spec-kit/src/specify_cli/__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
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

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 {}

# 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,
    },
    "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,
    },
}

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:
            msg = f"GitHub API returned {status} for {api_url}"
            if debug:
                msg += f"\nResponse headers: {response.headers}\nBody (truncated 500): {response.text[:500]}"
            raise RuntimeError(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:
                body_sample = response.text[:400]
                raise RuntimeError(f"Download failed with {response.status_code}\nHeaders: {response.headers}\nBody (truncated): {body_sample}")
            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}")

@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, or q"),
    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)"),
):
    """
    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)

    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"),
        ("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)

            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]")

def main():
    app()

if __name__ == "__main__":
    main()