
+    """Right context panel with Jira, TODOs, and Problems tabs."""
 
     DEFAULT_CSS = """
     ContextPanel {
@@ -61,16 +62,31 @@ class ContextPanel(Vertical):
             super().__init__()
 
     class TodoClicked(Message):
-        """Emitted when a TODO is clicked."""
+        """Emitted when a code TODO is clicked."""
 
         def __init__(self, item: TodoItem) -> None:
             self.item = item
             super().__init__()
 
+    class ProjectTodoClicked(Message):
+        """Emitted when a project TODO (from TODO.md) is clicked."""
+
+        def __init__(self, item: ProjectTodoItem) -> None:
+            self.item = item
+            super().__init__()
+
     class JiraRefreshRequested(Message):
         """Emitted when Jira refresh is requested."""
+
         pass
 
+    class TodoMdCreated(Message):
+        """Emitted when TODO.md has been created."""
+
+        def __init__(self, path: Path) -> None:
+            self.path = path
+            super().__init__()
+
     # Reactive state with counts for tab badges
     problem_count: reactive[int] = reactive(0)
     todo_count: reactive[int] = reactive(0)
@@ -79,20 +95,22 @@ class ContextPanel(Vertical):
     def __init__(
         self,
         jira_enabled: bool = True,
+        project_path: Path | None = None,
         **kwargs,
     ) -> None:
         super().__init__(**kwargs)
         self._jira_enabled = jira_enabled
+        self._project_path = project_path or Path.cwd()
         self.id = "panel-context"
 
     def compose(self) -> ComposeResult:
         with TabbedContent(id="context-tabs"):
-            with TabPane("Problems", id="context-problems"):
-                yield ProblemsView(id="problems-view")
-            with TabPane("TODOs", id="context-todos"):
-                yield TodosView(id="todos-view")
             with TabPane("Jira", id="context-jira"):
                 yield JiraView(enabled=self._jira_enabled, id="jira-view")
+            with TabPane("TODOs", id="context-todos"):
+                yield TodosView(project_path=self._project_path, id="todos-view")
+            with TabPane("Problems", id="context-problems"):
+                yield ProblemsView(id="problems-view")
         # Tab bar with counts at bottom
         with Horizontal(classes="context-tab-bar"):
             yield Static("", id="tab-counts")
@@ -120,15 +138,15 @@ class ContextPanel(Vertical):
             problem_style = "error-count" if self.problem_count > 0 else "success-count"
             todo_style = "warning-count" if self.todo_count > 0 else "success-count"
 
-            # Build count display
+            # Build count display (order matches tab order: TODOs, Problems)
             parts = []
+            parts.append(f"[{todo_style}]☐ {self.todo_count}[/]")
+
             if self.problem_count > 0:
                 parts.append(f"[{problem_style}]⚠ {self.problem_count}[/]")
             else:
                 parts.append(f"[{problem_style}]✓ 0[/]")
 
-            parts.append(f"[{todo_style}]☐ {self.todo_count}[/]")
-
             counts.update(" │ ".join(parts))
         except Exception:
             pass
@@ -142,12 +160,19 @@ class ContextPanel(Vertical):
         except Exception:
             pass
 
-    def update_todos(self, items: list[TodoItem]) -> None:
+    def update_todos(
+        self,
+        items: list[TodoItem],
+        project_items: list[ProjectTodoItem] | None = None,
+    ) -> None:
         """Update TODOs view and count."""
-        self.todo_count = len(items)
+        project_items = project_items or []
+        # Count includes both code TODOs and unchecked project TODOs
+        unchecked_project = sum(1 for p in project_items if not p.checked)
+        self.todo_count = len(items) + unchecked_project
         try:
             view = self.query_one("#todos-view", TodosView)
-            view.update_items(items)
+            view.update_items(items, project_items)
         except Exception:
             pass
 
@@ -201,12 +226,26 @@ class ContextPanel(Vertical):
         self.post_message(self.ProblemClicked(event.problem))
 
     def on_todos_view_todo_clicked(self, event: TodosView.TodoClicked) -> None:
-        """Forward todo click."""
+        """Forward code todo click."""
         self.post_message(self.TodoClicked(event.item))
 
+    def on_todos_view_project_todo_clicked(
+        self,
+        event: TodosView.ProjectTodoClicked,
+    ) -> None:
+        """Forward project todo click."""
+        self.post_message(self.ProjectTodoClicked(event.item))
+
     def on_jira_view_refresh_requested(
         self,
         event: JiraView.RefreshRequested,
     ) -> None:
         """Forward Jira refresh request."""
         self.post_message(self.JiraRefreshRequested())
+
+    def on_todos_view_todo_md_created(
+        self,
+        event: TodosView.TodoMdCreated,
+    ) -> None:
+        """Forward TODO.md created event."""
+        self.post_message(self.TodoMdCreated(event.path))

pyproject.toml

@@ -111,6 +111,11 @@ select = [
 ]
 ignore = [
     "E501",   # line too long (handled by formatter)
+    "ARG002", # unused method argument (Textual event handlers require these)
+    "SIM102", # nested if (sometimes clearer)
+    "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)
 ]
 
 [tool.ruff.lint.isort]