__init__.py

#!/usr/bin/env python3
# /// script
# requires-python = ">=3.11"
# dependencies = [
#     "typer",
#     "rich",
#     "platformdirs",
#     "readchar",
#     "httpx",
#     "json5",
# ]
# ///
"""
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 json
import json5
import stat
import yaml
from pathlib import Path
from typing import Any, 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, CLI tool requirement, and commands subdirectory
AGENT_CONFIG = {
    "copilot": {
        "name": "GitHub Copilot",
        "folder": ".github/",
        "commands_subdir": "agents",  # Special: uses agents/ not commands/
        "install_url": None,  # IDE-based, no CLI check needed
        "requires_cli": False,
    },
    "claude": {
        "name": "Claude Code",
        "folder": ".claude/",
        "commands_subdir": "commands",
        "install_url": "https://docs.anthropic.com/en/docs/claude-code/setup",
        "requires_cli": True,
    },
    "gemini": {
        "name": "Gemini CLI",
        "folder": ".gemini/",
        "commands_subdir": "commands",
        "install_url": "https://github.com/google-gemini/gemini-cli",
        "requires_cli": True,
    },
    "cursor-agent": {
        "name": "Cursor",
        "folder": ".cursor/",
        "commands_subdir": "commands",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "qwen": {
        "name": "Qwen Code",
        "folder": ".qwen/",
        "commands_subdir": "commands",
        "install_url": "https://github.com/QwenLM/qwen-code",
        "requires_cli": True,
    },
    "opencode": {
        "name": "opencode",
        "folder": ".opencode/",
        "commands_subdir": "command",  # Special: singular 'command' not 'commands'
        "install_url": "https://opencode.ai",
        "requires_cli": True,
    },
    "codex": {
        "name": "Codex CLI",
        "folder": ".agents/",
        "commands_subdir": "skills",  # Codex now uses project skills directly
        "install_url": "https://github.com/openai/codex",
        "requires_cli": True,
    },
    "windsurf": {
        "name": "Windsurf",
        "folder": ".windsurf/",
        "commands_subdir": "workflows",  # Special: uses workflows/ not commands/
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "junie": {
        "name": "Junie",
        "folder": ".junie/",
        "commands_subdir": "commands",
        "install_url": "https://junie.jetbrains.com/",
        "requires_cli": True,
    },
    "kilocode": {
        "name": "Kilo Code",
        "folder": ".kilocode/",
        "commands_subdir": "workflows",  # Special: uses workflows/ not commands/
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "auggie": {
        "name": "Auggie CLI",
        "folder": ".augment/",
        "commands_subdir": "commands",
        "install_url": "https://docs.augmentcode.com/cli/setup-auggie/install-auggie-cli",
        "requires_cli": True,
    },
    "codebuddy": {
        "name": "CodeBuddy",
        "folder": ".codebuddy/",
        "commands_subdir": "commands",
        "install_url": "https://www.codebuddy.ai/cli",
        "requires_cli": True,
    },
    "qodercli": {
        "name": "Qoder CLI",
        "folder": ".qoder/",
        "commands_subdir": "commands",
        "install_url": "https://qoder.com/cli",
        "requires_cli": True,
    },
    "roo": {
        "name": "Roo Code",
        "folder": ".roo/",
        "commands_subdir": "commands",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "kiro-cli": {
        "name": "Kiro CLI",
        "folder": ".kiro/",
        "commands_subdir": "prompts",  # Special: uses prompts/ not commands/
        "install_url": "https://kiro.dev/docs/cli/",
        "requires_cli": True,
    },
    "amp": {
        "name": "Amp",
        "folder": ".agents/",
        "commands_subdir": "commands",
        "install_url": "https://ampcode.com/manual#install",
        "requires_cli": True,
    },
    "shai": {
        "name": "SHAI",
        "folder": ".shai/",
        "commands_subdir": "commands",
        "install_url": "https://github.com/ovh/shai",
        "requires_cli": True,
    },
    "tabnine": {
        "name": "Tabnine CLI",
        "folder": ".tabnine/agent/",
        "commands_subdir": "commands",
        "install_url": "https://docs.tabnine.com/main/getting-started/tabnine-cli",
        "requires_cli": True,
    },
    "agy": {
        "name": "Antigravity",
        "folder": ".agent/",
        "commands_subdir": "commands",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "bob": {
        "name": "IBM Bob",
        "folder": ".bob/",
        "commands_subdir": "commands",
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "vibe": {
        "name": "Mistral Vibe",
        "folder": ".vibe/",
        "commands_subdir": "prompts",
        "install_url": "https://github.com/mistralai/mistral-vibe",
        "requires_cli": True,
    },
    "kimi": {
        "name": "Kimi Code",
        "folder": ".kimi/",
        "commands_subdir": "skills",  # Kimi uses /skill:<name> with .kimi/skills/<name>/SKILL.md
        "install_url": "https://code.kimi.com/",
        "requires_cli": True,
    },
    "trae": {
        "name": "Trae",
        "folder": ".trae/",
        "commands_subdir": "rules",  # Trae uses .trae/rules/ for project rules
        "install_url": None,  # IDE-based
        "requires_cli": False,
    },
    "pi": {
        "name": "Pi Coding Agent",
        "folder": ".pi/",
        "commands_subdir": "prompts",
        "install_url": "https://www.npmjs.com/package/@mariozechner/pi-coding-agent",
        "requires_cli": True,
    },
    "iflow": {
        "name": "iFlow CLI",
        "folder": ".iflow/",
        "commands_subdir": "commands",
        "install_url": "https://docs.iflow.cn/en/cli/quickstart",
        "requires_cli": True,
    },
    "generic": {
        "name": "Generic (bring your own agent)",
        "folder": None,  # Set dynamically via --ai-commands-dir
        "commands_subdir": "commands",
        "install_url": None,
        "requires_cli": False,
    },
}

AI_ASSISTANT_ALIASES = {
    "kiro": "kiro-cli",
}

# Agents that use TOML command format (others use Markdown)
_TOML_AGENTS = frozenset({"gemini", "tabnine"})

def _build_ai_assistant_help() -> str:
    """Build the --ai help text from AGENT_CONFIG so it stays in sync with runtime config."""

    non_generic_agents = sorted(agent for agent in AGENT_CONFIG if agent != "generic")
    base_help = (
        f"AI assistant to use: {', '.join(non_generic_agents)}, "
        "or generic (requires --ai-commands-dir)."
    )

    if not AI_ASSISTANT_ALIASES:
        return base_help

    alias_phrases = []
    for alias, target in sorted(AI_ASSISTANT_ALIASES.items()):
        alias_phrases.append(f"'{alias}' as an alias for '{target}'")

    if len(alias_phrases) == 1:
        aliases_text = alias_phrases[0]
    else:
        aliases_text = ', '.join(alias_phrases[:-1]) + ' and ' + alias_phrases[-1]

    return base_help + " Use " + aliases_text + "."
AI_ASSISTANT_HELP = _build_ai_assistant_help()

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
    
    if tool == "kiro-cli":
        # Kiro currently supports both executable names. Prefer kiro-cli and
        # accept kiro as a compatibility fallback.
        found = shutil.which("kiro-cli") is not None or shutil.which("kiro") is not None
    else:
        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.

    Note: when merge produces changes, rewritten output is normalized JSON and
    existing JSONC comments/trailing commas are not preserved.
    """
    def log(message, color="green"):
        if verbose and not tracker:
            console.print(f"[{color}]{message}[/] {rel_path}")

    def atomic_write_json(target_file: Path, payload: dict[str, Any]) -> None:
        """Atomically write JSON while preserving existing mode bits when possible."""
        temp_path: Optional[Path] = None
        try:
            with tempfile.NamedTemporaryFile(
                mode='w',
                encoding='utf-8',
                dir=target_file.parent,
                prefix=f"{target_file.name}.",
                suffix=".tmp",
                delete=False,
            ) as f:
                temp_path = Path(f.name)
                json.dump(payload, f, indent=4)
                f.write('\n')

            if target_file.exists():
                try:
                    existing_stat = target_file.stat()
                    os.chmod(temp_path, stat.S_IMODE(existing_stat.st_mode))
                    if hasattr(os, "chown"):
                        try:
                            os.chown(temp_path, existing_stat.st_uid, existing_stat.st_gid)
                        except PermissionError:
                            # Best-effort owner/group preservation without requiring elevated privileges.
                            pass
                except OSError:
                    # Best-effort metadata preservation; data safety is prioritized.
                    pass

            os.replace(temp_path, target_file)
        except Exception:
            if temp_path and temp_path.exists():
                temp_path.unlink()
            raise

    try:
        with open(sub_item, 'r', encoding='utf-8') as f:
            # json5 natively supports comments and trailing commas (JSONC)
            new_settings = json5.load(f)

        if dest_file.exists():
            merged = merge_json_files(dest_file, new_settings, verbose=verbose and not tracker)
            if merged is not None:
                atomic_write_json(dest_file, merged)
                log("Merged:", "green")
                log("Note: comments/trailing commas are normalized when rewritten", "yellow")
            else:
                log("Skipped merge (preserved existing settings)", "yellow")
        else:
            shutil.copy2(sub_item, dest_file)
            log("Copied (no existing settings.json):", "blue")

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


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

    Performs a polite deep merge where:
    - New keys are added
    - Existing keys are preserved (not overwritten) unless both values are dictionaries
    - Nested dictionaries are merged recursively only when both sides are dictionaries
    - Lists and other values are preserved from base if they exist

    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, or None if the existing file should be left untouched.
    """
    # Load existing content first to have a safe fallback
    existing_content = None
    exists = existing_path.exists()

    if exists:
        try:
            with open(existing_path, 'r', encoding='utf-8') as f:
                # Handle comments (JSONC) natively with json5
                # Note: json5 handles BOM automatically
                existing_content = json5.load(f)
        except FileNotFoundError:
            # Handle race condition where file is deleted after exists() check
            exists = False
        except Exception as e:
            if verbose:
                console.print(f"[yellow]Warning: Could not read or parse existing JSON in {existing_path.name} ({e}).[/yellow]")
            # Skip merge to preserve existing file if unparseable or inaccessible (e.g. PermissionError)
            return None

    # Validate template content
    if not isinstance(new_content, dict):
        if verbose:
            console.print(f"[yellow]Warning: Template content for {existing_path.name} is not a dictionary. Preserving existing settings.[/yellow]")
        return None

    if not exists:
        return new_content

    # If existing content parsed but is not a dict, skip merge to avoid data loss
    if not isinstance(existing_content, dict):
        if verbose:
            console.print(f"[yellow]Warning: Existing JSON in {existing_path.name} is not an object. Skipping merge to avoid data loss.[/yellow]")
        return None

    def deep_merge_polite(base: dict[str, Any], update: dict[str, Any]) -> dict[str, Any]:
        """Recursively merge update dict into base dict, preserving base values."""
        result = base.copy()
        for key, value in update.items():
            if key not in result:
                # Add new key
                result[key] = value
            elif isinstance(result[key], dict) and isinstance(value, dict):
                # Recursively merge nested dictionaries
                result[key] = deep_merge_polite(result[key], value)
            else:
                # Key already exists and values are not both dicts; preserve existing value.
                # This ensures user settings aren't overwritten by template defaults.
                pass
        return result

    merged = deep_merge_polite(existing_content, new_content)

    # Detect if anything actually changed. If not, return None so the caller
    # can skip rewriting the file (preserving user's comments/formatting).
    if merged == existing_content:
        return None

    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("[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("[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("[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,
    *,
    skip_legacy_codex_prompts: 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)

    Note:
        ``skip_legacy_codex_prompts`` suppresses the legacy top-level
        ``.codex`` directory from older template archives in Codex skills mode.
        The name is kept for backward compatibility with existing callers.
    """
    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:
            def _validate_zip_members_within(root: Path) -> None:
                """Validate all ZIP members stay within ``root`` (Zip Slip guard)."""
                root_resolved = root.resolve()
                for member in zip_ref.namelist():
                    member_path = (root / member).resolve()
                    try:
                        member_path.relative_to(root_resolved)
                    except ValueError:
                        raise RuntimeError(
                            f"Unsafe path in ZIP archive: {member} "
                            "(potential path traversal)"
                        )

            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)
                    _validate_zip_members_within(temp_path)
                    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("[cyan]Found nested directory structure[/cyan]")

                    for item in source_dir.iterdir():
                        # In Codex skills mode, do not materialize the legacy
                        # top-level .codex directory from older prompt-based
                        # template archives.
                        if skip_legacy_codex_prompts and ai_assistant == "codex" and item.name == ".codex":
                            continue
                        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("[cyan]Template files merged into current directory[/cyan]")
            else:
                _validate_zip_members_within(project_path)
                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("[cyan]Flattened nested directory structure[/cyan]")

                # For fresh-directory Codex skills init, suppress legacy
                # top-level .codex layout extracted from older archives.
                if skip_legacy_codex_prompts and ai_assistant == "codex":
                    legacy_codex_dir = project_path / ".codex"
                    if legacy_codex_dir.is_dir():
                        shutil.rmtree(legacy_codex_dir, ignore_errors=True)

    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 _locate_core_pack() -> Path | None:
    """Return the filesystem path to the bundled core_pack directory, or None.

    Only present in wheel installs: hatchling's force-include copies
    templates/, scripts/ etc. into specify_cli/core_pack/ at build time.

    Source-checkout and editable installs do NOT have this directory.
    Callers that need to work in both environments must check the repo-root
    trees (templates/, scripts/) as a fallback when this returns None.
    """
    # Wheel install: core_pack is a sibling directory of this file
    candidate = Path(__file__).parent / "core_pack"
    if candidate.is_dir():
        return candidate
    return None


def _locate_release_script() -> tuple[Path, str]:
    """Return (script_path, shell_cmd) for the platform-appropriate release script.

    Checks the bundled core_pack first, then falls back to the source checkout.
    Returns the bash script on Unix and the PowerShell script on Windows.
    Raises FileNotFoundError if neither can be found.
    """
    if os.name == "nt":
        name = "create-release-packages.ps1"
        shell = shutil.which("pwsh")
        if not shell:
            raise FileNotFoundError(
                "'pwsh' (PowerShell 7+) not found on PATH. "
                "The bundled release script requires PowerShell 7+ (pwsh), "
                "not Windows PowerShell 5.x (powershell.exe). "
                "Install from https://aka.ms/powershell to use offline scaffolding."
            )
    else:
        name = "create-release-packages.sh"
        shell = "bash"

    # Wheel install: core_pack/release_scripts/
    candidate = Path(__file__).parent / "core_pack" / "release_scripts" / name
    if candidate.is_file():
        return candidate, shell

    # Source-checkout fallback
    repo_root = Path(__file__).parent.parent.parent
    candidate = repo_root / ".github" / "workflows" / "scripts" / name
    if candidate.is_file():
        return candidate, shell

    raise FileNotFoundError(f"Release script '{name}' not found in core_pack or source checkout")


def scaffold_from_core_pack(
    project_path: Path,
    ai_assistant: str,
    script_type: str,
    is_current_dir: bool = False,
    *,
    tracker: StepTracker | None = None,
) -> bool:
    """Scaffold a project from bundled core_pack assets — no network access required.

    Invokes the bundled create-release-packages script (bash on Unix, PowerShell
    on Windows) to generate the full project scaffold for a single agent.  This
    guarantees byte-for-byte parity between ``specify init`` and the GitHub
    release ZIPs because both use the exact same script.

    Returns True on success.  Returns False if offline scaffolding failed for
    any reason, including missing or unreadable assets, missing required tools
    (bash, pwsh, zip), release-script failure or timeout, or unexpected runtime
    exceptions.  When ``--offline`` is active the caller should treat False as
    a hard error rather than falling back to a network download.
    """
    # --- Locate asset sources ---
    core = _locate_core_pack()

    # Command templates
    if core and (core / "commands").is_dir():
        commands_dir = core / "commands"
    else:
        repo_root = Path(__file__).parent.parent.parent
        commands_dir = repo_root / "templates" / "commands"
        if not commands_dir.is_dir():
            if tracker:
                tracker.error("scaffold", "command templates not found")
            return False

    # Scripts directory (parent of bash/ and powershell/)
    if core and (core / "scripts").is_dir():
        scripts_dir = core / "scripts"
    else:
        repo_root = Path(__file__).parent.parent.parent
        scripts_dir = repo_root / "scripts"
        if not scripts_dir.is_dir():
            if tracker:
                tracker.error("scaffold", "scripts directory not found")
            return False

    # Page templates (spec-template.md, plan-template.md, vscode-settings.json, etc.)
    if core and (core / "templates").is_dir():
        templates_dir = core / "templates"
    else:
        repo_root = Path(__file__).parent.parent.parent
        templates_dir = repo_root / "templates"
        if not templates_dir.is_dir():
            if tracker:
                tracker.error("scaffold", "page templates not found")
            return False

    # Release script
    try:
        release_script, shell_cmd = _locate_release_script()
    except FileNotFoundError as exc:
        if tracker:
            tracker.error("scaffold", str(exc))
        return False

    # Preflight: verify required external tools are available
    if os.name != "nt":
        if not shutil.which("bash"):
            msg = "'bash' not found on PATH. Required for offline scaffolding."
            if tracker:
                tracker.error("scaffold", msg)
            return False
        if not shutil.which("zip"):
            msg = "'zip' not found on PATH. Required for offline scaffolding. Install with: apt install zip / brew install zip"
            if tracker:
                tracker.error("scaffold", msg)
            return False

    if tracker:
        tracker.start("scaffold", "applying bundled assets")

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

        with tempfile.TemporaryDirectory() as tmpdir:
            tmp = Path(tmpdir)

            # Set up a repo-like directory layout in the temp dir so the
            # release script finds templates/commands/, scripts/, etc.
            tmpl_cmds = tmp / "templates" / "commands"
            tmpl_cmds.mkdir(parents=True)
            for f in commands_dir.iterdir():
                if f.is_file():
                    shutil.copy2(f, tmpl_cmds / f.name)

            # Page templates (needed for vscode-settings.json etc.)
            if templates_dir.is_dir():
                tmpl_root = tmp / "templates"
                for f in templates_dir.iterdir():
                    if f.is_file():
                        shutil.copy2(f, tmpl_root / f.name)

            # Scripts (bash/ and powershell/)
            for subdir in ("bash", "powershell"):
                src = scripts_dir / subdir
                if src.is_dir():
                    dst = tmp / "scripts" / subdir
                    dst.mkdir(parents=True, exist_ok=True)
                    for f in src.iterdir():
                        if f.is_file():
                            shutil.copy2(f, dst / f.name)

            # Run the release script for this single agent + script type
            env = os.environ.copy()
            # Pin GENRELEASES_DIR inside the temp dir so a user-exported
            # value cannot redirect output or cause rm -rf outside the sandbox.
            env["GENRELEASES_DIR"] = str(tmp / ".genreleases")
            if os.name == "nt":
                cmd = [
                    shell_cmd, "-File", str(release_script),
                    "-Version", "v0.0.0",
                    "-Agents", ai_assistant,
                    "-Scripts", script_type,
                ]
            else:
                cmd = [shell_cmd, str(release_script), "v0.0.0"]
                env["AGENTS"] = ai_assistant
                env["SCRIPTS"] = script_type

            try:
                result = subprocess.run(
                    cmd, cwd=str(tmp), env=env,
                    capture_output=True, text=True,
                    timeout=120,
                )
            except subprocess.TimeoutExpired:
                msg = "release script timed out after 120 seconds"
                if tracker:
                    tracker.error("scaffold", msg)
                else:
                    console.print(f"[red]Error:[/red] {msg}")
                return False

            if result.returncode != 0:
                msg = result.stderr.strip() or result.stdout.strip() or "unknown error"
                if tracker:
                    tracker.error("scaffold", f"release script failed: {msg}")
                else:
                    console.print(f"[red]Release script failed:[/red] {msg}")
                return False

            # Copy the generated files to the project directory
            build_dir = tmp / ".genreleases" / f"sdd-{ai_assistant}-package-{script_type}"
            if not build_dir.is_dir():
                if tracker:
                    tracker.error("scaffold", "release script produced no output")
                return False

            for item in build_dir.rglob("*"):
                if item.is_file():
                    rel = item.relative_to(build_dir)
                    dest = project_path / rel
                    dest.parent.mkdir(parents=True, exist_ok=True)
                    # When scaffolding into an existing directory (--here),
                    # use the same merge semantics as the GitHub-download path.
                    if is_current_dir and dest.name == "settings.json" and dest.parent.name == ".vscode":
                        handle_vscode_settings(item, dest, rel, verbose=False, tracker=tracker)
                    else:
                        shutil.copy2(item, dest)

        if tracker:
            tracker.complete("scaffold", "bundled assets applied")
        return True

    except Exception as e:
        if tracker:
            tracker.error("scaffold", str(e))
        else:
            console.print(f"[red]Error scaffolding from bundled assets:[/red] {e}")
        return False


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("[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]")


INIT_OPTIONS_FILE = ".specify/init-options.json"


def save_init_options(project_path: Path, options: dict[str, Any]) -> None:
    """Persist the CLI options used during ``specify init``.

    Writes a small JSON file to ``.specify/init-options.json`` so that
    later operations (e.g. preset install) can adapt their behaviour
    without scanning the filesystem.
    """
    dest = project_path / INIT_OPTIONS_FILE
    dest.parent.mkdir(parents=True, exist_ok=True)
    dest.write_text(json.dumps(options, indent=2, sort_keys=True))


def load_init_options(project_path: Path) -> dict[str, Any]:
    """Load the init options previously saved by ``specify init``.

    Returns an empty dict if the file does not exist or cannot be parsed.
    """
    path = project_path / INIT_OPTIONS_FILE
    if not path.exists():
        return {}
    try:
        return json.loads(path.read_text())
    except (json.JSONDecodeError, OSError):
        return {}


# Default skills directory for agents not in AGENT_CONFIG
DEFAULT_SKILLS_DIR = ".agents/skills"

# Agents whose downloaded template already contains skills in the final layout.
#
# Technical debt note:
# - Spec-kit currently has multiple SKILL.md generators:
#   1) release packaging scripts that build the template zip (native skills),
#   2) `install_ai_skills()` which converts extracted command templates to skills,
#   3) extension/preset overrides via `agents.CommandRegistrar.render_skill_command()`.
# - Keep the skills frontmatter schema aligned across all generators
#   (at minimum: name/description/compatibility/metadata.{author,source}).
# - When adding fields here, update the release scripts and override writers too.
NATIVE_SKILLS_AGENTS = {"codex", "kimi"}

# Enhanced descriptions for each spec-kit command skill
SKILL_DESCRIPTIONS = {
    "specify": "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.",
    "plan": "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.",
    "tasks": "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.",
    "implement": "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.",
    "analyze": "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.",
    "clarify": "Structured clarification workflow for underspecified requirements. Use before planning to resolve ambiguities through coverage-based questioning. Records answers in spec clarifications section.",
    "constitution": "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.",
    "checklist": "Generate custom quality checklists for validating requirements completeness and clarity. Use to create unit tests for English that ensure spec quality before implementation.",
    "taskstoissues": "Convert tasks from tasks.md into GitHub issues. Use after task breakdown to track work items in GitHub project management.",
}


def _get_skills_dir(project_path: Path, selected_ai: str) -> Path:
    """Resolve the agent-specific skills directory for the given AI assistant.

    Uses ``AGENT_CONFIG[agent]["folder"] + "skills"`` and falls back to
    ``DEFAULT_SKILLS_DIR`` for unknown agents.
    """
    agent_config = AGENT_CONFIG.get(selected_ai, {})
    agent_folder = agent_config.get("folder", "")
    if agent_folder:
        return project_path / agent_folder.rstrip("/") / "skills"

    return project_path / DEFAULT_SKILLS_DIR


def install_ai_skills(
    project_path: Path,
    selected_ai: str,
    tracker: StepTracker | None = None,
    *,
    overwrite_existing: bool = False,
) -> bool:
    """Install Prompt.MD files from templates/commands/ as agent skills.

    Skills are written to the agent-specific skills directory following the
    `agentskills.io <https://agentskills.io/specification>`_ specification.
    Installation is additive by default — existing files are never removed and
    prompt command files in the agent's commands directory are left untouched.

    Args:
        project_path: Target project directory.
        selected_ai: AI assistant key from ``AGENT_CONFIG``.
        tracker: Optional progress tracker.
        overwrite_existing: When True, overwrite any existing ``SKILL.md`` file
            in the target skills directory (including user-authored content).
            Defaults to False.

    Returns:
        ``True`` if at least one skill was installed or all skills were
        already present (idempotent re-run), ``False`` otherwise.
    """
    # Locate command templates in the agent's extracted commands directory.
    # download_and_extract_template() already placed the .md files here.
    agent_config = AGENT_CONFIG.get(selected_ai, {})
    agent_folder = agent_config.get("folder", "")
    commands_subdir = agent_config.get("commands_subdir", "commands")
    if agent_folder:
        templates_dir = project_path / agent_folder.rstrip("/") / commands_subdir
    else:
        templates_dir = project_path / commands_subdir

    # Only consider speckit.*.md templates so that user-authored command
    # files (e.g. custom slash commands, agent files) coexisting in the
    # same commands directory are not incorrectly converted into skills.
    template_glob = "speckit.*.md"

    if not templates_dir.exists() or not any(templates_dir.glob(template_glob)):
        # Fallback: try the repo-relative path (for running from source checkout)
        # This also covers agents whose extracted commands are in a different
        # format (e.g. gemini/tabnine use .toml, not .md).
        script_dir = Path(__file__).parent.parent.parent  # up from src/specify_cli/
        fallback_dir = script_dir / "templates" / "commands"
        if fallback_dir.exists() and any(fallback_dir.glob("*.md")):
            templates_dir = fallback_dir
            template_glob = "*.md"

    if not templates_dir.exists() or not any(templates_dir.glob(template_glob)):
        if tracker:
            tracker.error("ai-skills", "command templates not found")
        else:
            console.print("[yellow]Warning: command templates not found, skipping skills installation[/yellow]")
        return False

    command_files = sorted(templates_dir.glob(template_glob))
    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

    # Resolve the correct skills directory for this agent
    skills_dir = _get_skills_dir(project_path, selected_ai)
    skills_dir.mkdir(parents=True, exist_ok=True)

    if tracker:
        tracker.start("ai-skills")

    installed_count = 0
    skipped_count = 0
    for command_file in command_files:
        try:
            content = command_file.read_text(encoding="utf-8")

            # Parse YAML frontmatter
            if content.startswith("---"):
                parts = content.split("---", 2)
                if len(parts) >= 3:
                    frontmatter = yaml.safe_load(parts[1])
                    if not isinstance(frontmatter, dict):
                        frontmatter = {}
                    body = parts[2].strip()
                else:
                    # File starts with --- but has no closing ---
                    console.print(f"[yellow]Warning: {command_file.name} has malformed frontmatter (no closing ---), treating as plain content[/yellow]")
                    frontmatter = {}
                    body = content
            else:
                frontmatter = {}
                body = content

            command_name = command_file.stem
            # Normalize: extracted commands may be named "speckit.<cmd>.md"
            # or "speckit.<cmd>.agent.md"; strip the "speckit." prefix and
            # any trailing ".agent" suffix so skill names stay clean and
            # SKILL_DESCRIPTIONS lookups work.
            if command_name.startswith("speckit."):
                command_name = command_name[len("speckit."):]
            if command_name.endswith(".agent"):
                command_name = command_name[:-len(".agent")]
            skill_name = f"speckit-{command_name.replace('.', '-')}"

            # Create skill directory (additive — never removes existing content)
            skill_dir = skills_dir / skill_name
            skill_dir.mkdir(parents=True, exist_ok=True)

            # Select the best description available
            original_desc = frontmatter.get("description", "")
            enhanced_desc = SKILL_DESCRIPTIONS.get(command_name, original_desc or f"Spec-kit workflow command: {command_name}")

            # Build SKILL.md following agentskills.io spec
            # Use yaml.safe_dump to safely serialise the frontmatter and
            # avoid YAML injection from descriptions containing colons,
            # quotes, or newlines.
            # Normalize source filename for metadata — strip speckit. prefix
            # so it matches the canonical templates/commands/<cmd>.md path.
            source_name = command_file.name
            if source_name.startswith("speckit."):
                source_name = source_name[len("speckit."):]
            if source_name.endswith(".agent.md"):
                source_name = source_name[:-len(".agent.md")] + ".md"

            frontmatter_data = {
                "name": skill_name,
                "description": enhanced_desc,
                "compatibility": "Requires spec-kit project structure with .specify/ directory",
                "metadata": {
                    "author": "github-spec-kit",
                    "source": f"templates/commands/{source_name}",
                },
            }
            frontmatter_text = yaml.safe_dump(frontmatter_data, sort_keys=False).strip()
            skill_content = (
                f"---\n"
                f"{frontmatter_text}\n"
                f"---\n\n"
                f"# Speckit {command_name.title()} Skill\n\n"
                f"{body}\n"
            )

            skill_file = skill_dir / "SKILL.md"
            if skill_file.exists():
                if not overwrite_existing:
                    # Default behavior: do not overwrite user-customized skills on re-runs
                    skipped_count += 1
                    continue
            skill_file.write_text(skill_content, encoding="utf-8")
            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 and skipped_count > 0:
            tracker.complete("ai-skills", f"{installed_count} new + {skipped_count} existing skills in {skills_dir.relative_to(project_path)}")
        elif installed_count > 0:
            tracker.complete("ai-skills", f"{installed_count} skills → {skills_dir.relative_to(project_path)}")
        elif skipped_count > 0:
            tracker.complete("ai-skills", f"{skipped_count} skills already present")
        else:
            tracker.error("ai-skills", "no skills installed")
    else:
        if installed_count > 0:
            console.print(f"[green]✓[/green] Installed {installed_count} agent skills to {skills_dir.relative_to(project_path)}/")
        elif skipped_count > 0:
            console.print(f"[green]✓[/green] {skipped_count} agent skills already present in {skills_dir.relative_to(project_path)}/")
        else:
            console.print("[yellow]No skills were installed[/yellow]")

    return installed_count > 0 or skipped_count > 0


def _has_bundled_skills(project_path: Path, selected_ai: str) -> bool:
    """Return True when a native-skills agent has spec-kit bundled skills."""
    skills_dir = _get_skills_dir(project_path, selected_ai)
    if not skills_dir.is_dir():
        return False

    return any(skills_dir.glob("speckit-*/SKILL.md"))


def _migrate_legacy_kimi_dotted_skills(skills_dir: Path) -> tuple[int, int]:
    """Migrate legacy Kimi dotted skill dirs (speckit.xxx) to hyphenated format.

    Temporary migration helper:
    - Intended removal window: after 2026-06-25.
    - Purpose: one-time cleanup for projects initialized before Kimi moved to
      hyphenated skills (speckit-xxx).

    Returns:
        Tuple[migrated_count, removed_count]
        - migrated_count: old dotted dir renamed to hyphenated dir
        - removed_count: old dotted dir deleted when equivalent hyphenated dir existed
    """
    if not skills_dir.is_dir():
        return (0, 0)

    migrated_count = 0
    removed_count = 0

    for legacy_dir in sorted(skills_dir.glob("speckit.*")):
        if not legacy_dir.is_dir():
            continue
        if not (legacy_dir / "SKILL.md").exists():
            continue

        suffix = legacy_dir.name[len("speckit."):]
        if not suffix:
            continue

        target_dir = skills_dir / f"speckit-{suffix.replace('.', '-')}"

        if not target_dir.exists():
            shutil.move(str(legacy_dir), str(target_dir))
            migrated_count += 1
            continue

        # If the new target already exists, avoid destructive cleanup unless
        # both SKILL.md files are byte-identical.
        target_skill = target_dir / "SKILL.md"
        legacy_skill = legacy_dir / "SKILL.md"
        if target_skill.is_file():
            try:
                if target_skill.read_bytes() == legacy_skill.read_bytes():
                    # Preserve legacy directory when it contains extra user files.
                    has_extra_entries = any(
                        child.name != "SKILL.md" for child in legacy_dir.iterdir()
                    )
                    if not has_extra_entries:
                        shutil.rmtree(legacy_dir)
                        removed_count += 1
            except OSError:
                # Best-effort migration: preserve legacy dir on read failures.
                pass

    return (migrated_count, removed_count)


AGENT_SKILLS_MIGRATIONS = {
    "agy": {
        "error": "Explicit command support was deprecated in Antigravity version 1.20.5.",
        "usage": "specify init <project> --ai agy --ai-skills",
        "interactive_note": (
            "'agy' was selected interactively; enabling [cyan]--ai-skills[/cyan] "
            "automatically for compatibility (explicit .agent/commands usage is deprecated)."
        ),
    },
    "codex": {
        "error": (
            "Custom prompt-based spec-kit initialization is deprecated for Codex CLI; "
            "use agent skills instead."
        ),
        "usage": "specify init <project> --ai codex --ai-skills",
        "interactive_note": (
            "'codex' was selected interactively; enabling [cyan]--ai-skills[/cyan] "
            "automatically for compatibility (.agents/skills is the recommended Codex layout)."
        ),
    },
}


def _handle_agent_skills_migration(console: Console, agent_key: str) -> None:
    """Print a fail-fast migration error for agents that now require skills."""
    migration = AGENT_SKILLS_MIGRATIONS[agent_key]
    console.print(f"\n[red]Error:[/red] {migration['error']}")
    console.print("Please use [cyan]--ai-skills[/cyan] when initializing to install templates as agent skills instead.")
    console.print(f"[yellow]Usage:[/yellow] {migration['usage']}")
    raise typer.Exit(1)

@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_HELP),
    ai_commands_dir: str = typer.Option(None, "--ai-commands-dir", help="Directory for agent command files (required with --ai generic, e.g. .myagent/commands/)"),
    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)"),
    offline: bool = typer.Option(False, "--offline", help="Use assets bundled in the specify-cli package instead of downloading from GitHub (no network access required). Bundled assets will become the default in v0.6.0 and this flag will be removed."),
    preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
    branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, ...) or 'timestamp' (YYYYMMDD-HHMMSS)"),
):
    """
    Initialize a new Specify project.

    By default, project files are downloaded from the latest GitHub release.
    Use --offline to scaffold from assets bundled inside the specify-cli
    package instead (no internet access required, ideal for air-gapped or
    enterprise environments).

    NOTE: Starting with v0.6.0, bundled assets will be used by default and
    the --offline flag will be removed. The GitHub download path will be
    retired because bundled assets eliminate the need for network access,
    avoid proxy/firewall issues, and guarantee that templates always match
    the installed CLI version.

    This command will:
    1. Check that required tools are installed (git is optional)
    2. Let you choose your AI assistant
    3. Download template from GitHub (or use bundled assets with --offline)
    4. Initialize a fresh git repository (if not --no-git and no existing repo)
    5. 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 --ai-skills
        specify init --here --ai codebuddy
        specify init --here --ai vibe      # Initialize with Mistral Vibe support
        specify init --here
        specify init --here --force  # Skip confirmation when current directory not empty
        specify init my-project --ai claude --ai-skills   # Install agent skills
        specify init --here --ai gemini --ai-skills
        specify init my-project --ai generic --ai-commands-dir .myagent/commands/  # Unsupported agent
        specify init my-project --offline  # Use bundled assets (no network access)
        specify init my-project --ai claude --preset healthcare-compliance  # With preset
    """

    show_banner()

    # Detect when option values are likely misinterpreted flags (parameter ordering issue)
    if ai_assistant and ai_assistant.startswith("--"):
        console.print(f"[red]Error:[/red] Invalid value for --ai: '{ai_assistant}'")
        console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai?")
        console.print("[yellow]Example:[/yellow] specify init --ai claude --here")
        console.print(f"[yellow]Available agents:[/yellow] {', '.join(AGENT_CONFIG.keys())}")
        raise typer.Exit(1)
    
    if ai_commands_dir and ai_commands_dir.startswith("--"):
        console.print(f"[red]Error:[/red] Invalid value for --ai-commands-dir: '{ai_commands_dir}'")
        console.print("[yellow]Hint:[/yellow] Did you forget to provide a value for --ai-commands-dir?")
        console.print("[yellow]Example:[/yellow] specify init --ai generic --ai-commands-dir .myagent/commands/")
        raise typer.Exit(1)

    if ai_assistant:
        ai_assistant = AI_ASSISTANT_ALIASES.get(ai_assistant, ai_assistant)

    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 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)

    BRANCH_NUMBERING_CHOICES = {"sequential", "timestamp"}
    if branch_numbering and branch_numbering not in BRANCH_NUMBERING_CHOICES:
        console.print(f"[red]Error:[/red] Invalid --branch-numbering value '{branch_numbering}'. Choose from: {', '.join(sorted(BRANCH_NUMBERING_CHOICES))}")
        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)

    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"
        )

    # Agents that have moved from explicit commands/prompts to agent skills.
    if selected_ai in AGENT_SKILLS_MIGRATIONS and not ai_skills:
        # If selected interactively (no --ai provided), automatically enable
        # ai_skills so the agent remains usable without requiring an extra flag.
        # Preserve fail-fast behavior only for explicit '--ai <agent>' without skills.
        if ai_assistant:
            _handle_agent_skills_migration(console, selected_ai)
        else:
            ai_skills = True
            console.print(f"\n[yellow]Note:[/yellow] {AGENT_SKILLS_MIGRATIONS[selected_ai]['interactive_note']}")

    # Validate --ai-commands-dir usage
    if selected_ai == "generic":
        if not ai_commands_dir:
            console.print("[red]Error:[/red] --ai-commands-dir is required when using --ai generic")
            console.print("[dim]Example: specify init my-project --ai generic --ai-commands-dir .myagent/commands/[/dim]")
            raise typer.Exit(1)
    elif ai_commands_dir:
        console.print(f"[red]Error:[/red] --ai-commands-dir can only be used with --ai generic (not '{selected_ai}')")
        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 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)

    # Determine whether to use bundled assets or download from GitHub (default).
    # --offline opts in to bundled assets; without it, always use GitHub.
    # When --offline is set, scaffold_from_core_pack() will try the wheel's
    # core_pack/ first, then fall back to source-checkout paths. If neither
    # location has the required assets it returns False and we error out.
    _core = _locate_core_pack()

    use_github = not offline

    if use_github and _core is not None:
        console.print(
            "[yellow]Note:[/yellow] Bundled assets are available in this install. "
            "Use [bold]--offline[/bold] to skip the GitHub download — faster, "
            "no network required, and guaranteed version match.\n"
            "This will become the default in v0.6.0."
        )

    if use_github:
        for key, label in [
            ("fetch", "Fetch latest release"),
            ("download", "Download template"),
            ("extract", "Extract template"),
            ("zip-list", "Archive contents"),
            ("extracted-summary", "Extraction summary"),
        ]:
            tracker.add(key, label)
    else:
        tracker.add("scaffold", "Apply bundled assets")

    for key, label in [
        ("chmod", "Ensure scripts executable"),
        ("constitution", "Constitution setup"),
    ]:
        tracker.add(key, label)
    if ai_skills:
        tracker.add("ai-skills", "Install agent skills")
    for key, label in [
        ("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

            if use_github:
                with httpx.Client(verify=local_ssl_context) as local_client:
                    download_and_extract_template(
                        project_path,
                        selected_ai,
                        selected_script,
                        here,
                        skip_legacy_codex_prompts=(selected_ai == "codex" and ai_skills),
                        verbose=False,
                        tracker=tracker,
                        client=local_client,
                        debug=debug,
                        github_token=github_token,
                    )
            else:
                scaffold_ok = scaffold_from_core_pack(project_path, selected_ai, selected_script, here, tracker=tracker)
                if not scaffold_ok:
                    # --offline explicitly requested: never attempt a network download
                    console.print(
                        "\n[red]Error:[/red] --offline was specified but scaffolding from bundled assets failed.\n"
                        "Common causes: missing bash/pwsh, script permission errors, or incomplete wheel.\n"
                        "Remove --offline to attempt a GitHub download instead."
                    )
                    # Surface the specific failure reason from the tracker
                    for step in tracker.steps:
                        if step["key"] == "scaffold" and step["detail"]:
                            console.print(f"[red]Detail:[/red] {step['detail']}")
                            break
                    # Clean up partial project directory (same as the GitHub-download failure path)
                    if not here and project_path.exists():
                        shutil.rmtree(project_path)
                    raise typer.Exit(1)
            # For generic agent, rename placeholder directory to user-specified path
            if selected_ai == "generic" and ai_commands_dir:
                placeholder_dir = project_path / ".speckit" / "commands"
                target_dir = project_path / ai_commands_dir
                if placeholder_dir.is_dir():
                    target_dir.parent.mkdir(parents=True, exist_ok=True)
                    shutil.move(str(placeholder_dir), str(target_dir))
                    # Clean up empty .speckit dir if it's now empty
                    speckit_dir = project_path / ".speckit"
                    if speckit_dir.is_dir() and not any(speckit_dir.iterdir()):
                        speckit_dir.rmdir()

            ensure_executable_scripts(project_path, tracker=tracker)

            ensure_constitution_from_template(project_path, tracker=tracker)

            # Determine skills directory and migrate any legacy Kimi dotted skills.
            migrated_legacy_kimi_skills = 0
            removed_legacy_kimi_skills = 0
            skills_dir: Optional[Path] = None
            if selected_ai in NATIVE_SKILLS_AGENTS:
                skills_dir = _get_skills_dir(project_path, selected_ai)
                if selected_ai == "kimi" and skills_dir.is_dir():
                    (
                        migrated_legacy_kimi_skills,
                        removed_legacy_kimi_skills,
                    ) = _migrate_legacy_kimi_dotted_skills(skills_dir)

            if ai_skills:
                if selected_ai in NATIVE_SKILLS_AGENTS:
                    bundled_found = _has_bundled_skills(project_path, selected_ai)
                    if bundled_found:
                        detail = f"bundled skills → {skills_dir.relative_to(project_path)}"
                        if migrated_legacy_kimi_skills or removed_legacy_kimi_skills:
                            detail += (
                                f" (migrated {migrated_legacy_kimi_skills}, "
                                f"removed {removed_legacy_kimi_skills} legacy Kimi dotted skills)"
                            )
                        if tracker:
                            tracker.start("ai-skills")
                            tracker.complete("ai-skills", detail)
                        else:
                            console.print(f"[green]✓[/green] Using {detail}")
                    else:
                        # Compatibility fallback: convert command templates to skills
                        # when an older template archive does not include native skills.
                        # This keeps `specify init --here --ai codex --ai-skills` usable
                        # in repos that already contain unrelated skills under .agents/skills.
                        fallback_ok = install_ai_skills(
                            project_path,
                            selected_ai,
                            tracker=tracker,
                            overwrite_existing=True,
                        )
                        if not fallback_ok:
                            raise RuntimeError(
                                f"Expected bundled agent skills in {skills_dir.relative_to(project_path)}, "
                                "but none were found and fallback conversion failed. "
                                "Re-run with an up-to-date template."
                            )
                else:
                    skills_ok = install_ai_skills(project_path, selected_ai, tracker=tracker)

                    # When --ai-skills is used on a NEW project and skills were
                    # successfully installed, remove the command files that the
                    # template archive just created.  Skills replace commands, so
                    # keeping both would be confusing.  For --here on an existing
                    # repo we leave pre-existing commands untouched to avoid a
                    # breaking change.  We only delete AFTER skills succeed so the
                    # project always has at least one of {commands, skills}.
                    if skills_ok and not here:
                        agent_cfg = AGENT_CONFIG.get(selected_ai, {})
                        agent_folder = agent_cfg.get("folder", "")
                        commands_subdir = agent_cfg.get("commands_subdir", "commands")
                        if agent_folder:
                            cmds_dir = project_path / agent_folder.rstrip("/") / commands_subdir
                            if cmds_dir.exists():
                                try:
                                    shutil.rmtree(cmds_dir)
                                except OSError:
                                    # Best-effort cleanup: skills are already installed,
                                    # so leaving stale commands is non-fatal.
                                    console.print("[yellow]Warning: could not remove extracted commands directory[/yellow]")

            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")

            # Persist the CLI options so later operations (e.g. preset add)
            # can adapt their behaviour without re-scanning the filesystem.
            # Must be saved BEFORE preset install so _get_skills_dir() works.
            save_init_options(project_path, {
                "ai": selected_ai,
                "ai_skills": ai_skills,
                "ai_commands_dir": ai_commands_dir,
                "branch_numbering": branch_numbering or "sequential",
                "here": here,
                "preset": preset,
                "offline": offline,
                "script": selected_script,
                "speckit_version": get_speckit_version(),
            })

            # Install preset if specified
            if preset:
                try:
                    from .presets import PresetManager, PresetCatalog, PresetError
                    preset_manager = PresetManager(project_path)
                    speckit_ver = get_speckit_version()

                    # Try local directory first, then catalog
                    local_path = Path(preset).resolve()
                    if local_path.is_dir() and (local_path / "preset.yml").exists():
                        preset_manager.install_from_directory(local_path, speckit_ver)
                    else:
                        preset_catalog = PresetCatalog(project_path)
                        pack_info = preset_catalog.get_pack_info(preset)
                        if not pack_info:
                            console.print(f"[yellow]Warning:[/yellow] Preset '{preset}' not found in catalog. Skipping.")
                        else:
                            try:
                                zip_path = preset_catalog.download_pack(preset)
                                preset_manager.install_from_zip(zip_path, speckit_ver)
                                # Clean up downloaded ZIP to avoid cache accumulation
                                try:
                                    zip_path.unlink(missing_ok=True)
                                except OSError:
                                    # Best-effort cleanup; failure to delete is non-fatal
                                    pass
                            except PresetError as preset_err:
                                console.print(f"[yellow]Warning:[/yellow] Failed to install preset '{preset}': {preset_err}")
                except Exception as preset_err:
                    console.print(f"[yellow]Warning:[/yellow] Failed to install preset: {preset_err}")

            # Scaffold path has no zip archive to clean up
            if not use_github:
                tracker.skip("cleanup", "not needed (no download)")

            tracker.complete("final", "project ready")
        except (typer.Exit, SystemExit):
            raise
        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 = ai_commands_dir if selected_ai == "generic" else agent_config["folder"]
        if agent_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

    if selected_ai == "codex" and ai_skills:
        steps_lines.append(f"{step_num}. Start Codex in this project directory; spec-kit skills were installed to [cyan].agents/skills[/cyan]")
        step_num += 1

    codex_skill_mode = selected_ai == "codex" and ai_skills
    kimi_skill_mode = selected_ai == "kimi"
    native_skill_mode = codex_skill_mode or kimi_skill_mode
    usage_label = "skills" if native_skill_mode else "slash commands"

    def _display_cmd(name: str) -> str:
        if codex_skill_mode:
            return f"$speckit-{name}"
        if kimi_skill_mode:
            return f"/skill:speckit-{name}"
        return f"/speckit.{name}"

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

    steps_lines.append(f"   {step_num}.1 [cyan]{_display_cmd('constitution')}[/] - Establish project principles")
    steps_lines.append(f"   {step_num}.2 [cyan]{_display_cmd('specify')}[/] - Create baseline specification")
    steps_lines.append(f"   {step_num}.3 [cyan]{_display_cmd('plan')}[/] - Create implementation plan")
    steps_lines.append(f"   {step_num}.4 [cyan]{_display_cmd('tasks')}[/] - Generate actionable tasks")
    steps_lines.append(f"   {step_num}.5 [cyan]{_display_cmd('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_intro = (
        "Optional skills that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]"
        if native_skill_mode
        else "Optional commands that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]"
    )
    enhancement_lines = [
        enhancement_intro,
        "",
        f"○ [cyan]{_display_cmd('clarify')}[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]{_display_cmd('plan')}[/] if used)",
        f"○ [cyan]{_display_cmd('analyze')}[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]{_display_cmd('tasks')}[/], before [cyan]{_display_cmd('implement')}[/])",
        f"○ [cyan]{_display_cmd('checklist')}[/] [bright_black](optional)[/bright_black] - Generate quality checklists to validate requirements completeness, clarity, and consistency (after [cyan]{_display_cmd('plan')}[/])"
    ]
    enhancements_title = "Enhancement Skills" if native_skill_mode else "Enhancement Commands"
    enhancements_panel = Panel("\n".join(enhancement_lines), title=enhancements_title, 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():
        if agent_key == "generic":
            continue  # Generic is not a real agent to check
        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")
    check_tool("code", tracker=tracker)

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

catalog_app = typer.Typer(
    name="catalog",
    help="Manage extension catalogs",
    add_completion=False,
)
extension_app.add_typer(catalog_app, name="catalog")

preset_app = typer.Typer(
    name="preset",
    help="Manage spec-kit presets",
    add_completion=False,
)
app.add_typer(preset_app, name="preset")

preset_catalog_app = typer.Typer(
    name="catalog",
    help="Manage preset catalogs",
    add_completion=False,
)
preset_app.add_typer(preset_catalog_app, name="catalog")


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"


# ===== Preset Commands =====


@preset_app.command("list")
def preset_list():
    """List installed presets."""
    from .presets import PresetManager

    project_root = Path.cwd()

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

    if not installed:
        console.print("[yellow]No presets installed.[/yellow]")
        console.print("\nInstall a preset with:")
        console.print("  [cyan]specify preset add <pack-name>[/cyan]")
        return

    console.print("\n[bold cyan]Installed Presets:[/bold cyan]\n")
    for pack in installed:
        status = "[green]enabled[/green]" if pack.get("enabled", True) else "[red]disabled[/red]"
        pri = pack.get('priority', 10)
        console.print(f"  [bold]{pack['name']}[/bold] ({pack['id']}) v{pack['version']} — {status} — priority {pri}")
        console.print(f"    {pack['description']}")
        if pack.get("tags"):
            tags_str = ", ".join(pack["tags"])
            console.print(f"    [dim]Tags: {tags_str}[/dim]")
        console.print(f"    [dim]Templates: {pack['template_count']}[/dim]")
        console.print()


@preset_app.command("add")
def preset_add(
    pack_id: str = typer.Argument(None, help="Preset ID to install from catalog"),
    from_url: str = typer.Option(None, "--from", help="Install from a URL (ZIP file)"),
    dev: str = typer.Option(None, "--dev", help="Install from local directory (development mode)"),
    priority: int = typer.Option(10, "--priority", help="Resolution priority (lower = higher precedence, default 10)"),
):
    """Install a preset."""
    from .presets import (
        PresetManager,
        PresetCatalog,
        PresetError,
        PresetValidationError,
        PresetCompatibilityError,
    )

    project_root = Path.cwd()

    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)

    # Validate priority
    if priority < 1:
        console.print("[red]Error:[/red] Priority must be a positive integer (1 or higher)")
        raise typer.Exit(1)

    manager = PresetManager(project_root)
    speckit_version = get_speckit_version()

    try:
        if dev:
            dev_path = Path(dev).resolve()
            if not dev_path.exists():
                console.print(f"[red]Error:[/red] Directory not found: {dev}")
                raise typer.Exit(1)

            console.print(f"Installing preset from [cyan]{dev_path}[/cyan]...")
            manifest = manager.install_from_directory(dev_path, speckit_version, priority)
            console.print(f"[green]✓[/green] Preset '{manifest.name}' v{manifest.version} installed (priority {priority})")

        elif from_url:
            # Validate URL scheme before downloading
            from urllib.parse import urlparse as _urlparse
            _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(f"[red]Error:[/red] URL must use HTTPS (got {_parsed.scheme}://). HTTP is only allowed for localhost.")
                raise typer.Exit(1)

            console.print(f"Installing preset from [cyan]{from_url}[/cyan]...")
            import urllib.request
            import urllib.error
            import tempfile

            with tempfile.TemporaryDirectory() as tmpdir:
                zip_path = Path(tmpdir) / "preset.zip"
                try:
                    with urllib.request.urlopen(from_url, timeout=60) as response:
                        zip_path.write_bytes(response.read())
                except urllib.error.URLError as e:
                    console.print(f"[red]Error:[/red] Failed to download: {e}")
                    raise typer.Exit(1)

                manifest = manager.install_from_zip(zip_path, speckit_version, priority)

            console.print(f"[green]✓[/green] Preset '{manifest.name}' v{manifest.version} installed (priority {priority})")

        elif pack_id:
            catalog = PresetCatalog(project_root)
            pack_info = catalog.get_pack_info(pack_id)

            if not pack_info:
                console.print(f"[red]Error:[/red] Preset '{pack_id}' not found in catalog")
                raise typer.Exit(1)

            if not pack_info.get("_install_allowed", True):
                catalog_name = pack_info.get("_catalog_name", "unknown")
                console.print(f"[red]Error:[/red] Preset '{pack_id}' is from the '{catalog_name}' catalog which is discovery-only (install not allowed).")
                console.print("Add the catalog with --install-allowed or install from the preset's repository directly with --from.")
                raise typer.Exit(1)

            console.print(f"Installing preset [cyan]{pack_info.get('name', pack_id)}[/cyan]...")

            try:
                zip_path = catalog.download_pack(pack_id)
                manifest = manager.install_from_zip(zip_path, speckit_version, priority)
                console.print(f"[green]✓[/green] Preset '{manifest.name}' v{manifest.version} installed (priority {priority})")
            finally:
                if 'zip_path' in locals() and zip_path.exists():
                    zip_path.unlink(missing_ok=True)
        else:
            console.print("[red]Error:[/red] Specify a preset ID, --from URL, or --dev path")
            raise typer.Exit(1)

    except PresetCompatibilityError as e:
        console.print(f"[red]Compatibility Error:[/red] {e}")
        raise typer.Exit(1)
    except PresetValidationError as e:
        console.print(f"[red]Validation Error:[/red] {e}")
        raise typer.Exit(1)
    except PresetError as e:
        console.print(f"[red]Error:[/red] {e}")
        raise typer.Exit(1)


@preset_app.command("remove")
def preset_remove(
    pack_id: str = typer.Argument(..., help="Preset ID to remove"),
):
    """Remove an installed preset."""
    from .presets import PresetManager

    project_root = Path.cwd()

    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 = PresetManager(project_root)

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

    if manager.remove(pack_id):
        console.print(f"[green]✓[/green] Preset '{pack_id}' removed successfully")
    else:
        console.print(f"[red]Error:[/red] Failed to remove preset '{pack_id}'")
        raise typer.Exit(1)


@preset_app.command("search")
def preset_search(
    query: str = typer.Argument(None, help="Search query"),
    tag: str = typer.Option(None, "--tag", help="Filter by tag"),
    author: str = typer.Option(None, "--author", help="Filter by author"),
):
    """Search for presets in the catalog."""
    from .presets import PresetCatalog, PresetError

    project_root = Path.cwd()

    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 = PresetCatalog(project_root)

    try:
        results = catalog.search(query=query, tag=tag, author=author)
    except PresetError as e:
        console.print(f"[red]Error:[/red] {e}")
        raise typer.Exit(1)

    if not results:
        console.print("[yellow]No presets found matching your criteria.[/yellow]")
        return

    console.print(f"\n[bold cyan]Presets ({len(results)} found):[/bold cyan]\n")
    for pack in results:
        console.print(f"  [bold]{pack.get('name', pack['id'])}[/bold] ({pack['id']}) v{pack.get('version', '?')}")
        console.print(f"    {pack.get('description', '')}")
        if pack.get("tags"):
            tags_str = ", ".join(pack["tags"])
            console.print(f"    [dim]Tags: {tags_str}[/dim]")
        console.print()


@preset_app.command("resolve")
def preset_resolve(
    template_name: str = typer.Argument(..., help="Template name to resolve (e.g., spec-template)"),
):
    """Show which template will be resolved for a given name."""
    from .presets import PresetResolver

    project_root = Path.cwd()

    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)

    resolver = PresetResolver(project_root)
    result = resolver.resolve_with_source(template_name)

    if result:
        console.print(f"  [bold]{template_name}[/bold]: {result['path']}")
        console.print(f"    [dim](from: {result['source']})[/dim]")
    else:
        console.print(f"  [yellow]{template_name}[/yellow]: not found")
        console.print("    [dim]No template with this name exists in the resolution stack[/dim]")


@preset_app.command("info")
def preset_info(
    pack_id: str = typer.Argument(..., help="Preset ID to get info about"),
):
    """Show detailed information about a preset."""
    from .extensions import normalize_priority
    from .presets import PresetCatalog, PresetManager, PresetError

    project_root = Path.cwd()

    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)

    # Check if installed locally first
    manager = PresetManager(project_root)
    local_pack = manager.get_pack(pack_id)

    if local_pack:
        console.print(f"\n[bold cyan]Preset: {local_pack.name}[/bold cyan]\n")
        console.print(f"  ID:          {local_pack.id}")
        console.print(f"  Version:     {local_pack.version}")
        console.print(f"  Description: {local_pack.description}")
        if local_pack.author:
            console.print(f"  Author:      {local_pack.author}")
        if local_pack.tags:
            console.print(f"  Tags:        {', '.join(local_pack.tags)}")
        console.print(f"  Templates:   {len(local_pack.templates)}")
        for tmpl in local_pack.templates:
            console.print(f"    - {tmpl['name']} ({tmpl['type']}): {tmpl.get('description', '')}")
        repo = local_pack.data.get("preset", {}).get("repository")
        if repo:
            console.print(f"  Repository:  {repo}")
        license_val = local_pack.data.get("preset", {}).get("license")
        if license_val:
            console.print(f"  License:     {license_val}")
        console.print("\n  [green]Status: installed[/green]")
        # Get priority from registry
        pack_metadata = manager.registry.get(pack_id)
        priority = normalize_priority(pack_metadata.get("priority") if isinstance(pack_metadata, dict) else None)
        console.print(f"  [dim]Priority:[/dim] {priority}")
        console.print()
        return

    # Fall back to catalog
    catalog = PresetCatalog(project_root)
    try:
        pack_info = catalog.get_pack_info(pack_id)
    except PresetError:
        pack_info = None

    if not pack_info:
        console.print(f"[red]Error:[/red] Preset '{pack_id}' not found (not installed and not in catalog)")
        raise typer.Exit(1)

    console.print(f"\n[bold cyan]Preset: {pack_info.get('name', pack_id)}[/bold cyan]\n")
    console.print(f"  ID:          {pack_info['id']}")
    console.print(f"  Version:     {pack_info.get('version', '?')}")
    console.print(f"  Description: {pack_info.get('description', '')}")
    if pack_info.get("author"):
        console.print(f"  Author:      {pack_info['author']}")
    if pack_info.get("tags"):
        console.print(f"  Tags:        {', '.join(pack_info['tags'])}")
    if pack_info.get("repository"):
        console.print(f"  Repository:  {pack_info['repository']}")
    if pack_info.get("license"):
        console.print(f"  License:     {pack_info['license']}")
    console.print("\n  [yellow]Status: not installed[/yellow]")
    console.print(f"  Install with: [cyan]specify preset add {pack_id}[/cyan]")
    console.print()


@preset_app.command("set-priority")
def preset_set_priority(
    pack_id: str = typer.Argument(help="Preset ID"),
    priority: int = typer.Argument(help="New priority (lower = higher precedence)"),
):
    """Set the resolution priority of an installed preset."""
    from .presets import PresetManager

    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)

    # Validate priority
    if priority < 1:
        console.print("[red]Error:[/red] Priority must be a positive integer (1 or higher)")
        raise typer.Exit(1)

    manager = PresetManager(project_root)

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

    # Get current metadata
    metadata = manager.registry.get(pack_id)
    if metadata is None or not isinstance(metadata, dict):
        console.print(f"[red]Error:[/red] Preset '{pack_id}' not found in registry (corrupted state)")
        raise typer.Exit(1)

    from .extensions import normalize_priority
    raw_priority = metadata.get("priority")
    # Only skip if the stored value is already a valid int equal to requested priority
    # This ensures corrupted values (e.g., "high") get repaired even when setting to default (10)
    if isinstance(raw_priority, int) and raw_priority == priority:
        console.print(f"[yellow]Preset '{pack_id}' already has priority {priority}[/yellow]")
        raise typer.Exit(0)

    old_priority = normalize_priority(raw_priority)

    # Update priority
    manager.registry.update(pack_id, {"priority": priority})

    console.print(f"[green]✓[/green] Preset '{pack_id}' priority changed: {old_priority} → {priority}")
    console.print("\n[dim]Lower priority = higher precedence in template resolution[/dim]")


@preset_app.command("enable")
def preset_enable(
    pack_id: str = typer.Argument(help="Preset ID to enable"),
):
    """Enable a disabled preset."""
    from .presets import PresetManager

    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 = PresetManager(project_root)

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

    # Get current metadata
    metadata = manager.registry.get(pack_id)
    if metadata is None or not isinstance(metadata, dict):
        console.print(f"[red]Error:[/red] Preset '{pack_id}' not found in registry (corrupted state)")
        raise typer.Exit(1)

    if metadata.get("enabled", True):
        console.print(f"[yellow]Preset '{pack_id}' is already enabled[/yellow]")
        raise typer.Exit(0)

    # Enable the preset
    manager.registry.update(pack_id, {"enabled": True})

    console.print(f"[green]✓[/green] Preset '{pack_id}' enabled")
    console.print("\nTemplates from this preset will now be included in resolution.")
    console.print("[dim]Note: Previously registered commands/skills remain active.[/dim]")


@preset_app.command("disable")
def preset_disable(
    pack_id: str = typer.Argument(help="Preset ID to disable"),
):
    """Disable a preset without removing it."""
    from .presets import PresetManager

    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 = PresetManager(project_root)

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

    # Get current metadata
    metadata = manager.registry.get(pack_id)
    if metadata is None or not isinstance(metadata, dict):
        console.print(f"[red]Error:[/red] Preset '{pack_id}' not found in registry (corrupted state)")
        raise typer.Exit(1)

    if not metadata.get("enabled", True):
        console.print(f"[yellow]Preset '{pack_id}' is already disabled[/yellow]")
        raise typer.Exit(0)

    # Disable the preset
    manager.registry.update(pack_id, {"enabled": False})

    console.print(f"[green]✓[/green] Preset '{pack_id}' disabled")
    console.print("\nTemplates from this preset will be skipped during resolution.")
    console.print("[dim]Note: Previously registered commands/skills remain active until preset removal.[/dim]")
    console.print(f"To re-enable: specify preset enable {pack_id}")


# ===== Preset Catalog Commands =====


@preset_catalog_app.command("list")
def preset_catalog_list():
    """List all active preset catalogs."""
    from .presets import PresetCatalog, PresetValidationError

    project_root = Path.cwd()

    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 = PresetCatalog(project_root)

    try:
        active_catalogs = catalog.get_active_catalogs()
    except PresetValidationError as e:
        console.print(f"[red]Error:[/red] {e}")
        raise typer.Exit(1)

    console.print("\n[bold cyan]Active Preset Catalogs:[/bold cyan]\n")
    for entry in active_catalogs:
        install_str = (
            "[green]install allowed[/green]"
            if entry.install_allowed
            else "[yellow]discovery only[/yellow]"
        )
        console.print(f"  [bold]{entry.name}[/bold] (priority {entry.priority})")
        if entry.description:
            console.print(f"     {entry.description}")
        console.print(f"     URL: {entry.url}")
        console.print(f"     Install: {install_str}")
        console.print()

    config_path = project_root / ".specify" / "preset-catalogs.yml"
    user_config_path = Path.home() / ".specify" / "preset-catalogs.yml"
    if os.environ.get("SPECKIT_PRESET_CATALOG_URL"):
        console.print("[dim]Catalog configured via SPECKIT_PRESET_CATALOG_URL environment variable.[/dim]")
    else:
        try:
            proj_loaded = config_path.exists() and catalog._load_catalog_config(config_path) is not None
        except PresetValidationError:
            proj_loaded = False
        if proj_loaded:
            console.print(f"[dim]Config: {config_path.relative_to(project_root)}[/dim]")
        else:
            try:
                user_loaded = user_config_path.exists() and catalog._load_catalog_config(user_config_path) is not None
            except PresetValidationError:
                user_loaded = False
            if user_loaded:
                console.print("[dim]Config: ~/.specify/preset-catalogs.yml[/dim]")
            else:
                console.print("[dim]Using built-in default catalog stack.[/dim]")
                console.print(
                    "[dim]Add .specify/preset-catalogs.yml to customize.[/dim]"
                )


@preset_catalog_app.command("add")
def preset_catalog_add(
    url: str = typer.Argument(help="Catalog URL (must use HTTPS)"),
    name: str = typer.Option(..., "--name", help="Catalog name"),
    priority: int = typer.Option(10, "--priority", help="Priority (lower = higher priority)"),
    install_allowed: bool = typer.Option(
        False, "--install-allowed/--no-install-allowed",
        help="Allow presets from this catalog to be installed",
    ),
    description: str = typer.Option("", "--description", help="Description of the catalog"),
):
    """Add a catalog to .specify/preset-catalogs.yml."""
    from .presets import PresetCatalog, PresetValidationError

    project_root = Path.cwd()

    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)

    # Validate URL
    tmp_catalog = PresetCatalog(project_root)
    try:
        tmp_catalog._validate_catalog_url(url)
    except PresetValidationError as e:
        console.print(f"[red]Error:[/red] {e}")
        raise typer.Exit(1)

    config_path = specify_dir / "preset-catalogs.yml"

    # Load existing config
    if config_path.exists():
        try:
            config = yaml.safe_load(config_path.read_text(encoding="utf-8")) or {}
        except Exception as e:
            console.print(f"[red]Error:[/red] Failed to read {config_path}: {e}")
            raise typer.Exit(1)
    else:
        config = {}

    catalogs = config.get("catalogs", [])
    if not isinstance(catalogs, list):
        console.print("[red]Error:[/red] Invalid catalog config: 'catalogs' must be a list.")
        raise typer.Exit(1)

    # Check for duplicate name
    for existing in catalogs:
        if isinstance(existing, dict) and existing.get("name") == name:
            console.print(f"[yellow]Warning:[/yellow] A catalog named '{name}' already exists.")
            console.print("Use 'specify preset catalog remove' first, or choose a different name.")
            raise typer.Exit(1)

    catalogs.append({
        "name": name,
        "url": url,
        "priority": priority,
        "install_allowed": install_allowed,
        "description": description,
    })

    config["catalogs"] = catalogs
    config_path.write_text(yaml.dump(config, default_flow_style=False, sort_keys=False, allow_unicode=True), encoding="utf-8")

    install_label = "install allowed" if install_allowed else "discovery only"
    console.print(f"\n[green]✓[/green] Added catalog '[bold]{name}[/bold]' ({install_label})")
    console.print(f"  URL: {url}")
    console.print(f"  Priority: {priority}")
    console.print(f"\nConfig saved to {config_path.relative_to(project_root)}")


@preset_catalog_app.command("remove")
def preset_catalog_remove(
    name: str = typer.Argument(help="Catalog name to remove"),
):
    """Remove a catalog from .specify/preset-catalogs.yml."""
    project_root = Path.cwd()

    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)

    config_path = specify_dir / "preset-catalogs.yml"
    if not config_path.exists():
        console.print("[red]Error:[/red] No preset catalog config found. Nothing to remove.")
        raise typer.Exit(1)

    try:
        config = yaml.safe_load(config_path.read_text(encoding="utf-8")) or {}
    except Exception:
        console.print("[red]Error:[/red] Failed to read preset catalog config.")
        raise typer.Exit(1)

    catalogs = config.get("catalogs", [])
    if not isinstance(catalogs, list):
        console.print("[red]Error:[/red] Invalid catalog config: 'catalogs' must be a list.")
        raise typer.Exit(1)
    original_count = len(catalogs)
    catalogs = [c for c in catalogs if isinstance(c, dict) and c.get("name") != name]

    if len(catalogs) == original_count:
        console.print(f"[red]Error:[/red] Catalog '{name}' not found.")
        raise typer.Exit(1)

    config["catalogs"] = catalogs
    config_path.write_text(yaml.dump(config, default_flow_style=False, sort_keys=False, allow_unicode=True), encoding="utf-8")

    console.print(f"[green]✓[/green] Removed catalog '{name}'")
    if not catalogs:
        console.print("\n[dim]No catalogs remain in config. Built-in defaults will be used.[/dim]")


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


def _resolve_installed_extension(
    argument: str,
    installed_extensions: list,
    command_name: str = "command",
    allow_not_found: bool = False,
) -> tuple[Optional[str], Optional[str]]:
    """Resolve an extension argument (ID or display name) to an installed extension.

    Args:
        argument: Extension ID or display name provided by user
        installed_extensions: List of installed extension dicts from manager.list_installed()
        command_name: Name of the command for error messages (e.g., "enable", "disable")
        allow_not_found: If True, return (None, None) when not found instead of raising

    Returns:
        Tuple of (extension_id, display_name), or (None, None) if allow_not_found=True and not found

    Raises:
        typer.Exit: If extension not found (and allow_not_found=False) or name is ambiguous
    """
    from rich.table import Table

    # First, try exact ID match
    for ext in installed_extensions:
        if ext["id"] == argument:
            return (ext["id"], ext["name"])

    # If not found by ID, try display name match
    name_matches = [ext for ext in installed_extensions if ext["name"].lower() == argument.lower()]

    if len(name_matches) == 1:
        # Unique display-name match
        return (name_matches[0]["id"], name_matches[0]["name"])
    elif len(name_matches) > 1:
        # Ambiguous display-name match
        console.print(
            f"[red]Error:[/red] Extension name '{argument}' is ambiguous. "
            "Multiple installed extensions share this name:"
        )
        table = Table(title="Matching extensions")
        table.add_column("ID", style="cyan", no_wrap=True)
        table.add_column("Name", style="white")
        table.add_column("Version", style="green")
        for ext in name_matches:
            table.add_row(ext.get("id", ""), ext.get("name", ""), str(ext.get("version", "")))
        console.print(table)
        console.print("\nPlease rerun using the extension ID:")
        console.print(f"  [bold]specify extension {command_name} <extension-id>[/bold]")
        raise typer.Exit(1)
    else:
        # No match by ID or display name
        if allow_not_found:
            return (None, None)
        console.print(f"[red]Error:[/red] Extension '{argument}' is not installed")
        raise typer.Exit(1)


def _resolve_catalog_extension(
    argument: str,
    catalog,
    command_name: str = "info",
) -> tuple[Optional[dict], Optional[Exception]]:
    """Resolve an extension argument (ID or display name) from the catalog.

    Args:
        argument: Extension ID or display name provided by user
        catalog: ExtensionCatalog instance
        command_name: Name of the command for error messages

    Returns:
        Tuple of (extension_info, catalog_error)
        - If found: (ext_info_dict, None)
        - If catalog error: (None, error)
        - If not found: (None, None)
    """
    from rich.table import Table
    from .extensions import ExtensionError

    try:
        # First try by ID
        ext_info = catalog.get_extension_info(argument)
        if ext_info:
            return (ext_info, None)

        # Try by display name - search using argument as query, then filter for exact match
        search_results = catalog.search(query=argument)
        name_matches = [ext for ext in search_results if ext["name"].lower() == argument.lower()]

        if len(name_matches) == 1:
            return (name_matches[0], None)
        elif len(name_matches) > 1:
            # Ambiguous display-name match in catalog
            console.print(
                f"[red]Error:[/red] Extension name '{argument}' is ambiguous. "
                "Multiple catalog extensions share this name:"
            )
            table = Table(title="Matching extensions")
            table.add_column("ID", style="cyan", no_wrap=True)
            table.add_column("Name", style="white")
            table.add_column("Version", style="green")
            table.add_column("Catalog", style="dim")
            for ext in name_matches:
                table.add_row(
                    ext.get("id", ""),
                    ext.get("name", ""),
                    str(ext.get("version", "")),
                    ext.get("_catalog_name", ""),
                )
            console.print(table)
            console.print("\nPlease rerun using the extension ID:")
            console.print(f"  [bold]specify extension {command_name} <extension-id>[/bold]")
            raise typer.Exit(1)

        # Not found
        return (None, None)

    except ExtensionError as e:
        return (None, e)


@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"     [dim]{ext['id']}[/dim]")
            console.print(f"     {ext['description']}")
            console.print(f"     Commands: {ext['command_count']} | Hooks: {ext['hook_count']} | Priority: {ext['priority']} | 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]")


@catalog_app.command("list")
def catalog_list():
    """List all active extension catalogs."""
    from .extensions import ExtensionCatalog, ValidationError

    project_root = Path.cwd()

    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:
        active_catalogs = catalog.get_active_catalogs()
    except ValidationError as e:
        console.print(f"[red]Error:[/red] {e}")
        raise typer.Exit(1)

    console.print("\n[bold cyan]Active Extension Catalogs:[/bold cyan]\n")
    for entry in active_catalogs:
        install_str = (
            "[green]install allowed[/green]"
            if entry.install_allowed
            else "[yellow]discovery only[/yellow]"
        )
        console.print(f"  [bold]{entry.name}[/bold] (priority {entry.priority})")
        if entry.description:
            console.print(f"     {entry.description}")
        console.print(f"     URL: {entry.url}")
        console.print(f"     Install: {install_str}")
        console.print()

    config_path = project_root / ".specify" / "extension-catalogs.yml"
    user_config_path = Path.home() / ".specify" / "extension-catalogs.yml"
    if os.environ.get("SPECKIT_CATALOG_URL"):
        console.print("[dim]Catalog configured via SPECKIT_CATALOG_URL environment variable.[/dim]")
    else:
        try:
            proj_loaded = config_path.exists() and catalog._load_catalog_config(config_path) is not None
        except ValidationError:
            proj_loaded = False
        if proj_loaded:
            console.print(f"[dim]Config: {config_path.relative_to(project_root)}[/dim]")
        else:
            try:
                user_loaded = user_config_path.exists() and catalog._load_catalog_config(user_config_path) is not None
            except ValidationError:
                user_loaded = False
            if user_loaded:
                console.print("[dim]Config: ~/.specify/extension-catalogs.yml[/dim]")
            else:
                console.print("[dim]Using built-in default catalog stack.[/dim]")
                console.print(
                    "[dim]Add .specify/extension-catalogs.yml to customize.[/dim]"
                )


@catalog_app.command("add")
def catalog_add(
    url: str = typer.Argument(help="Catalog URL (must use HTTPS)"),
    name: str = typer.Option(..., "--name", help="Catalog name"),
    priority: int = typer.Option(10, "--priority", help="Priority (lower = higher priority)"),
    install_allowed: bool = typer.Option(
        False, "--install-allowed/--no-install-allowed",
        help="Allow extensions from this catalog to be installed",
    ),
    description: str = typer.Option("", "--description", help="Description of the catalog"),
):
    """Add a catalog to .specify/extension-catalogs.yml."""
    from .extensions import ExtensionCatalog, ValidationError

    project_root = Path.cwd()

    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)

    # Validate URL
    tmp_catalog = ExtensionCatalog(project_root)
    try:
        tmp_catalog._validate_catalog_url(url)
    except ValidationError as e:
        console.print(f"[red]Error:[/red] {e}")
        raise typer.Exit(1)

    config_path = specify_dir / "extension-catalogs.yml"

    # Load existing config
    if config_path.exists():
        try:
            config = yaml.safe_load(config_path.read_text(encoding="utf-8")) or {}
        except Exception as e:
            console.print(f"[red]Error:[/red] Failed to read {config_path}: {e}")
            raise typer.Exit(1)
    else:
        config = {}

    catalogs = config.get("catalogs", [])
    if not isinstance(catalogs, list):
        console.print("[red]Error:[/red] Invalid catalog config: 'catalogs' must be a list.")
        raise typer.Exit(1)

    # Check for duplicate name
    for existing in catalogs:
        if isinstance(existing, dict) and existing.get("name") == name:
            console.print(f"[yellow]Warning:[/yellow] A catalog named '{name}' already exists.")
            console.print("Use 'specify extension catalog remove' first, or choose a different name.")
            raise typer.Exit(1)

    catalogs.append({
        "name": name,
        "url": url,
        "priority": priority,
        "install_allowed": install_allowed,
        "description": description,
    })

    config["catalogs"] = catalogs
    config_path.write_text(yaml.dump(config, default_flow_style=False, sort_keys=False, allow_unicode=True), encoding="utf-8")

    install_label = "install allowed" if install_allowed else "discovery only"
    console.print(f"\n[green]✓[/green] Added catalog '[bold]{name}[/bold]' ({install_label})")
    console.print(f"  URL: {url}")
    console.print(f"  Priority: {priority}")
    console.print(f"\nConfig saved to {config_path.relative_to(project_root)}")


@catalog_app.command("remove")
def catalog_remove(
    name: str = typer.Argument(help="Catalog name to remove"),
):
    """Remove a catalog from .specify/extension-catalogs.yml."""
    project_root = Path.cwd()

    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)

    config_path = specify_dir / "extension-catalogs.yml"
    if not config_path.exists():
        console.print("[red]Error:[/red] No catalog config found. Nothing to remove.")
        raise typer.Exit(1)

    try:
        config = yaml.safe_load(config_path.read_text(encoding="utf-8")) or {}
    except Exception:
        console.print("[red]Error:[/red] Failed to read catalog config.")
        raise typer.Exit(1)

    catalogs = config.get("catalogs", [])
    if not isinstance(catalogs, list):
        console.print("[red]Error:[/red] Invalid catalog config: 'catalogs' must be a list.")
        raise typer.Exit(1)
    original_count = len(catalogs)
    catalogs = [c for c in catalogs if isinstance(c, dict) and c.get("name") != name]

    if len(catalogs) == original_count:
        console.print(f"[red]Error:[/red] Catalog '{name}' not found.")
        raise typer.Exit(1)

    config["catalogs"] = catalogs
    config_path.write_text(yaml.dump(config, default_flow_style=False, sort_keys=False, allow_unicode=True), encoding="utf-8")

    console.print(f"[green]✓[/green] Removed catalog '{name}'")
    if not catalogs:
        console.print("\n[dim]No catalogs remain in config. Built-in defaults will be used.[/dim]")


@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"),
    priority: int = typer.Option(10, "--priority", help="Resolution priority (lower = higher precedence, default 10)"),
):
    """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)

    # Validate priority
    if priority < 1:
        console.print("[red]Error:[/red] Priority must be a positive integer (1 or higher)")
        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, priority=priority)

            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, priority=priority)
                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 (supports both ID and display name)
                ext_info, catalog_error = _resolve_catalog_extension(extension, catalog, "add")
                if catalog_error:
                    console.print(f"[red]Error:[/red] Could not query extension catalog: {catalog_error}")
                    raise typer.Exit(1)
                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)

                # Enforce install_allowed policy
                if not ext_info.get("_install_allowed", True):
                    catalog_name = ext_info.get("_catalog_name", "community")
                    console.print(
                        f"[red]Error:[/red] '{extension}' is available in the "
                        f"'{catalog_name}' catalog but installation is not allowed from that catalog."
                    )
                    console.print(
                        f"\nTo enable installation, add '{extension}' to an approved catalog "
                        f"(install_allowed: true) in .specify/extension-catalogs.yml."
                    )
                    raise typer.Exit(1)

                # Download extension ZIP (use resolved ID, not original argument which may be display name)
                extension_id = ext_info['id']
                console.print(f"Downloading {ext_info['name']} v{ext_info.get('version', 'unknown')}...")
                zip_path = catalog.download_extension(extension_id)

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

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

        # Report agent skills registration
        reg_meta = manager.registry.get(manifest.id)
        reg_skills = reg_meta.get("registered_skills", []) if reg_meta else []
        # Normalize to guard against corrupted registry entries
        if not isinstance(reg_skills, list):
            reg_skills = []
        if reg_skills:
            console.print(f"\n[green]✓[/green] {len(reg_skills)} agent skill(s) auto-registered")

        console.print("\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 or name 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)

    # Resolve extension ID from argument (handles ambiguous names)
    installed = manager.list_installed()
    extension_id, display_name = _resolve_installed_extension(extension, installed, "remove")

    # Get extension info for command and skill counts
    ext_manifest = manager.get_extension(extension_id)
    cmd_count = len(ext_manifest.commands) if ext_manifest else 0
    reg_meta = manager.registry.get(extension_id)
    raw_skills = reg_meta.get("registered_skills") if reg_meta else None
    skill_count = len(raw_skills) if isinstance(raw_skills, list) else 0

    # Confirm removal
    if not force:
        console.print("\n[yellow]⚠  This will remove:[/yellow]")
        console.print(f"   • {cmd_count} commands from AI agent")
        if skill_count:
            console.print(f"   • {skill_count} agent skill(s)")
        console.print(f"   • Extension directory: .specify/extensions/{extension_id}/")
        if not keep_config:
            console.print("   • 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_id, keep_config=keep_config)

    if success:
        console.print(f"\n[green]✓[/green] Extension '{display_name}' removed successfully")
        if keep_config:
            console.print(f"\nConfig files preserved in .specify/extensions/{extension_id}/")
        else:
            console.print(f"\nConfig files backed up to .specify/extensions/.backup/{extension_id}/")
        console.print(f"\nTo reinstall: specify extension add {extension_id}")
    else:
        console.print("[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}")

            # Source catalog
            catalog_name = ext.get("_catalog_name", "")
            install_allowed = ext.get("_install_allowed", True)
            if catalog_name:
                if install_allowed:
                    console.print(f"  [dim]Catalog:[/dim] {catalog_name}")
                else:
                    console.print(f"  [dim]Catalog:[/dim] {catalog_name} [yellow](discovery only — not installable)[/yellow]")

            # 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 (show warning if not installable)
            if install_allowed:
                console.print(f"\n  [cyan]Install:[/cyan] specify extension add {ext['id']}")
            else:
                console.print(f"\n  [yellow]⚠[/yellow]  Not directly installable from '{catalog_name}'.")
                console.print(
                    f"  Add to an approved catalog with install_allowed: true, "
                    f"or install from a ZIP URL: specify extension add {ext['id']} --from <zip-url>"
                )
            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, normalize_priority

    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)
    installed = manager.list_installed()

    # Try to resolve from installed extensions first (by ID or name)
    # Use allow_not_found=True since the extension may be catalog-only
    resolved_installed_id, resolved_installed_name = _resolve_installed_extension(
        extension, installed, "info", allow_not_found=True
    )

    # Try catalog lookup (with error handling)
    # If we resolved an installed extension by display name, use its ID for catalog lookup
    # to ensure we get the correct catalog entry (not a different extension with same name)
    lookup_key = resolved_installed_id if resolved_installed_id else extension
    ext_info, catalog_error = _resolve_catalog_extension(lookup_key, catalog, "info")

    # Case 1: Found in catalog - show full catalog info
    if ext_info:
        _print_extension_info(ext_info, manager)
        return

    # Case 2: Installed locally but catalog lookup failed or not in catalog
    if resolved_installed_id:
        # Get local manifest info
        ext_manifest = manager.get_extension(resolved_installed_id)
        metadata = manager.registry.get(resolved_installed_id)
        metadata_is_dict = isinstance(metadata, dict)
        if not metadata_is_dict:
            console.print(
                "[yellow]Warning:[/yellow] Extension metadata appears to be corrupted; "
                "some information may be unavailable."
            )
        version = metadata.get("version", "unknown") if metadata_is_dict else "unknown"

        console.print(f"\n[bold]{resolved_installed_name}[/bold] (v{version})")
        console.print(f"ID: {resolved_installed_id}")
        console.print()

        if ext_manifest:
            console.print(f"{ext_manifest.description}")
            console.print()
            # Author is optional in extension.yml, safely retrieve it
            author = ext_manifest.data.get("extension", {}).get("author")
            if author:
                console.print(f"[dim]Author:[/dim] {author}")
                console.print()

            if ext_manifest.commands:
                console.print("[bold]Commands:[/bold]")
                for cmd in ext_manifest.commands:
                    console.print(f"  • {cmd['name']}: {cmd.get('description', '')}")
                console.print()

        # Show catalog status
        if catalog_error:
            console.print(f"[yellow]Catalog unavailable:[/yellow] {catalog_error}")
            console.print("[dim]Note: Using locally installed extension; catalog info could not be verified.[/dim]")
        else:
            console.print("[yellow]Note:[/yellow] Not found in catalog (custom/local extension)")

        console.print()
        console.print("[green]✓ Installed[/green]")
        priority = normalize_priority(metadata.get("priority") if metadata_is_dict else None)
        console.print(f"[dim]Priority:[/dim] {priority}")
        console.print(f"\nTo remove: specify extension remove {resolved_installed_id}")
        return

    # Case 3: Not found anywhere
    if catalog_error:
        console.print(f"[red]Error:[/red] Could not query extension catalog: {catalog_error}")
        console.print("\nTry again when online, or use the extension ID directly.")
    else:
        console.print(f"[red]Error:[/red] Extension '{extension}' not found")
        console.print("\nTry: specify extension search")
    raise typer.Exit(1)


def _print_extension_info(ext_info: dict, manager):
    """Print formatted extension info from catalog data."""
    from .extensions import normalize_priority

    # 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')}")

    # Source catalog
    if ext_info.get("_catalog_name"):
        install_allowed = ext_info.get("_install_allowed", True)
        install_note = "" if install_allowed else " [yellow](discovery only)[/yellow]"
        console.print(f"[dim]Source catalog:[/dim] {ext_info['_catalog_name']}{install_note}")
    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'])
    install_allowed = ext_info.get("_install_allowed", True)
    if is_installed:
        console.print("[green]✓ Installed[/green]")
        metadata = manager.registry.get(ext_info['id'])
        priority = normalize_priority(metadata.get("priority") if isinstance(metadata, dict) else None)
        console.print(f"[dim]Priority:[/dim] {priority}")
        console.print(f"\nTo remove: specify extension remove {ext_info['id']}")
    elif install_allowed:
        console.print("[yellow]Not installed[/yellow]")
        console.print(f"\n[cyan]Install:[/cyan] specify extension add {ext_info['id']}")
    else:
        catalog_name = ext_info.get("_catalog_name", "community")
        console.print("[yellow]Not installed[/yellow]")
        console.print(
            f"\n[yellow]⚠[/yellow]  '{ext_info['id']}' is available in the '{catalog_name}' catalog "
            f"but not in your approved catalog. Add it to .specify/extension-catalogs.yml "
            f"with install_allowed: true to enable installation."
        )


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

    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)
    speckit_version = get_speckit_version()

    try:
        # Get list of extensions to update
        installed = manager.list_installed()
        if extension:
            # Update specific extension - resolve ID from argument (handles ambiguous names)
            extension_id, _ = _resolve_installed_extension(extension, installed, "update")
            extensions_to_update = [extension_id]
        else:
            # Update all extensions
            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)
            if metadata is None or not isinstance(metadata, dict) or "version" not in metadata:
                console.print(f"⚠  {ext_id}: Registry entry corrupted or missing (skipping)")
                continue
            try:
                installed_version = pkg_version.Version(metadata["version"])
            except pkg_version.InvalidVersion:
                console.print(
                    f"⚠  {ext_id}: Invalid installed version '{metadata.get('version')}' in registry (skipping)"
                )
                continue

            # 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

            # Check if installation is allowed from this catalog
            if not ext_info.get("_install_allowed", True):
                console.print(f"⚠  {ext_id}: Updates not allowed from '{ext_info.get('_catalog_name', 'catalog')}' (skipping)")
                continue

            try:
                catalog_version = pkg_version.Version(ext_info["version"])
            except pkg_version.InvalidVersion:
                console.print(
                    f"⚠  {ext_id}: Invalid catalog version '{ext_info.get('version')}' (skipping)"
                )
                continue

            if catalog_version > installed_version:
                updates_available.append(
                    {
                        "id": ext_id,
                        "name": ext_info.get("name", ext_id),  # Display name for status messages
                        "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 with atomic backup/restore
        console.print()
        updated_extensions = []
        failed_updates = []
        registrar = CommandRegistrar()
        hook_executor = HookExecutor(project_root)

        for update in updates_available:
            extension_id = update["id"]
            ext_name = update["name"]  # Use display name for user-facing messages
            console.print(f"📦 Updating {ext_name}...")

            # Backup paths
            backup_base = manager.extensions_dir / ".backup" / f"{extension_id}-update"
            backup_ext_dir = backup_base / "extension"
            backup_commands_dir = backup_base / "commands"
            backup_config_dir = backup_base / "config"

            # Store backup state
            backup_registry_entry = None
            backup_hooks = None  # None means no hooks key in config; {} means hooks key existed
            backed_up_command_files = {}

            try:
                # 1. Backup registry entry (always, even if extension dir doesn't exist)
                backup_registry_entry = manager.registry.get(extension_id)

                # 2. Backup extension directory
                extension_dir = manager.extensions_dir / extension_id
                if extension_dir.exists():
                    backup_base.mkdir(parents=True, exist_ok=True)
                    if backup_ext_dir.exists():
                        shutil.rmtree(backup_ext_dir)
                    shutil.copytree(extension_dir, backup_ext_dir)

                    # Backup config files separately so they can be restored
                    # after a successful install (install_from_directory clears dest dir).
                    config_files = list(extension_dir.glob("*-config.yml")) + list(
                        extension_dir.glob("*-config.local.yml")
                    )
                    for cfg_file in config_files:
                        backup_config_dir.mkdir(parents=True, exist_ok=True)
                        shutil.copy2(cfg_file, backup_config_dir / cfg_file.name)

                # 3. Backup command files for all agents
                registered_commands = backup_registry_entry.get("registered_commands", {})
                for agent_name, cmd_names in registered_commands.items():
                    if agent_name not in registrar.AGENT_CONFIGS:
                        continue
                    agent_config = registrar.AGENT_CONFIGS[agent_name]
                    commands_dir = project_root / agent_config["dir"]

                    for cmd_name in cmd_names:
                        cmd_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
                        if cmd_file.exists():
                            backup_cmd_path = backup_commands_dir / agent_name / cmd_file.name
                            backup_cmd_path.parent.mkdir(parents=True, exist_ok=True)
                            shutil.copy2(cmd_file, backup_cmd_path)
                            backed_up_command_files[str(cmd_file)] = str(backup_cmd_path)

                        # Also backup copilot prompt files
                        if agent_name == "copilot":
                            prompt_file = project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
                            if prompt_file.exists():
                                backup_prompt_path = backup_commands_dir / "copilot-prompts" / prompt_file.name
                                backup_prompt_path.parent.mkdir(parents=True, exist_ok=True)
                                shutil.copy2(prompt_file, backup_prompt_path)
                                backed_up_command_files[str(prompt_file)] = str(backup_prompt_path)

                # 4. Backup hooks from extensions.yml
                # Use backup_hooks=None to indicate config had no "hooks" key (don't create on restore)
                # Use backup_hooks={} to indicate config had "hooks" key with no hooks for this extension
                config = hook_executor.get_project_config()
                if "hooks" in config:
                    backup_hooks = {}  # Config has hooks key - preserve this fact
                    for hook_name, hook_list in config["hooks"].items():
                        ext_hooks = [h for h in hook_list if h.get("extension") == extension_id]
                        if ext_hooks:
                            backup_hooks[hook_name] = ext_hooks

                # 5. Download new version
                zip_path = catalog.download_extension(extension_id)
                try:
                    # 6. Validate extension ID from ZIP BEFORE modifying installation
                    # Handle both root-level and nested extension.yml (GitHub auto-generated ZIPs)
                    with zipfile.ZipFile(zip_path, "r") as zf:
                        import yaml
                        manifest_data = None
                        namelist = zf.namelist()

                        # First try root-level extension.yml
                        if "extension.yml" in namelist:
                            with zf.open("extension.yml") as f:
                                manifest_data = yaml.safe_load(f) or {}
                        else:
                            # Look for extension.yml in a single top-level subdirectory
                            # (e.g., "repo-name-branch/extension.yml")
                            manifest_paths = [n for n in namelist if n.endswith("/extension.yml") and n.count("/") == 1]
                            if len(manifest_paths) == 1:
                                with zf.open(manifest_paths[0]) as f:
                                    manifest_data = yaml.safe_load(f) or {}

                        if manifest_data is None:
                            raise ValueError("Downloaded extension archive is missing 'extension.yml'")

                    zip_extension_id = manifest_data.get("extension", {}).get("id")
                    if zip_extension_id != extension_id:
                        raise ValueError(
                            f"Extension ID mismatch: expected '{extension_id}', got '{zip_extension_id}'"
                        )

                    # 7. Remove old extension (handles command file cleanup and registry removal)
                    manager.remove(extension_id, keep_config=True)

                    # 8. Install new version
                    _ = manager.install_from_zip(zip_path, speckit_version)

                    # Restore user config files from backup after successful install.
                    new_extension_dir = manager.extensions_dir / extension_id
                    if backup_config_dir.exists() and new_extension_dir.exists():
                        for cfg_file in backup_config_dir.iterdir():
                            if cfg_file.is_file():
                                shutil.copy2(cfg_file, new_extension_dir / cfg_file.name)

                    # 9. Restore metadata from backup (installed_at, enabled state)
                    if backup_registry_entry and isinstance(backup_registry_entry, dict):
                        # Copy current registry entry to avoid mutating internal
                        # registry state before explicit restore().
                        current_metadata = manager.registry.get(extension_id)
                        if current_metadata is None or not isinstance(current_metadata, dict):
                            raise RuntimeError(
                                f"Registry entry for '{extension_id}' missing or corrupted after install — update incomplete"
                            )
                        new_metadata = dict(current_metadata)

                        # Preserve the original installation timestamp
                        if "installed_at" in backup_registry_entry:
                            new_metadata["installed_at"] = backup_registry_entry["installed_at"]

                        # Preserve the original priority (normalized to handle corruption)
                        if "priority" in backup_registry_entry:
                            new_metadata["priority"] = normalize_priority(backup_registry_entry["priority"])

                        # If extension was disabled before update, disable it again
                        if not backup_registry_entry.get("enabled", True):
                            new_metadata["enabled"] = False

                        # Use restore() instead of update() because update() always
                        # preserves the existing installed_at, ignoring our override
                        manager.registry.restore(extension_id, new_metadata)

                        # Also disable hooks in extensions.yml if extension was disabled
                        if not backup_registry_entry.get("enabled", True):
                            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_id:
                                            hook["enabled"] = False
                                hook_executor.save_project_config(config)
                finally:
                    # Clean up downloaded ZIP
                    if zip_path.exists():
                        zip_path.unlink()

                # 10. Clean up backup on success
                if backup_base.exists():
                    shutil.rmtree(backup_base)

                console.print(f"   [green]✓[/green] Updated to v{update['available']}")
                updated_extensions.append(ext_name)

            except KeyboardInterrupt:
                raise
            except Exception as e:
                console.print(f"   [red]✗[/red] Failed: {e}")
                failed_updates.append((ext_name, str(e)))

                # Rollback on failure
                console.print(f"   [yellow]↩[/yellow] Rolling back {ext_name}...")

                try:
                    # Restore extension directory
                    # Only perform destructive rollback if backup exists (meaning we
                    # actually modified the extension). This avoids deleting a valid
                    # installation when failure happened before changes were made.
                    extension_dir = manager.extensions_dir / extension_id
                    if backup_ext_dir.exists():
                        if extension_dir.exists():
                            shutil.rmtree(extension_dir)
                        shutil.copytree(backup_ext_dir, extension_dir)

                    # Remove any NEW command files created by failed install
                    # (files that weren't in the original backup)
                    try:
                        new_registry_entry = manager.registry.get(extension_id)
                        if new_registry_entry is None or not isinstance(new_registry_entry, dict):
                            new_registered_commands = {}
                        else:
                            new_registered_commands = new_registry_entry.get("registered_commands", {})
                        for agent_name, cmd_names in new_registered_commands.items():
                            if agent_name not in registrar.AGENT_CONFIGS:
                                continue
                            agent_config = registrar.AGENT_CONFIGS[agent_name]
                            commands_dir = project_root / agent_config["dir"]

                            for cmd_name in cmd_names:
                                cmd_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
                                # Delete if it exists and wasn't in our backup
                                if cmd_file.exists() and str(cmd_file) not in backed_up_command_files:
                                    cmd_file.unlink()

                                # Also handle copilot prompt files
                                if agent_name == "copilot":
                                    prompt_file = project_root / ".github" / "prompts" / f"{cmd_name}.prompt.md"
                                    if prompt_file.exists() and str(prompt_file) not in backed_up_command_files:
                                        prompt_file.unlink()
                    except KeyError:
                        pass  # No new registry entry exists, nothing to clean up

                    # Restore backed up command files
                    for original_path, backup_path in backed_up_command_files.items():
                        backup_file = Path(backup_path)
                        if backup_file.exists():
                            original_file = Path(original_path)
                            original_file.parent.mkdir(parents=True, exist_ok=True)
                            shutil.copy2(backup_file, original_file)

                    # Restore hooks in extensions.yml
                    # - backup_hooks=None means original config had no "hooks" key
                    # - backup_hooks={} or {...} means config had hooks key
                    config = hook_executor.get_project_config()
                    if "hooks" in config:
                        modified = False

                        if backup_hooks is None:
                            # Original config had no "hooks" key; remove it entirely
                            del config["hooks"]
                            modified = True
                        else:
                            # Remove any hooks for this extension added by failed install
                            for hook_name, hooks_list in config["hooks"].items():
                                original_len = len(hooks_list)
                                config["hooks"][hook_name] = [
                                    h for h in hooks_list
                                    if h.get("extension") != extension_id
                                ]
                                if len(config["hooks"][hook_name]) != original_len:
                                    modified = True

                            # Add back the backed up hooks if any
                            if backup_hooks:
                                for hook_name, hooks in backup_hooks.items():
                                    if hook_name not in config["hooks"]:
                                        config["hooks"][hook_name] = []
                                    config["hooks"][hook_name].extend(hooks)
                                    modified = True

                        if modified:
                            hook_executor.save_project_config(config)

                    # Restore registry entry (use restore() since entry was removed)
                    if backup_registry_entry:
                        manager.registry.restore(extension_id, backup_registry_entry)

                    console.print("   [green]✓[/green] Rollback successful")
                    # Clean up backup directory only on successful rollback
                    if backup_base.exists():
                        shutil.rmtree(backup_base)
                except Exception as rollback_error:
                    console.print(f"   [red]✗[/red] Rollback failed: {rollback_error}")
                    console.print(f"   [dim]Backup preserved at: {backup_base}[/dim]")

        # Summary
        console.print()
        if updated_extensions:
            console.print(f"[green]✓[/green] Successfully updated {len(updated_extensions)} extension(s)")
        if failed_updates:
            console.print(f"[red]✗[/red] Failed to update {len(failed_updates)} extension(s):")
            for ext_name, error in failed_updates:
                console.print(f"   • {ext_name}: {error}")
            raise typer.Exit(1)

    except ValidationError as e:
        console.print(f"\n[red]Validation 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("enable")
def extension_enable(
    extension: str = typer.Argument(help="Extension ID or name 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)

    # Resolve extension ID from argument (handles ambiguous names)
    installed = manager.list_installed()
    extension_id, display_name = _resolve_installed_extension(extension, installed, "enable")

    # Update registry
    metadata = manager.registry.get(extension_id)
    if metadata is None or not isinstance(metadata, dict):
        console.print(f"[red]Error:[/red] Extension '{extension_id}' not found in registry (corrupted state)")
        raise typer.Exit(1)

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

    manager.registry.update(extension_id, {"enabled": True})

    # 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_id:
                    hook["enabled"] = True
        hook_executor.save_project_config(config)

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


@extension_app.command("disable")
def extension_disable(
    extension: str = typer.Argument(help="Extension ID or name 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)

    # Resolve extension ID from argument (handles ambiguous names)
    installed = manager.list_installed()
    extension_id, display_name = _resolve_installed_extension(extension, installed, "disable")

    # Update registry
    metadata = manager.registry.get(extension_id)
    if metadata is None or not isinstance(metadata, dict):
        console.print(f"[red]Error:[/red] Extension '{extension_id}' not found in registry (corrupted state)")
        raise typer.Exit(1)

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

    manager.registry.update(extension_id, {"enabled": False})

    # 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_id:
                    hook["enabled"] = False
        hook_executor.save_project_config(config)

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


@extension_app.command("set-priority")
def extension_set_priority(
    extension: str = typer.Argument(help="Extension ID or name"),
    priority: int = typer.Argument(help="New priority (lower = higher precedence)"),
):
    """Set the resolution priority of an installed 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)

    # Validate priority
    if priority < 1:
        console.print("[red]Error:[/red] Priority must be a positive integer (1 or higher)")
        raise typer.Exit(1)

    manager = ExtensionManager(project_root)

    # Resolve extension ID from argument (handles ambiguous names)
    installed = manager.list_installed()
    extension_id, display_name = _resolve_installed_extension(extension, installed, "set-priority")

    # Get current metadata
    metadata = manager.registry.get(extension_id)
    if metadata is None or not isinstance(metadata, dict):
        console.print(f"[red]Error:[/red] Extension '{extension_id}' not found in registry (corrupted state)")
        raise typer.Exit(1)

    from .extensions import normalize_priority
    raw_priority = metadata.get("priority")
    # Only skip if the stored value is already a valid int equal to requested priority
    # This ensures corrupted values (e.g., "high") get repaired even when setting to default (10)
    if isinstance(raw_priority, int) and raw_priority == priority:
        console.print(f"[yellow]Extension '{display_name}' already has priority {priority}[/yellow]")
        raise typer.Exit(0)

    old_priority = normalize_priority(raw_priority)

    # Update priority
    manager.registry.update(extension_id, {"priority": priority})

    console.print(f"[green]✓[/green] Extension '{display_name}' priority changed: {old_priority} → {priority}")
    console.print("\n[dim]Lower priority = higher precedence in template resolution[/dim]")


def main():
    app()

if __name__ == "__main__":
    main()