__init__.py

#!/usr/bin/env python3
# /// script
# requires-python = ">=3.11"
# dependencies = [
#     "typer",
#     "rich",
#     "platformdirs",
#     "readchar",
#     "httpx",
# ]
# ///
"""
Specify CLI - Setup tool for Specify projects

Usage:
    uvx specify-cli.py init <project-name>
    uvx specify-cli.py init .
    uvx specify-cli.py init --here

Or install globally:
    uv tool install --from specify-cli.py specify-cli
    specify init <project-name>
    specify init .
    specify init --here
"""

import os
import subprocess
import sys
import zipfile
import tempfile
import shutil
import shlex
import json
import yaml
from pathlib import Path
from typing import Optional, Tuple

import typer
import httpx
from rich.console import Console
from rich.panel import Panel
from rich.progress import Progress, SpinnerColumn, TextColumn
from rich.text import Text
from rich.live import Live
from rich.align import Align
from rich.table import Table
from rich.tree import Tree
from typer.core import TyperGroup

# For cross-platform keyboard input
import readchar
import ssl
import truststore
from datetime import datetime, timezone

ssl_context = truststore.SSLContext(ssl.PROTOCOL_TLS_CLIENT)
client = httpx.Client(verify=ssl_context)

def _github_token(cli_token: str | None = None) -> str | None:
    """Return sanitized GitHub token (cli arg takes precedence) or None."""
    return ((cli_token or os.getenv("GH_TOKEN") or os.getenv("GITHUB_TOKEN") or "").strip()) or None

def _github_auth_headers(cli_token: str | None = None) -> dict:
    """Return Authorization header dict only when a non-empty token exists."""
    token = _github_token(cli_token)
    return {"Authorization": f"Bearer {token}"} if token else {}

def _parse_rate_limit_headers(headers: httpx.Headers) -> dict:
    """Extract and parse GitHub rate-limit headers."""
    info = {}
    
    # Standard GitHub rate-limit headers
    if "X-RateLimit-Limit" in headers:
        info["limit"] = headers.get("X-RateLimit-Limit")
    if "X-RateLimit-Remaining" in headers:
        info["remaining"] = headers.get("X-RateLimit-Remaining")
    if "X-RateLimit-Reset" in headers:
        reset_epoch = int(headers.get("X-RateLimit-Reset", "0"))
        if reset_epoch:
            reset_time = datetime.fromtimestamp(reset_epoch, tz=timezone.utc)
            info["reset_epoch"] = reset_epoch
            info["reset_time"] = reset_time
            info["reset_local"] = reset_time.astimezone()
    
    # Retry-After header (seconds or HTTP-date)
    if "Retry-After" in headers:
        retry_after = headers.get("Retry-After")
        try:
            info["retry_after_seconds"] = int(retry_after)
        except ValueError:
            # HTTP-date format - not implemented, just store as string
            info["retry_after"] = retry_after
    
    return info

def _format_rate_limit_error(status_code: int, headers: httpx.Headers, url: str) -> str:
    """Format a user-friendly error message with rate-limit information."""
    rate_info = _parse_rate_limit_headers(headers)
    
    lines = [f"GitHub API returned status {status_code} for {url}"]
    lines.append("")
    
    if rate_info:
        lines.append("[bold]Rate Limit Information:[/bold]")
        if "limit" in rate_info:
            lines.append(f"  • Rate Limit: {rate_info['limit']} requests/hour")
        if "remaining" in rate_info:
            lines.append(f"  • Remaining: {rate_info['remaining']}")
        if "reset_local" in rate_info:
            reset_str = rate_info["reset_local"].strftime("%Y-%m-%d %H:%M:%S %Z")
            lines.append(f"  • Resets at: {reset_str}")
        if "retry_after_seconds" in rate_info:
            lines.append(f"  • Retry after: {rate_info['retry_after_seconds']} seconds")
        lines.append("")
    
    # Add troubleshooting guidance
    lines.append("[bold]Troubleshooting Tips:[/bold]")
    lines.append("  • If you're on a shared CI or corporate environment, you may be rate-limited.")
    lines.append("  • Consider using a GitHub token via --github-token or the GH_TOKEN/GITHUB_TOKEN")
    lines.append("    environment variable to increase rate limits.")
    lines.append("  • Authenticated requests have a limit of 5,000/hour vs 60/hour for unauthenticated.")
    
    return "\n".join(lines)

# Agent configuration with name, folder, install URL, and CLI tool requirement
AGENT_CONFIG = {
    "copilot": {
        "name": "GitHub Copilot",
        "folder": ".github/",
        "install_url": None,  # IDE-based, no CLI check needed
        "requires_cli": False,
    },
    "claude": {
        "name": "Claude Code",
        "folder": ".claude/",
        "install_url": "https://docs.anthropic.com/en/docs/claude-code/setup",
        "requires_cli": True,
    },
    "gemini": {
        "name": "Gemini CLI",
        "folder": ".gemini/",
        "install_url": "https://github.com/google-gemini/gemini-cli",
        "requires_cli": True,
    },
    "cursor-agent": {
        "name": "Cursor",
        "folder": ".cursor/",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "qwen": {
        "name": "Qwen Code",
        "folder": ".qwen/",
        "install_url": "https://github.com/QwenLM/qwen-code",
        "requires_cli": True,
    },
    "opencode": {
        "name": "opencode",
        "folder": ".opencode/",
        "install_url": "https://opencode.ai",
        "requires_cli": True,
    },
    "codex": {
        "name": "Codex CLI",
        "folder": ".codex/",
        "install_url": "https://github.com/openai/codex",
        "requires_cli": True,
    },
    "windsurf": {
        "name": "Windsurf",
        "folder": ".windsurf/",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "kilocode": {
        "name": "Kilo Code",
        "folder": ".kilocode/",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "auggie": {
        "name": "Auggie CLI",
        "folder": ".augment/",
        "install_url": "https://docs.augmentcode.com/cli/setup-auggie/install-auggie-cli",
        "requires_cli": True,
    },
    "codebuddy": {
        "name": "CodeBuddy",
        "folder": ".codebuddy/",
        "install_url": "https://www.codebuddy.ai/cli",
        "requires_cli": True,
    },
    "qoder": {
        "name": "Qoder CLI",
        "folder": ".qoder/",
        "install_url": "https://qoder.com/cli",
        "requires_cli": True,
    },
    "roo": {
        "name": "Roo Code",
        "folder": ".roo/",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "q": {
        "name": "Amazon Q Developer CLI",
        "folder": ".amazonq/",
        "install_url": "https://aws.amazon.com/developer/learning/q-developer-cli/",
        "requires_cli": True,
    },
    "amp": {
        "name": "Amp",
        "folder": ".agents/",
        "install_url": "https://ampcode.com/manual#install",
        "requires_cli": True,
    },
    "shai": {
        "name": "SHAI",
        "folder": ".shai/",
        "install_url": "https://github.com/ovh/shai",
        "requires_cli": True,
    },
    "bob": {
        "name": "IBM Bob",
        "folder": ".bob/",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
}

SCRIPT_TYPE_CHOICES = {"sh": "POSIX Shell (bash/zsh)", "ps": "PowerShell"}

CLAUDE_LOCAL_PATH = Path.home() / ".claude" / "local" / "claude"

BANNER = """
███████╗██████╗ ███████╗ ██████╗██╗███████╗██╗   ██╗
██╔════╝██╔══██╗██╔════╝██╔════╝██║██╔════╝╚██╗ ██╔╝
███████╗██████╔╝█████╗  ██║     ██║█████╗   ╚████╔╝ 
╚════██║██╔═══╝ ██╔══╝  ██║     ██║██╔══╝    ╚██╔╝  
███████║██║     ███████╗╚██████╗██║██║        ██║   
╚══════╝╚═╝     ╚══════╝ ╚═════╝╚═╝╚═╝        ╚═╝   
"""

TAGLINE = "GitHub Spec Kit - Spec-Driven Development Toolkit"
class StepTracker:
    """Track and render hierarchical steps without emojis, similar to Claude Code tree output.
    Supports live auto-refresh via an attached refresh callback.
    """
    def __init__(self, title: str):
        self.title = title
        self.steps = []  # list of dicts: {key, label, status, detail}
        self.status_order = {"pending": 0, "running": 1, "done": 2, "error": 3, "skipped": 4}
        self._refresh_cb = None  # callable to trigger UI refresh

    def attach_refresh(self, cb):
        self._refresh_cb = cb

    def add(self, key: str, label: str):
        if key not in [s["key"] for s in self.steps]:
            self.steps.append({"key": key, "label": label, "status": "pending", "detail": ""})
            self._maybe_refresh()

    def start(self, key: str, detail: str = ""):
        self._update(key, status="running", detail=detail)

    def complete(self, key: str, detail: str = ""):
        self._update(key, status="done", detail=detail)

    def error(self, key: str, detail: str = ""):
        self._update(key, status="error", detail=detail)

    def skip(self, key: str, detail: str = ""):
        self._update(key, status="skipped", detail=detail)

    def _update(self, key: str, status: str, detail: str):
        for s in self.steps:
            if s["key"] == key:
                s["status"] = status
                if detail:
                    s["detail"] = detail
                self._maybe_refresh()
                return

        self.steps.append({"key": key, "label": key, "status": status, "detail": detail})
        self._maybe_refresh()

    def _maybe_refresh(self):
        if self._refresh_cb:
            try:
                self._refresh_cb()
            except Exception:
                pass

    def render(self):
        tree = Tree(f"[cyan]{self.title}[/cyan]", guide_style="grey50")
        for step in self.steps:
            label = step["label"]
            detail_text = step["detail"].strip() if step["detail"] else ""

            status = step["status"]
            if status == "done":
                symbol = "[green]●[/green]"
            elif status == "pending":
                symbol = "[green dim]○[/green dim]"
            elif status == "running":
                symbol = "[cyan]○[/cyan]"
            elif status == "error":
                symbol = "[red]●[/red]"
            elif status == "skipped":
                symbol = "[yellow]○[/yellow]"
            else:
                symbol = " "

            if status == "pending":
                # Entire line light gray (pending)
                if detail_text:
                    line = f"{symbol} [bright_black]{label} ({detail_text})[/bright_black]"
                else:
                    line = f"{symbol} [bright_black]{label}[/bright_black]"
            else:
                # Label white, detail (if any) light gray in parentheses
                if detail_text:
                    line = f"{symbol} [white]{label}[/white] [bright_black]({detail_text})[/bright_black]"
                else:
                    line = f"{symbol} [white]{label}[/white]"

            tree.add(line)
        return tree

def get_key():
    """Get a single keypress in a cross-platform way using readchar."""
    key = readchar.readkey()

    if key == readchar.key.UP or key == readchar.key.CTRL_P:
        return 'up'
    if key == readchar.key.DOWN or key == readchar.key.CTRL_N:
        return 'down'

    if key == readchar.key.ENTER:
        return 'enter'

    if key == readchar.key.ESC:
        return 'escape'

    if key == readchar.key.CTRL_C:
        raise KeyboardInterrupt

    return key

def select_with_arrows(options: dict, prompt_text: str = "Select an option", default_key: str = None) -> str:
    """
    Interactive selection using arrow keys with Rich Live display.
    
    Args:
        options: Dict with keys as option keys and values as descriptions
        prompt_text: Text to show above the options
        default_key: Default option key to start with
        
    Returns:
        Selected option key
    """
    option_keys = list(options.keys())
    if default_key and default_key in option_keys:
        selected_index = option_keys.index(default_key)
    else:
        selected_index = 0

    selected_key = None

    def create_selection_panel():
        """Create the selection panel with current selection highlighted."""
        table = Table.grid(padding=(0, 2))
        table.add_column(style="cyan", justify="left", width=3)
        table.add_column(style="white", justify="left")

        for i, key in enumerate(option_keys):
            if i == selected_index:
                table.add_row("▶", f"[cyan]{key}[/cyan] [dim]({options[key]})[/dim]")
            else:
                table.add_row(" ", f"[cyan]{key}[/cyan] [dim]({options[key]})[/dim]")

        table.add_row("", "")
        table.add_row("", "[dim]Use ↑/↓ to navigate, Enter to select, Esc to cancel[/dim]")

        return Panel(
            table,
            title=f"[bold]{prompt_text}[/bold]",
            border_style="cyan",
            padding=(1, 2)
        )

    console.print()

    def run_selection_loop():
        nonlocal selected_key, selected_index
        with Live(create_selection_panel(), console=console, transient=True, auto_refresh=False) as live:
            while True:
                try:
                    key = get_key()
                    if key == 'up':
                        selected_index = (selected_index - 1) % len(option_keys)
                    elif key == 'down':
                        selected_index = (selected_index + 1) % len(option_keys)
                    elif key == 'enter':
                        selected_key = option_keys[selected_index]
                        break
                    elif key == 'escape':
                        console.print("\n[yellow]Selection cancelled[/yellow]")
                        raise typer.Exit(1)

                    live.update(create_selection_panel(), refresh=True)

                except KeyboardInterrupt:
                    console.print("\n[yellow]Selection cancelled[/yellow]")
                    raise typer.Exit(1)

    run_selection_loop()

    if selected_key is None:
        console.print("\n[red]Selection failed.[/red]")
        raise typer.Exit(1)

    return selected_key

console = Console()

class BannerGroup(TyperGroup):
    """Custom group that shows banner before help."""

    def format_help(self, ctx, formatter):
        # Show banner before help
        show_banner()
        super().format_help(ctx, formatter)


app = typer.Typer(
    name="specify",
    help="Setup tool for Specify spec-driven development projects",
    add_completion=False,
    invoke_without_command=True,
    cls=BannerGroup,
)

def show_banner():
    """Display the ASCII art banner."""
    banner_lines = BANNER.strip().split('\n')
    colors = ["bright_blue", "blue", "cyan", "bright_cyan", "white", "bright_white"]

    styled_banner = Text()
    for i, line in enumerate(banner_lines):
        color = colors[i % len(colors)]
        styled_banner.append(line + "\n", style=color)

    console.print(Align.center(styled_banner))
    console.print(Align.center(Text(TAGLINE, style="italic bright_yellow")))
    console.print()

@app.callback()
def callback(ctx: typer.Context):
    """Show banner when no subcommand is provided."""
    if ctx.invoked_subcommand is None and "--help" not in sys.argv and "-h" not in sys.argv:
        show_banner()
        console.print(Align.center("[dim]Run 'specify --help' for usage information[/dim]"))
        console.print()

def run_command(cmd: list[str], check_return: bool = True, capture: bool = False, shell: bool = False) -> Optional[str]:
    """Run a shell command and optionally capture output."""
    try:
        if capture:
            result = subprocess.run(cmd, check=check_return, capture_output=True, text=True, shell=shell)
            return result.stdout.strip()
        else:
            subprocess.run(cmd, check=check_return, shell=shell)
            return None
    except subprocess.CalledProcessError as e:
        if check_return:
            console.print(f"[red]Error running command:[/red] {' '.join(cmd)}")
            console.print(f"[red]Exit code:[/red] {e.returncode}")
            if hasattr(e, 'stderr') and e.stderr:
                console.print(f"[red]Error output:[/red] {e.stderr}")
            raise
        return None

def check_tool(tool: str, tracker: StepTracker = None) -> bool:
    """Check if a tool is installed. Optionally update tracker.
    
    Args:
        tool: Name of the tool to check
        tracker: Optional StepTracker to update with results
        
    Returns:
        True if tool is found, False otherwise
    """
    # Special handling for Claude CLI after `claude migrate-installer`
    # See: https://github.com/github/spec-kit/issues/123
    # The migrate-installer command REMOVES the original executable from PATH
    # and creates an alias at ~/.claude/local/claude instead
    # This path should be prioritized over other claude executables in PATH
    if tool == "claude":
        if CLAUDE_LOCAL_PATH.exists() and CLAUDE_LOCAL_PATH.is_file():
            if tracker:
                tracker.complete(tool, "available")
            return True
    
    found = shutil.which(tool) is not None
    
    if tracker:
        if found:
            tracker.complete(tool, "available")
        else:
            tracker.error(tool, "not found")
    
    return found

def is_git_repo(path: Path = None) -> bool:
    """Check if the specified path is inside a git repository."""
    if path is None:
        path = Path.cwd()
    
    if not path.is_dir():
        return False

    try:
        # Use git command to check if inside a work tree
        subprocess.run(
            ["git", "rev-parse", "--is-inside-work-tree"],
            check=True,
            capture_output=True,
            cwd=path,
        )
        return True
    except (subprocess.CalledProcessError, FileNotFoundError):
        return False

def init_git_repo(project_path: Path, quiet: bool = False) -> Tuple[bool, Optional[str]]:
    """Initialize a git repository in the specified path.
    
    Args:
        project_path: Path to initialize git repository in
        quiet: if True suppress console output (tracker handles status)
    
    Returns:
        Tuple of (success: bool, error_message: Optional[str])
    """
    try:
        original_cwd = Path.cwd()
        os.chdir(project_path)
        if not quiet:
            console.print("[cyan]Initializing git repository...[/cyan]")
        subprocess.run(["git", "init"], check=True, capture_output=True, text=True)
        subprocess.run(["git", "add", "."], check=True, capture_output=True, text=True)
        subprocess.run(["git", "commit", "-m", "Initial commit from Specify template"], check=True, capture_output=True, text=True)
        if not quiet:
            console.print("[green]✓[/green] Git repository initialized")
        return True, None

    except subprocess.CalledProcessError as e:
        error_msg = f"Command: {' '.join(e.cmd)}\nExit code: {e.returncode}"
        if e.stderr:
            error_msg += f"\nError: {e.stderr.strip()}"
        elif e.stdout:
            error_msg += f"\nOutput: {e.stdout.strip()}"
        
        if not quiet:
            console.print(f"[red]Error initializing git repository:[/red] {e}")
        return False, error_msg
    finally:
        os.chdir(original_cwd)

def handle_vscode_settings(sub_item, dest_file, rel_path, verbose=False, tracker=None) -> None:
    """Handle merging or copying of .vscode/settings.json files."""
    def log(message, color="green"):
        if verbose and not tracker:
            console.print(f"[{color}]{message}[/] {rel_path}")

    try:
        with open(sub_item, 'r', encoding='utf-8') as f:
            new_settings = json.load(f)

        if dest_file.exists():
            merged = merge_json_files(dest_file, new_settings, verbose=verbose and not tracker)
            with open(dest_file, 'w', encoding='utf-8') as f:
                json.dump(merged, f, indent=4)
                f.write('\n')
            log("Merged:", "green")
        else:
            shutil.copy2(sub_item, dest_file)
            log("Copied (no existing settings.json):", "blue")

    except Exception as e:
        log(f"Warning: Could not merge, copying instead: {e}", "yellow")
        shutil.copy2(sub_item, dest_file)

def merge_json_files(existing_path: Path, new_content: dict, verbose: bool = False) -> dict:
    """Merge new JSON content into existing JSON file.

    Performs a deep merge where:
    - New keys are added
    - Existing keys are preserved unless overwritten by new content
    - Nested dictionaries are merged recursively
    - Lists and other values are replaced (not merged)

    Args:
        existing_path: Path to existing JSON file
        new_content: New JSON content to merge in
        verbose: Whether to print merge details

    Returns:
        Merged JSON content as dict
    """
    try:
        with open(existing_path, 'r', encoding='utf-8') as f:
            existing_content = json.load(f)
    except (FileNotFoundError, json.JSONDecodeError):
        # If file doesn't exist or is invalid, just use new content
        return new_content

    def deep_merge(base: dict, update: dict) -> dict:
        """Recursively merge update dict into base dict."""
        result = base.copy()
        for key, value in update.items():
            if key in result and isinstance(result[key], dict) and isinstance(value, dict):
                # Recursively merge nested dictionaries
                result[key] = deep_merge(result[key], value)
            else:
                # Add new key or replace existing value
                result[key] = value
        return result

    merged = deep_merge(existing_content, new_content)

    if verbose:
        console.print(f"[cyan]Merged JSON file:[/cyan] {existing_path.name}")

    return merged

def download_template_from_github(ai_assistant: str, download_dir: Path, *, script_type: str = "sh", verbose: bool = True, show_progress: bool = True, client: httpx.Client = None, debug: bool = False, github_token: str = None) -> Tuple[Path, dict]:
    repo_owner = "github"
    repo_name = "spec-kit"
    if client is None:
        client = httpx.Client(verify=ssl_context)

    if verbose:
        console.print("[cyan]Fetching latest release information...[/cyan]")
    api_url = f"https://api.github.com/repos/{repo_owner}/{repo_name}/releases/latest"

    try:
        response = client.get(
            api_url,
            timeout=30,
            follow_redirects=True,
            headers=_github_auth_headers(github_token),
        )
        status = response.status_code
        if status != 200:
            # Format detailed error message with rate-limit info
            error_msg = _format_rate_limit_error(status, response.headers, api_url)
            if debug:
                error_msg += f"\n\n[dim]Response body (truncated 500):[/dim]\n{response.text[:500]}"
            raise RuntimeError(error_msg)
        try:
            release_data = response.json()
        except ValueError as je:
            raise RuntimeError(f"Failed to parse release JSON: {je}\nRaw (truncated 400): {response.text[:400]}")
    except Exception as e:
        console.print(f"[red]Error fetching release information[/red]")
        console.print(Panel(str(e), title="Fetch Error", border_style="red"))
        raise typer.Exit(1)

    assets = release_data.get("assets", [])
    pattern = f"spec-kit-template-{ai_assistant}-{script_type}"
    matching_assets = [
        asset for asset in assets
        if pattern in asset["name"] and asset["name"].endswith(".zip")
    ]

    asset = matching_assets[0] if matching_assets else None

    if asset is None:
        console.print(f"[red]No matching release asset found[/red] for [bold]{ai_assistant}[/bold] (expected pattern: [bold]{pattern}[/bold])")
        asset_names = [a.get('name', '?') for a in assets]
        console.print(Panel("\n".join(asset_names) or "(no assets)", title="Available Assets", border_style="yellow"))
        raise typer.Exit(1)

    download_url = asset["browser_download_url"]
    filename = asset["name"]
    file_size = asset["size"]

    if verbose:
        console.print(f"[cyan]Found template:[/cyan] {filename}")
        console.print(f"[cyan]Size:[/cyan] {file_size:,} bytes")
        console.print(f"[cyan]Release:[/cyan] {release_data['tag_name']}")

    zip_path = download_dir / filename
    if verbose:
        console.print(f"[cyan]Downloading template...[/cyan]")

    try:
        with client.stream(
            "GET",
            download_url,
            timeout=60,
            follow_redirects=True,
            headers=_github_auth_headers(github_token),
        ) as response:
            if response.status_code != 200:
                # Handle rate-limiting on download as well
                error_msg = _format_rate_limit_error(response.status_code, response.headers, download_url)
                if debug:
                    error_msg += f"\n\n[dim]Response body (truncated 400):[/dim]\n{response.text[:400]}"
                raise RuntimeError(error_msg)
            total_size = int(response.headers.get('content-length', 0))
            with open(zip_path, 'wb') as f:
                if total_size == 0:
                    for chunk in response.iter_bytes(chunk_size=8192):
                        f.write(chunk)
                else:
                    if show_progress:
                        with Progress(
                            SpinnerColumn(),
                            TextColumn("[progress.description]{task.description}"),
                            TextColumn("[progress.percentage]{task.percentage:>3.0f}%"),
                            console=console,
                        ) as progress:
                            task = progress.add_task("Downloading...", total=total_size)
                            downloaded = 0
                            for chunk in response.iter_bytes(chunk_size=8192):
                                f.write(chunk)
                                downloaded += len(chunk)
                                progress.update(task, completed=downloaded)
                    else:
                        for chunk in response.iter_bytes(chunk_size=8192):
                            f.write(chunk)
    except Exception as e:
        console.print(f"[red]Error downloading template[/red]")
        detail = str(e)
        if zip_path.exists():
            zip_path.unlink()
        console.print(Panel(detail, title="Download Error", border_style="red"))
        raise typer.Exit(1)
    if verbose:
        console.print(f"Downloaded: {filename}")
    metadata = {
        "filename": filename,
        "size": file_size,
        "release": release_data["tag_name"],
        "asset_url": download_url
    }
    return zip_path, metadata

def download_and_extract_template(project_path: Path, ai_assistant: str, script_type: str, is_current_dir: bool = False, *, verbose: bool = True, tracker: StepTracker | None = None, client: httpx.Client = None, debug: bool = False, github_token: str = None) -> Path:
    """Download the latest release and extract it to create a new project.
    Returns project_path. Uses tracker if provided (with keys: fetch, download, extract, cleanup)
    """
    current_dir = Path.cwd()

    if tracker:
        tracker.start("fetch", "contacting GitHub API")
    try:
        zip_path, meta = download_template_from_github(
            ai_assistant,
            current_dir,
            script_type=script_type,
            verbose=verbose and tracker is None,
            show_progress=(tracker is None),
            client=client,
            debug=debug,
            github_token=github_token
        )
        if tracker:
            tracker.complete("fetch", f"release {meta['release']} ({meta['size']:,} bytes)")
            tracker.add("download", "Download template")
            tracker.complete("download", meta['filename'])
    except Exception as e:
        if tracker:
            tracker.error("fetch", str(e))
        else:
            if verbose:
                console.print(f"[red]Error downloading template:[/red] {e}")
        raise

    if tracker:
        tracker.add("extract", "Extract template")
        tracker.start("extract")
    elif verbose:
        console.print("Extracting template...")

    try:
        if not is_current_dir:
            project_path.mkdir(parents=True)

        with zipfile.ZipFile(zip_path, 'r') as zip_ref:
            zip_contents = zip_ref.namelist()
            if tracker:
                tracker.start("zip-list")
                tracker.complete("zip-list", f"{len(zip_contents)} entries")
            elif verbose:
                console.print(f"[cyan]ZIP contains {len(zip_contents)} items[/cyan]")

            if is_current_dir:
                with tempfile.TemporaryDirectory() as temp_dir:
                    temp_path = Path(temp_dir)
                    zip_ref.extractall(temp_path)

                    extracted_items = list(temp_path.iterdir())
                    if tracker:
                        tracker.start("extracted-summary")
                        tracker.complete("extracted-summary", f"temp {len(extracted_items)} items")
                    elif verbose:
                        console.print(f"[cyan]Extracted {len(extracted_items)} items to temp location[/cyan]")

                    source_dir = temp_path
                    if len(extracted_items) == 1 and extracted_items[0].is_dir():
                        source_dir = extracted_items[0]
                        if tracker:
                            tracker.add("flatten", "Flatten nested directory")
                            tracker.complete("flatten")
                        elif verbose:
                            console.print(f"[cyan]Found nested directory structure[/cyan]")

                    for item in source_dir.iterdir():
                        dest_path = project_path / item.name
                        if item.is_dir():
                            if dest_path.exists():
                                if verbose and not tracker:
                                    console.print(f"[yellow]Merging directory:[/yellow] {item.name}")
                                for sub_item in item.rglob('*'):
                                    if sub_item.is_file():
                                        rel_path = sub_item.relative_to(item)
                                        dest_file = dest_path / rel_path
                                        dest_file.parent.mkdir(parents=True, exist_ok=True)
                                        # Special handling for .vscode/settings.json - merge instead of overwrite
                                        if dest_file.name == "settings.json" and dest_file.parent.name == ".vscode":
                                            handle_vscode_settings(sub_item, dest_file, rel_path, verbose, tracker)
                                        else:
                                            shutil.copy2(sub_item, dest_file)
                            else:
                                shutil.copytree(item, dest_path)
                        else:
                            if dest_path.exists() and verbose and not tracker:
                                console.print(f"[yellow]Overwriting file:[/yellow] {item.name}")
                            shutil.copy2(item, dest_path)
                    if verbose and not tracker:
                        console.print(f"[cyan]Template files merged into current directory[/cyan]")
            else:
                zip_ref.extractall(project_path)

                extracted_items = list(project_path.iterdir())
                if tracker:
                    tracker.start("extracted-summary")
                    tracker.complete("extracted-summary", f"{len(extracted_items)} top-level items")
                elif verbose:
                    console.print(f"[cyan]Extracted {len(extracted_items)} items to {project_path}:[/cyan]")
                    for item in extracted_items:
                        console.print(f"  - {item.name} ({'dir' if item.is_dir() else 'file'})")

                if len(extracted_items) == 1 and extracted_items[0].is_dir():
                    nested_dir = extracted_items[0]
                    temp_move_dir = project_path.parent / f"{project_path.name}_temp"

                    shutil.move(str(nested_dir), str(temp_move_dir))

                    project_path.rmdir()

                    shutil.move(str(temp_move_dir), str(project_path))
                    if tracker:
                        tracker.add("flatten", "Flatten nested directory")
                        tracker.complete("flatten")
                    elif verbose:
                        console.print(f"[cyan]Flattened nested directory structure[/cyan]")

    except Exception as e:
        if tracker:
            tracker.error("extract", str(e))
        else:
            if verbose:
                console.print(f"[red]Error extracting template:[/red] {e}")
                if debug:
                    console.print(Panel(str(e), title="Extraction Error", border_style="red"))

        if not is_current_dir and project_path.exists():
            shutil.rmtree(project_path)
        raise typer.Exit(1)
    else:
        if tracker:
            tracker.complete("extract")
    finally:
        if tracker:
            tracker.add("cleanup", "Remove temporary archive")

        if zip_path.exists():
            zip_path.unlink()
            if tracker:
                tracker.complete("cleanup")
            elif verbose:
                console.print(f"Cleaned up: {zip_path.name}")

    return project_path


def ensure_executable_scripts(project_path: Path, tracker: StepTracker | None = None) -> None:
    """Ensure POSIX .sh scripts under .specify/scripts (recursively) have execute bits (no-op on Windows)."""
    if os.name == "nt":
        return  # Windows: skip silently
    scripts_root = project_path / ".specify" / "scripts"
    if not scripts_root.is_dir():
        return
    failures: list[str] = []
    updated = 0
    for script in scripts_root.rglob("*.sh"):
        try:
            if script.is_symlink() or not script.is_file():
                continue
            try:
                with script.open("rb") as f:
                    if f.read(2) != b"#!":
                        continue
            except Exception:
                continue
            st = script.stat(); mode = st.st_mode
            if mode & 0o111:
                continue
            new_mode = mode
            if mode & 0o400: new_mode |= 0o100
            if mode & 0o040: new_mode |= 0o010
            if mode & 0o004: new_mode |= 0o001
            if not (new_mode & 0o100):
                new_mode |= 0o100
            os.chmod(script, new_mode)
            updated += 1
        except Exception as e:
            failures.append(f"{script.relative_to(scripts_root)}: {e}")
    if tracker:
        detail = f"{updated} updated" + (f", {len(failures)} failed" if failures else "")
        tracker.add("chmod", "Set script permissions recursively")
        (tracker.error if failures else tracker.complete)("chmod", detail)
    else:
        if updated:
            console.print(f"[cyan]Updated execute permissions on {updated} script(s) recursively[/cyan]")
        if failures:
            console.print("[yellow]Some scripts could not be updated:[/yellow]")
            for f in failures:
                console.print(f"  - {f}")

def ensure_constitution_from_template(project_path: Path, tracker: StepTracker | None = None) -> None:
    """Copy constitution template to memory if it doesn't exist (preserves existing constitution on reinitialization)."""
    memory_constitution = project_path / ".specify" / "memory" / "constitution.md"
    template_constitution = project_path / ".specify" / "templates" / "constitution-template.md"

    # If constitution already exists in memory, preserve it
    if memory_constitution.exists():
        if tracker:
            tracker.add("constitution", "Constitution setup")
            tracker.skip("constitution", "existing file preserved")
        return

    # If template doesn't exist, something went wrong with extraction
    if not template_constitution.exists():
        if tracker:
            tracker.add("constitution", "Constitution setup")
            tracker.error("constitution", "template not found")
        return

    # Copy template to memory directory
    try:
        memory_constitution.parent.mkdir(parents=True, exist_ok=True)
        shutil.copy2(template_constitution, memory_constitution)
        if tracker:
            tracker.add("constitution", "Constitution setup")
            tracker.complete("constitution", "copied from template")
        else:
            console.print(f"[cyan]Initialized constitution from template[/cyan]")
    except Exception as e:
        if tracker:
            tracker.add("constitution", "Constitution setup")
            tracker.error("constitution", str(e))
        else:
            console.print(f"[yellow]Warning: Could not initialize constitution: {e}[/yellow]")


def install_ai_skills(project_path: Path, tracker: StepTracker = None) -> bool:
    """
    Install Prompt.MD files from templates/commands/ as agent skills per agentskills.io spec.
    
    Args:
        project_path: Target project directory
        tracker: Optional progress tracker
    
    Returns:
        True if installation successful, False otherwise
    """
    # Find the project-local templates directory
    # Use the extracted templates under the initialized project, consistent with ensure_constitution_from_template
    templates_dir = project_path / ".specify" / "templates" / "commands"
    
    if not templates_dir.exists():
        if tracker:
            tracker.error("ai-skills", "project .specify/templates/commands not found")
        else:
            console.print("[yellow]Warning: project .specify/templates/commands directory not found, skipping skills installation[/yellow]")
        return False
    
    # Get all markdown files
    command_files = list(templates_dir.glob("*.md"))
    if not command_files:
        if tracker:
            tracker.skip("ai-skills", "no command templates found")
        else:
            console.print("[yellow]No command templates found to install[/yellow]")
        return False
    
    # Create skills directory
    skills_dir = project_path / ".agent" / "skills"
    skills_dir.mkdir(parents=True, exist_ok=True)
    
    if tracker:
        tracker.add("ai-skills", f"Install {len(command_files)} agent skills")
        tracker.start("ai-skills")
    
    installed_count = 0
    for command_file in command_files:
        try:
            # Read the template file
            with open(command_file, 'r', encoding='utf-8') as f:
                content = f.read()
            
            # Parse YAML frontmatter
            if content.startswith('---'):
                parts = content.split('---', 2)
                if len(parts) >= 3:
                    frontmatter = yaml.safe_load(parts[1])
                    body = parts[2].strip()
                else:
                    frontmatter = {}
                    body = content
            else:
                frontmatter = {}
                body = content
            
            # Generate skill name: speckit-<command-name>
            command_name = command_file.stem
            skill_name = f"speckit-{command_name}"
            
            # Create skill directory
            skill_dir = skills_dir / skill_name
            skill_dir.mkdir(parents=True, exist_ok=True)
            
            # Generate enhanced description
            original_desc = frontmatter.get('description', '')
            if command_name == 'specify':
                enhanced_desc = "Create or update feature specifications from natural language descriptions. Use when starting new features or refining requirements. Generates spec.md with user stories, functional requirements, and acceptance criteria following spec-driven development methodology."
            elif command_name == 'plan':
                enhanced_desc = "Generate technical implementation plans from feature specifications. Use after creating a spec to define architecture, tech stack, and implementation phases. Creates plan.md with detailed technical design."
            elif command_name == 'tasks':
                enhanced_desc = "Break down implementation plans into actionable task lists. Use after planning to create a structured task breakdown. Generates tasks.md with ordered, dependency-aware tasks."
            elif command_name == 'implement':
                enhanced_desc = "Execute all tasks from the task breakdown to build the feature. Use after task generation to systematically implement the planned solution following TDD approach where applicable."
            elif command_name == 'analyze':
                enhanced_desc = "Perform cross-artifact consistency analysis across spec.md, plan.md, and tasks.md. Use after task generation to identify gaps, duplications, and inconsistencies before implementation."
            elif command_name == 'clarify':
                enhanced_desc = "Structured clarification workflow for underspecified requirements. Use before planning to resolve ambiguities through coverage-based questioning. Records answers in spec clarifications section."
            elif command_name == 'constitution':
                enhanced_desc = "Create or update project governing principles and development guidelines. Use at project start to establish code quality, testing standards, and architectural constraints that guide all development."
            elif command_name == 'checklist':
                enhanced_desc = "Generate custom quality checklists for validating requirements completeness and clarity. Use to create unit tests for English that ensure spec quality before implementation."
            elif command_name == 'taskstoissues':
                enhanced_desc = "Convert tasks from tasks.md into GitHub issues. Use after task breakdown to track work items in GitHub project management."
            else:
                enhanced_desc = original_desc or f"Spec-kit workflow command: {command_name}"
            
            # Create SKILL.md following agentskills.io spec
            skill_content = f"""---
name: {skill_name}
description: {enhanced_desc}
compatibility: Requires git and spec-kit project structure with .agent/skills/ directory
---

# Speckit {command_name.title()} Skill

{body}
"""
            
            # Write SKILL.md
            skill_file = skill_dir / "SKILL.md"
            with open(skill_file, 'w', encoding='utf-8') as f:
                f.write(skill_content)
            
            installed_count += 1
            
        except Exception as e:
            console.print(f"[yellow]Warning: Failed to install skill {command_file.stem}: {e}[/yellow]")
            continue
    
    if tracker:
        if installed_count > 0:
            tracker.complete("ai-skills", f"{installed_count} skills installed")
        else:
            tracker.error("ai-skills", "no skills installed")
    else:
        if installed_count > 0:
            console.print(f"[green]✓[/green] Installed {installed_count} agent skills to .agent/skills/")
        else:
            console.print("[yellow]No skills were installed[/yellow]")
    
    return installed_count > 0

@app.command()
def init(
    project_name: str = typer.Argument(None, help="Name for your new project directory (optional if using --here, or use '.' for current directory)"),
    ai_assistant: str = typer.Option(None, "--ai", help="AI assistant to use: claude, gemini, copilot, cursor-agent, qwen, opencode, codex, windsurf, kilocode, auggie, codebuddy, amp, shai, q, bob, or qoder "),
    script_type: str = typer.Option(None, "--script", help="Script type to use: sh or ps"),
    ignore_agent_tools: bool = typer.Option(False, "--ignore-agent-tools", help="Skip checks for AI agent tools like Claude Code"),
    no_git: bool = typer.Option(False, "--no-git", help="Skip git repository initialization"),
    here: bool = typer.Option(False, "--here", help="Initialize project in the current directory instead of creating a new one"),
    force: bool = typer.Option(False, "--force", help="Force merge/overwrite when using --here (skip confirmation)"),
    skip_tls: bool = typer.Option(False, "--skip-tls", help="Skip SSL/TLS verification (not recommended)"),
    debug: bool = typer.Option(False, "--debug", help="Show verbose diagnostic output for network and extraction failures"),
    github_token: str = typer.Option(None, "--github-token", help="GitHub token to use for API requests (or set GH_TOKEN or GITHUB_TOKEN environment variable)"),
    ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
):
    """
    Initialize a new Specify project from the latest template.
    
    This command will:
    1. Check that required tools are installed (git is optional)
    2. Let you choose your AI assistant
    3. Download the appropriate template from GitHub
    4. Extract the template to a new project directory or current directory
    5. Initialize a fresh git repository (if not --no-git and no existing repo)
    6. Optionally set up AI assistant commands
    
    Examples:
        specify init my-project
        specify init my-project --ai claude
        specify init my-project --ai copilot --no-git
        specify init --ignore-agent-tools my-project
        specify init . --ai claude         # Initialize in current directory
        specify init .                     # Initialize in current directory (interactive AI selection)
        specify init --here --ai claude    # Alternative syntax for current directory
        specify init --here --ai codex
        specify init --here --ai codebuddy
        specify init --here
        specify init --here --force  # Skip confirmation when current directory not empty
    """

    show_banner()

    if project_name == ".":
        here = True
        project_name = None  # Clear project_name to use existing validation logic

    if here and project_name:
        console.print("[red]Error:[/red] Cannot specify both project name and --here flag")
        raise typer.Exit(1)

    if not here and not project_name:
        console.print("[red]Error:[/red] Must specify either a project name, use '.' for current directory, or use --here flag")
        raise typer.Exit(1)

    # Validate --ai-skills requires --ai
    if ai_skills and not ai_assistant:
        console.print("[red]Error:[/red] --ai-skills requires --ai to be specified")
        console.print("[yellow]Usage:[/yellow] specify init <project> --ai <agent> --ai-skills")
        raise typer.Exit(1)


    if here:
        project_name = Path.cwd().name
        project_path = Path.cwd()

        existing_items = list(project_path.iterdir())
        if existing_items:
            console.print(f"[yellow]Warning:[/yellow] Current directory is not empty ({len(existing_items)} items)")
            console.print("[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]")
            if force:
                console.print("[cyan]--force supplied: skipping confirmation and proceeding with merge[/cyan]")
            else:
                response = typer.confirm("Do you want to continue?")
                if not response:
                    console.print("[yellow]Operation cancelled[/yellow]")
                    raise typer.Exit(0)
    else:
        project_path = Path(project_name).resolve()
        if project_path.exists():
            error_panel = Panel(
                f"Directory '[cyan]{project_name}[/cyan]' already exists\n"
                "Please choose a different project name or remove the existing directory.",
                title="[red]Directory Conflict[/red]",
                border_style="red",
                padding=(1, 2)
            )
            console.print()
            console.print(error_panel)
            raise typer.Exit(1)

    current_dir = Path.cwd()

    setup_lines = [
        "[cyan]Specify Project Setup[/cyan]",
        "",
        f"{'Project':<15} [green]{project_path.name}[/green]",
        f"{'Working Path':<15} [dim]{current_dir}[/dim]",
    ]

    if not here:
        setup_lines.append(f"{'Target Path':<15} [dim]{project_path}[/dim]")

    console.print(Panel("\n".join(setup_lines), border_style="cyan", padding=(1, 2)))

    should_init_git = False
    if not no_git:
        should_init_git = check_tool("git")
        if not should_init_git:
            console.print("[yellow]Git not found - will skip repository initialization[/yellow]")

    if ai_assistant:
        if ai_assistant not in AGENT_CONFIG:
            console.print(f"[red]Error:[/red] Invalid AI assistant '{ai_assistant}'. Choose from: {', '.join(AGENT_CONFIG.keys())}")
            raise typer.Exit(1)
        selected_ai = ai_assistant
    else:
        # Create options dict for selection (agent_key: display_name)
        ai_choices = {key: config["name"] for key, config in AGENT_CONFIG.items()}
        selected_ai = select_with_arrows(
            ai_choices, 
            "Choose your AI assistant:", 
            "copilot"
        )

    if not ignore_agent_tools:
        agent_config = AGENT_CONFIG.get(selected_ai)
        if agent_config and agent_config["requires_cli"]:
            install_url = agent_config["install_url"]
            if not check_tool(selected_ai):
                error_panel = Panel(
                    f"[cyan]{selected_ai}[/cyan] not found\n"
                    f"Install from: [cyan]{install_url}[/cyan]\n"
                    f"{agent_config['name']} is required to continue with this project type.\n\n"
                    "Tip: Use [cyan]--ignore-agent-tools[/cyan] to skip this check",
                    title="[red]Agent Detection Error[/red]",
                    border_style="red",
                    padding=(1, 2)
                )
                console.print()
                console.print(error_panel)
                raise typer.Exit(1)

    if script_type:
        if script_type not in SCRIPT_TYPE_CHOICES:
            console.print(f"[red]Error:[/red] Invalid script type '{script_type}'. Choose from: {', '.join(SCRIPT_TYPE_CHOICES.keys())}")
            raise typer.Exit(1)
        selected_script = script_type
    else:
        default_script = "ps" if os.name == "nt" else "sh"

        if sys.stdin.isatty():
            selected_script = select_with_arrows(SCRIPT_TYPE_CHOICES, "Choose script type (or press Enter)", default_script)
        else:
            selected_script = default_script

    console.print(f"[cyan]Selected AI assistant:[/cyan] {selected_ai}")
    console.print(f"[cyan]Selected script type:[/cyan] {selected_script}")

    tracker = StepTracker("Initialize Specify Project")

    sys._specify_tracker_active = True

    tracker.add("precheck", "Check required tools")
    tracker.complete("precheck", "ok")
    tracker.add("ai-select", "Select AI assistant")
    tracker.complete("ai-select", f"{selected_ai}")
    tracker.add("script-select", "Select script type")
    tracker.complete("script-select", selected_script)
    for key, label in [
        ("fetch", "Fetch latest release"),
        ("download", "Download template"),
        ("extract", "Extract template"),
        ("zip-list", "Archive contents"),
        ("extracted-summary", "Extraction summary"),
        ("chmod", "Ensure scripts executable"),
        ("constitution", "Constitution setup"),
        ("cleanup", "Cleanup"),
        ("git", "Initialize git repository"),
        ("final", "Finalize")
    ]:
        tracker.add(key, label)

    # Track git error message outside Live context so it persists
    git_error_message = None

    with Live(tracker.render(), console=console, refresh_per_second=8, transient=True) as live:
        tracker.attach_refresh(lambda: live.update(tracker.render()))
        try:
            verify = not skip_tls
            local_ssl_context = ssl_context if verify else False
            local_client = httpx.Client(verify=local_ssl_context)

            download_and_extract_template(project_path, selected_ai, selected_script, here, verbose=False, tracker=tracker, client=local_client, debug=debug, github_token=github_token)

            ensure_executable_scripts(project_path, tracker=tracker)

            ensure_constitution_from_template(project_path, tracker=tracker)

            # Install agent skills if requested
            if ai_skills:
                install_ai_skills(project_path, tracker=tracker)

            if not no_git:
                tracker.start("git")
                if is_git_repo(project_path):
                    tracker.complete("git", "existing repo detected")
                elif should_init_git:
                    success, error_msg = init_git_repo(project_path, quiet=True)
                    if success:
                        tracker.complete("git", "initialized")
                    else:
                        tracker.error("git", "init failed")
                        git_error_message = error_msg
                else:
                    tracker.skip("git", "git not available")
            else:
                tracker.skip("git", "--no-git flag")

            tracker.complete("final", "project ready")
        except Exception as e:
            tracker.error("final", str(e))
            console.print(Panel(f"Initialization failed: {e}", title="Failure", border_style="red"))
            if debug:
                _env_pairs = [
                    ("Python", sys.version.split()[0]),
                    ("Platform", sys.platform),
                    ("CWD", str(Path.cwd())),
                ]
                _label_width = max(len(k) for k, _ in _env_pairs)
                env_lines = [f"{k.ljust(_label_width)} → [bright_black]{v}[/bright_black]" for k, v in _env_pairs]
                console.print(Panel("\n".join(env_lines), title="Debug Environment", border_style="magenta"))
            if not here and project_path.exists():
                shutil.rmtree(project_path)
            raise typer.Exit(1)
        finally:
            pass

    console.print(tracker.render())
    console.print("\n[bold green]Project ready.[/bold green]")
    
    # Show git error details if initialization failed
    if git_error_message:
        console.print()
        git_error_panel = Panel(
            f"[yellow]Warning:[/yellow] Git repository initialization failed\n\n"
            f"{git_error_message}\n\n"
            f"[dim]You can initialize git manually later with:[/dim]\n"
            f"[cyan]cd {project_path if not here else '.'}[/cyan]\n"
            f"[cyan]git init[/cyan]\n"
            f"[cyan]git add .[/cyan]\n"
            f"[cyan]git commit -m \"Initial commit\"[/cyan]",
            title="[red]Git Initialization Failed[/red]",
            border_style="red",
            padding=(1, 2)
        )
        console.print(git_error_panel)

    # Agent folder security notice
    agent_config = AGENT_CONFIG.get(selected_ai)
    if agent_config:
        agent_folder = agent_config["folder"]
        security_notice = Panel(
            f"Some agents may store credentials, auth tokens, or other identifying and private artifacts in the agent folder within your project.\n"
            f"Consider adding [cyan]{agent_folder}[/cyan] (or parts of it) to [cyan].gitignore[/cyan] to prevent accidental credential leakage.",
            title="[yellow]Agent Folder Security[/yellow]",
            border_style="yellow",
            padding=(1, 2)
        )
        console.print()
        console.print(security_notice)

    steps_lines = []
    if not here:
        steps_lines.append(f"1. Go to the project folder: [cyan]cd {project_name}[/cyan]")
        step_num = 2
    else:
        steps_lines.append("1. You're already in the project directory!")
        step_num = 2

    # Add Codex-specific setup step if needed
    if selected_ai == "codex":
        codex_path = project_path / ".codex"
        quoted_path = shlex.quote(str(codex_path))
        if os.name == "nt":  # Windows
            cmd = f"setx CODEX_HOME {quoted_path}"
        else:  # Unix-like systems
            cmd = f"export CODEX_HOME={quoted_path}"
        
        steps_lines.append(f"{step_num}. Set [cyan]CODEX_HOME[/cyan] environment variable before running Codex: [cyan]{cmd}[/cyan]")
        step_num += 1

    steps_lines.append(f"{step_num}. Start using slash commands with your AI agent:")

    steps_lines.append("   2.1 [cyan]/speckit.constitution[/] - Establish project principles")
    steps_lines.append("   2.2 [cyan]/speckit.specify[/] - Create baseline specification")
    steps_lines.append("   2.3 [cyan]/speckit.plan[/] - Create implementation plan")
    steps_lines.append("   2.4 [cyan]/speckit.tasks[/] - Generate actionable tasks")
    steps_lines.append("   2.5 [cyan]/speckit.implement[/] - Execute implementation")

    steps_panel = Panel("\n".join(steps_lines), title="Next Steps", border_style="cyan", padding=(1,2))
    console.print()
    console.print(steps_panel)

    enhancement_lines = [
        "Optional commands that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]",
        "",
        f"○ [cyan]/speckit.clarify[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]/speckit.plan[/] if used)",
        f"○ [cyan]/speckit.analyze[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]/speckit.tasks[/], before [cyan]/speckit.implement[/])",
        f"○ [cyan]/speckit.checklist[/] [bright_black](optional)[/bright_black] - Generate quality checklists to validate requirements completeness, clarity, and consistency (after [cyan]/speckit.plan[/])"
    ]
    enhancements_panel = Panel("\n".join(enhancement_lines), title="Enhancement Commands", border_style="cyan", padding=(1,2))
    console.print()
    console.print(enhancements_panel)



@app.command()
def check():
    """Check that all required tools are installed."""
    show_banner()
    console.print("[bold]Checking for installed tools...[/bold]\n")

    tracker = StepTracker("Check Available Tools")

    tracker.add("git", "Git version control")
    git_ok = check_tool("git", tracker=tracker)

    agent_results = {}
    for agent_key, agent_config in AGENT_CONFIG.items():
        agent_name = agent_config["name"]
        requires_cli = agent_config["requires_cli"]

        tracker.add(agent_key, agent_name)

        if requires_cli:
            agent_results[agent_key] = check_tool(agent_key, tracker=tracker)
        else:
            # IDE-based agent - skip CLI check and mark as optional
            tracker.skip(agent_key, "IDE-based, no CLI check")
            agent_results[agent_key] = False  # Don't count IDE agents as "found"

    # Check VS Code variants (not in agent config)
    tracker.add("code", "Visual Studio Code")
    code_ok = check_tool("code", tracker=tracker)

    tracker.add("code-insiders", "Visual Studio Code Insiders")
    code_insiders_ok = check_tool("code-insiders", tracker=tracker)

    console.print(tracker.render())

    console.print("\n[bold green]Specify CLI is ready to use![/bold green]")

    if not git_ok:
        console.print("[dim]Tip: Install git for repository management[/dim]")

    if not any(agent_results.values()):
        console.print("[dim]Tip: Install an AI assistant for the best experience[/dim]")



@app.command()
def version():
    """Display version and system information."""
    import platform
    import importlib.metadata
    
    show_banner()
    
    # Get CLI version from package metadata
    cli_version = "unknown"
    try:
        cli_version = importlib.metadata.version("specify-cli")
    except Exception:
        # Fallback: try reading from pyproject.toml if running from source
        try:
            import tomllib
            pyproject_path = Path(__file__).parent.parent.parent / "pyproject.toml"
            if pyproject_path.exists():
                with open(pyproject_path, "rb") as f:
                    data = tomllib.load(f)
                    cli_version = data.get("project", {}).get("version", "unknown")
        except Exception:
            pass
    
    # Fetch latest template release version
    repo_owner = "github"
    repo_name = "spec-kit"
    api_url = f"https://api.github.com/repos/{repo_owner}/{repo_name}/releases/latest"
    
    template_version = "unknown"
    release_date = "unknown"
    
    try:
        response = client.get(
            api_url,
            timeout=10,
            follow_redirects=True,
            headers=_github_auth_headers(),
        )
        if response.status_code == 200:
            release_data = response.json()
            template_version = release_data.get("tag_name", "unknown")
            # Remove 'v' prefix if present
            if template_version.startswith("v"):
                template_version = template_version[1:]
            release_date = release_data.get("published_at", "unknown")
            if release_date != "unknown":
                # Format the date nicely
                try:
                    dt = datetime.fromisoformat(release_date.replace('Z', '+00:00'))
                    release_date = dt.strftime("%Y-%m-%d")
                except Exception:
                    pass
    except Exception:
        pass

    info_table = Table(show_header=False, box=None, padding=(0, 2))
    info_table.add_column("Key", style="cyan", justify="right")
    info_table.add_column("Value", style="white")

    info_table.add_row("CLI Version", cli_version)
    info_table.add_row("Template Version", template_version)
    info_table.add_row("Released", release_date)
    info_table.add_row("", "")
    info_table.add_row("Python", platform.python_version())
    info_table.add_row("Platform", platform.system())
    info_table.add_row("Architecture", platform.machine())
    info_table.add_row("OS Version", platform.version())

    panel = Panel(
        info_table,
        title="[bold cyan]Specify CLI Information[/bold cyan]",
        border_style="cyan",
        padding=(1, 2)
    )

    console.print(panel)
    console.print()


# ===== Extension Commands =====

extension_app = typer.Typer(
    name="extension",
    help="Manage spec-kit extensions",
    add_completion=False,
)
app.add_typer(extension_app, name="extension")


def get_speckit_version() -> str:
    """Get current spec-kit version."""
    import importlib.metadata
    try:
        return importlib.metadata.version("specify-cli")
    except Exception:
        # Fallback: try reading from pyproject.toml
        try:
            import tomllib
            pyproject_path = Path(__file__).parent.parent.parent / "pyproject.toml"
            if pyproject_path.exists():
                with open(pyproject_path, "rb") as f:
                    data = tomllib.load(f)
                    return data.get("project", {}).get("version", "unknown")
        except Exception:
            # Intentionally ignore any errors while reading/parsing pyproject.toml.
            # If this lookup fails for any reason, we fall back to returning "unknown" below.
            pass
    return "unknown"


@extension_app.command("list")
def extension_list(
    available: bool = typer.Option(False, "--available", help="Show available extensions from catalog"),
    all_extensions: bool = typer.Option(False, "--all", help="Show both installed and available"),
):
    """List installed extensions."""
    from .extensions import ExtensionManager

    project_root = Path.cwd()

    # Check if we're in a spec-kit project
    specify_dir = project_root / ".specify"
    if not specify_dir.exists():
        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

    manager = ExtensionManager(project_root)
    installed = manager.list_installed()

    if not installed and not (available or all_extensions):
        console.print("[yellow]No extensions installed.[/yellow]")
        console.print("\nInstall an extension with:")
        console.print("  specify extension add <extension-name>")
        return

    if installed:
        console.print("\n[bold cyan]Installed Extensions:[/bold cyan]\n")

        for ext in installed:
            status_icon = "✓" if ext["enabled"] else "✗"
            status_color = "green" if ext["enabled"] else "red"

            console.print(f"  [{status_color}]{status_icon}[/{status_color}] [bold]{ext['name']}[/bold] (v{ext['version']})")
            console.print(f"     {ext['description']}")
            console.print(f"     Commands: {ext['command_count']} | Hooks: {ext['hook_count']} | Status: {'Enabled' if ext['enabled'] else 'Disabled'}")
            console.print()

    if available or all_extensions:
        console.print("\nInstall an extension:")
        console.print("  [cyan]specify extension add <name>[/cyan]")


@extension_app.command("add")
def extension_add(
    extension: str = typer.Argument(help="Extension name or path"),
    dev: bool = typer.Option(False, "--dev", help="Install from local directory"),
    from_url: Optional[str] = typer.Option(None, "--from", help="Install from custom URL"),
):
    """Install an extension."""
    from .extensions import ExtensionManager, ExtensionCatalog, ExtensionError, ValidationError, CompatibilityError

    project_root = Path.cwd()

    # Check if we're in a spec-kit project
    specify_dir = project_root / ".specify"
    if not specify_dir.exists():
        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

    manager = ExtensionManager(project_root)
    speckit_version = get_speckit_version()

    try:
        with console.status(f"[cyan]Installing extension: {extension}[/cyan]"):
            if dev:
                # Install from local directory
                source_path = Path(extension).expanduser().resolve()
                if not source_path.exists():
                    console.print(f"[red]Error:[/red] Directory not found: {source_path}")
                    raise typer.Exit(1)

                if not (source_path / "extension.yml").exists():
                    console.print(f"[red]Error:[/red] No extension.yml found in {source_path}")
                    raise typer.Exit(1)

                manifest = manager.install_from_directory(source_path, speckit_version)

            elif from_url:
                # Install from URL (ZIP file)
                import urllib.request
                import urllib.error
                from urllib.parse import urlparse

                # Validate URL
                parsed = urlparse(from_url)
                is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")

                if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
                    console.print("[red]Error:[/red] URL must use HTTPS for security.")
                    console.print("HTTP is only allowed for localhost URLs.")
                    raise typer.Exit(1)

                # Warn about untrusted sources
                console.print("[yellow]Warning:[/yellow] Installing from external URL.")
                console.print("Only install extensions from sources you trust.\n")
                console.print(f"Downloading from {from_url}...")

                # Download ZIP to temp location
                download_dir = project_root / ".specify" / "extensions" / ".cache" / "downloads"
                download_dir.mkdir(parents=True, exist_ok=True)
                zip_path = download_dir / f"{extension}-url-download.zip"

                try:
                    with urllib.request.urlopen(from_url, timeout=60) as response:
                        zip_data = response.read()
                    zip_path.write_bytes(zip_data)

                    # Install from downloaded ZIP
                    manifest = manager.install_from_zip(zip_path, speckit_version)
                except urllib.error.URLError as e:
                    console.print(f"[red]Error:[/red] Failed to download from {from_url}: {e}")
                    raise typer.Exit(1)
                finally:
                    # Clean up downloaded ZIP
                    if zip_path.exists():
                        zip_path.unlink()

            else:
                # Install from catalog
                catalog = ExtensionCatalog(project_root)

                # Check if extension exists in catalog
                ext_info = catalog.get_extension_info(extension)
                if not ext_info:
                    console.print(f"[red]Error:[/red] Extension '{extension}' not found in catalog")
                    console.print("\nSearch available extensions:")
                    console.print("  specify extension search")
                    raise typer.Exit(1)

                # Download extension ZIP
                console.print(f"Downloading {ext_info['name']} v{ext_info.get('version', 'unknown')}...")
                zip_path = catalog.download_extension(extension)

                try:
                    # Install from downloaded ZIP
                    manifest = manager.install_from_zip(zip_path, speckit_version)
                finally:
                    # Clean up downloaded ZIP
                    if zip_path.exists():
                        zip_path.unlink()

        console.print(f"\n[green]✓[/green] Extension installed successfully!")
        console.print(f"\n[bold]{manifest.name}[/bold] (v{manifest.version})")
        console.print(f"  {manifest.description}")
        console.print(f"\n[bold cyan]Provided commands:[/bold cyan]")
        for cmd in manifest.commands:
            console.print(f"  • {cmd['name']} - {cmd.get('description', '')}")

        console.print(f"\n[yellow]⚠[/yellow]  Configuration may be required")
        console.print(f"   Check: .specify/extensions/{manifest.id}/")

    except ValidationError as e:
        console.print(f"\n[red]Validation Error:[/red] {e}")
        raise typer.Exit(1)
    except CompatibilityError as e:
        console.print(f"\n[red]Compatibility Error:[/red] {e}")
        raise typer.Exit(1)
    except ExtensionError as e:
        console.print(f"\n[red]Error:[/red] {e}")
        raise typer.Exit(1)


@extension_app.command("remove")
def extension_remove(
    extension: str = typer.Argument(help="Extension ID to remove"),
    keep_config: bool = typer.Option(False, "--keep-config", help="Don't remove config files"),
    force: bool = typer.Option(False, "--force", help="Skip confirmation"),
):
    """Uninstall an extension."""
    from .extensions import ExtensionManager

    project_root = Path.cwd()

    # Check if we're in a spec-kit project
    specify_dir = project_root / ".specify"
    if not specify_dir.exists():
        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

    manager = ExtensionManager(project_root)

    # Check if extension is installed
    if not manager.registry.is_installed(extension):
        console.print(f"[red]Error:[/red] Extension '{extension}' is not installed")
        raise typer.Exit(1)

    # Get extension info
    ext_manifest = manager.get_extension(extension)
    if ext_manifest:
        ext_name = ext_manifest.name
        cmd_count = len(ext_manifest.commands)
    else:
        ext_name = extension
        cmd_count = 0

    # Confirm removal
    if not force:
        console.print(f"\n[yellow]⚠  This will remove:[/yellow]")
        console.print(f"   • {cmd_count} commands from AI agent")
        console.print(f"   • Extension directory: .specify/extensions/{extension}/")
        if not keep_config:
            console.print(f"   • Config files (will be backed up)")
        console.print()

        confirm = typer.confirm("Continue?")
        if not confirm:
            console.print("Cancelled")
            raise typer.Exit(0)

    # Remove extension
    success = manager.remove(extension, keep_config=keep_config)

    if success:
        console.print(f"\n[green]✓[/green] Extension '{ext_name}' removed successfully")
        if keep_config:
            console.print(f"\nConfig files preserved in .specify/extensions/{extension}/")
        else:
            console.print(f"\nConfig files backed up to .specify/extensions/.backup/{extension}/")
        console.print(f"\nTo reinstall: specify extension add {extension}")
    else:
        console.print(f"[red]Error:[/red] Failed to remove extension")
        raise typer.Exit(1)


@extension_app.command("search")
def extension_search(
    query: str = typer.Argument(None, help="Search query (optional)"),
    tag: Optional[str] = typer.Option(None, "--tag", help="Filter by tag"),
    author: Optional[str] = typer.Option(None, "--author", help="Filter by author"),
    verified: bool = typer.Option(False, "--verified", help="Show only verified extensions"),
):
    """Search for available extensions in catalog."""
    from .extensions import ExtensionCatalog, ExtensionError

    project_root = Path.cwd()

    # Check if we're in a spec-kit project
    specify_dir = project_root / ".specify"
    if not specify_dir.exists():
        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

    catalog = ExtensionCatalog(project_root)

    try:
        console.print("🔍 Searching extension catalog...")
        results = catalog.search(query=query, tag=tag, author=author, verified_only=verified)

        if not results:
            console.print("\n[yellow]No extensions found matching criteria[/yellow]")
            if query or tag or author or verified:
                console.print("\nTry:")
                console.print("  • Broader search terms")
                console.print("  • Remove filters")
                console.print("  • specify extension search (show all)")
            raise typer.Exit(0)

        console.print(f"\n[green]Found {len(results)} extension(s):[/green]\n")

        for ext in results:
            # Extension header
            verified_badge = " [green]✓ Verified[/green]" if ext.get("verified") else ""
            console.print(f"[bold]{ext['name']}[/bold] (v{ext['version']}){verified_badge}")
            console.print(f"  {ext['description']}")

            # Metadata
            console.print(f"\n  [dim]Author:[/dim] {ext.get('author', 'Unknown')}")
            if ext.get('tags'):
                tags_str = ", ".join(ext['tags'])
                console.print(f"  [dim]Tags:[/dim] {tags_str}")

            # Stats
            stats = []
            if ext.get('downloads') is not None:
                stats.append(f"Downloads: {ext['downloads']:,}")
            if ext.get('stars') is not None:
                stats.append(f"Stars: {ext['stars']}")
            if stats:
                console.print(f"  [dim]{' | '.join(stats)}[/dim]")

            # Links
            if ext.get('repository'):
                console.print(f"  [dim]Repository:[/dim] {ext['repository']}")

            # Install command
            console.print(f"\n  [cyan]Install:[/cyan] specify extension add {ext['id']}")
            console.print()

    except ExtensionError as e:
        console.print(f"\n[red]Error:[/red] {e}")
        console.print("\nTip: The catalog may be temporarily unavailable. Try again later.")
        raise typer.Exit(1)


@extension_app.command("info")
def extension_info(
    extension: str = typer.Argument(help="Extension ID or name"),
):
    """Show detailed information about an extension."""
    from .extensions import ExtensionCatalog, ExtensionManager, ExtensionError

    project_root = Path.cwd()

    # Check if we're in a spec-kit project
    specify_dir = project_root / ".specify"
    if not specify_dir.exists():
        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

    catalog = ExtensionCatalog(project_root)
    manager = ExtensionManager(project_root)

    try:
        ext_info = catalog.get_extension_info(extension)

        if not ext_info:
            console.print(f"[red]Error:[/red] Extension '{extension}' not found in catalog")
            console.print("\nTry: specify extension search")
            raise typer.Exit(1)

        # Header
        verified_badge = " [green]✓ Verified[/green]" if ext_info.get("verified") else ""
        console.print(f"\n[bold]{ext_info['name']}[/bold] (v{ext_info['version']}){verified_badge}")
        console.print(f"ID: {ext_info['id']}")
        console.print()

        # Description
        console.print(f"{ext_info['description']}")
        console.print()

        # Author and License
        console.print(f"[dim]Author:[/dim] {ext_info.get('author', 'Unknown')}")
        console.print(f"[dim]License:[/dim] {ext_info.get('license', 'Unknown')}")
        console.print()

        # Requirements
        if ext_info.get('requires'):
            console.print("[bold]Requirements:[/bold]")
            reqs = ext_info['requires']
            if reqs.get('speckit_version'):
                console.print(f"  • Spec Kit: {reqs['speckit_version']}")
            if reqs.get('tools'):
                for tool in reqs['tools']:
                    tool_name = tool['name']
                    tool_version = tool.get('version', 'any')
                    required = " (required)" if tool.get('required') else " (optional)"
                    console.print(f"  • {tool_name}: {tool_version}{required}")
            console.print()

        # Provides
        if ext_info.get('provides'):
            console.print("[bold]Provides:[/bold]")
            provides = ext_info['provides']
            if provides.get('commands'):
                console.print(f"  • Commands: {provides['commands']}")
            if provides.get('hooks'):
                console.print(f"  • Hooks: {provides['hooks']}")
            console.print()

        # Tags
        if ext_info.get('tags'):
            tags_str = ", ".join(ext_info['tags'])
            console.print(f"[bold]Tags:[/bold] {tags_str}")
            console.print()

        # Statistics
        stats = []
        if ext_info.get('downloads') is not None:
            stats.append(f"Downloads: {ext_info['downloads']:,}")
        if ext_info.get('stars') is not None:
            stats.append(f"Stars: {ext_info['stars']}")
        if stats:
            console.print(f"[bold]Statistics:[/bold] {' | '.join(stats)}")
            console.print()

        # Links
        console.print("[bold]Links:[/bold]")
        if ext_info.get('repository'):
            console.print(f"  • Repository: {ext_info['repository']}")
        if ext_info.get('homepage'):
            console.print(f"  • Homepage: {ext_info['homepage']}")
        if ext_info.get('documentation'):
            console.print(f"  • Documentation: {ext_info['documentation']}")
        if ext_info.get('changelog'):
            console.print(f"  • Changelog: {ext_info['changelog']}")
        console.print()

        # Installation status and command
        is_installed = manager.registry.is_installed(ext_info['id'])
        if is_installed:
            console.print("[green]✓ Installed[/green]")
            console.print(f"\nTo remove: specify extension remove {ext_info['id']}")
        else:
            console.print("[yellow]Not installed[/yellow]")
            console.print(f"\n[cyan]Install:[/cyan] specify extension add {ext_info['id']}")

    except ExtensionError as e:
        console.print(f"\n[red]Error:[/red] {e}")
        raise typer.Exit(1)


@extension_app.command("update")
def extension_update(
    extension: str = typer.Argument(None, help="Extension ID to update (or all)"),
):
    """Update extension(s) to latest version."""
    from .extensions import ExtensionManager, ExtensionCatalog, ExtensionError
    from packaging import version as pkg_version

    project_root = Path.cwd()

    # Check if we're in a spec-kit project
    specify_dir = project_root / ".specify"
    if not specify_dir.exists():
        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

    manager = ExtensionManager(project_root)
    catalog = ExtensionCatalog(project_root)

    try:
        # Get list of extensions to update
        if extension:
            # Update specific extension
            if not manager.registry.is_installed(extension):
                console.print(f"[red]Error:[/red] Extension '{extension}' is not installed")
                raise typer.Exit(1)
            extensions_to_update = [extension]
        else:
            # Update all extensions
            installed = manager.list_installed()
            extensions_to_update = [ext["id"] for ext in installed]

        if not extensions_to_update:
            console.print("[yellow]No extensions installed[/yellow]")
            raise typer.Exit(0)

        console.print("🔄 Checking for updates...\n")

        updates_available = []

        for ext_id in extensions_to_update:
            # Get installed version
            metadata = manager.registry.get(ext_id)
            installed_version = pkg_version.Version(metadata["version"])

            # Get catalog info
            ext_info = catalog.get_extension_info(ext_id)
            if not ext_info:
                console.print(f"⚠  {ext_id}: Not found in catalog (skipping)")
                continue

            catalog_version = pkg_version.Version(ext_info["version"])

            if catalog_version > installed_version:
                updates_available.append(
                    {
                        "id": ext_id,
                        "installed": str(installed_version),
                        "available": str(catalog_version),
                        "download_url": ext_info.get("download_url"),
                    }
                )
            else:
                console.print(f"✓ {ext_id}: Up to date (v{installed_version})")

        if not updates_available:
            console.print("\n[green]All extensions are up to date![/green]")
            raise typer.Exit(0)

        # Show available updates
        console.print("\n[bold]Updates available:[/bold]\n")
        for update in updates_available:
            console.print(
                f"  • {update['id']}: {update['installed']} → {update['available']}"
            )

        console.print()
        confirm = typer.confirm("Update these extensions?")
        if not confirm:
            console.print("Cancelled")
            raise typer.Exit(0)

        # Perform updates
        console.print()
        for update in updates_available:
            ext_id = update["id"]
            console.print(f"📦 Updating {ext_id}...")

            # TODO: Implement download and reinstall from URL
            # For now, just show  message
            console.print(
                f"[yellow]Note:[/yellow] Automatic update not yet implemented. "
                f"Please update manually:"
            )
            console.print(f"  specify extension remove {ext_id} --keep-config")
            console.print(f"  specify extension add {ext_id}")

        console.print(
            "\n[cyan]Tip:[/cyan] Automatic updates will be available in a future version"
        )

    except ExtensionError as e:
        console.print(f"\n[red]Error:[/red] {e}")
        raise typer.Exit(1)


@extension_app.command("enable")
def extension_enable(
    extension: str = typer.Argument(help="Extension ID to enable"),
):
    """Enable a disabled extension."""
    from .extensions import ExtensionManager, HookExecutor

    project_root = Path.cwd()

    # Check if we're in a spec-kit project
    specify_dir = project_root / ".specify"
    if not specify_dir.exists():
        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

    manager = ExtensionManager(project_root)
    hook_executor = HookExecutor(project_root)

    if not manager.registry.is_installed(extension):
        console.print(f"[red]Error:[/red] Extension '{extension}' is not installed")
        raise typer.Exit(1)

    # Update registry
    metadata = manager.registry.get(extension)
    if metadata.get("enabled", True):
        console.print(f"[yellow]Extension '{extension}' is already enabled[/yellow]")
        raise typer.Exit(0)

    metadata["enabled"] = True
    manager.registry.add(extension, metadata)

    # Enable hooks in extensions.yml
    config = hook_executor.get_project_config()
    if "hooks" in config:
        for hook_name in config["hooks"]:
            for hook in config["hooks"][hook_name]:
                if hook.get("extension") == extension:
                    hook["enabled"] = True
        hook_executor.save_project_config(config)

    console.print(f"[green]✓[/green] Extension '{extension}' enabled")


@extension_app.command("disable")
def extension_disable(
    extension: str = typer.Argument(help="Extension ID to disable"),
):
    """Disable an extension without removing it."""
    from .extensions import ExtensionManager, HookExecutor

    project_root = Path.cwd()

    # Check if we're in a spec-kit project
    specify_dir = project_root / ".specify"
    if not specify_dir.exists():
        console.print("[red]Error:[/red] Not a spec-kit project (no .specify/ directory)")
        console.print("Run this command from a spec-kit project root")
        raise typer.Exit(1)

    manager = ExtensionManager(project_root)
    hook_executor = HookExecutor(project_root)

    if not manager.registry.is_installed(extension):
        console.print(f"[red]Error:[/red] Extension '{extension}' is not installed")
        raise typer.Exit(1)

    # Update registry
    metadata = manager.registry.get(extension)
    if not metadata.get("enabled", True):
        console.print(f"[yellow]Extension '{extension}' is already disabled[/yellow]")
        raise typer.Exit(0)

    metadata["enabled"] = False
    manager.registry.add(extension, metadata)

    # Disable hooks in extensions.yml
    config = hook_executor.get_project_config()
    if "hooks" in config:
        for hook_name in config["hooks"]:
            for hook in config["hooks"][hook_name]:
                if hook.get("extension") == extension:
                    hook["enabled"] = False
        hook_executor.save_project_config(config)

    console.print(f"[green]✓[/green] Extension '{extension}' disabled")
    console.print(f"\nCommands will no longer be available. Hooks will not execute.")
    console.print(f"To re-enable: specify extension enable {extension}")


def main():
    app()

if __name__ == "__main__":
    main()