mcp-vector-search 0.12.6__py3-none-any.whl → 1.1.22__py3-none-any.whl

mcp_vector_search/cli/commands/setup.py

@@ -0,0 +1,1184 @@
+"""Smart zero-config setup command for MCP Vector Search CLI.
+
+This module provides a zero-configuration setup command that intelligently detects
+project characteristics and configures everything automatically:
+
+1. Detects project root and characteristics
+2. Scans for file types in use (with timeout)
+3. Detects installed MCP platforms
+4. Initializes with optimal defaults
+5. Indexes codebase
+6. Configures all detected MCP platforms
+7. Sets up file watching
+
+Examples:
+    # Zero-config setup (recommended)
+    $ mcp-vector-search setup
+
+    # Force re-setup
+    $ mcp-vector-search setup --force
+
+    # Verbose output for debugging
+    $ mcp-vector-search setup --verbose
+"""
+
+import asyncio
+import os
+import shutil
+import subprocess
+import time
+from pathlib import Path
+
+import typer
+from loguru import logger
+
+# Import Platform enum to filter excluded platforms
+from py_mcp_installer import Platform
+from rich.console import Console
+from rich.panel import Panel
+
+from ...config.defaults import (
+    DEFAULT_EMBEDDING_MODELS,
+    DEFAULT_FILE_EXTENSIONS,
+    get_language_from_extension,
+)
+from ...core.exceptions import ProjectInitializationError
+from ...core.project import ProjectManager
+from ..didyoumean import create_enhanced_typer
+from ..output import (
+    print_error,
+    print_info,
+    print_next_steps,
+    print_success,
+    print_warning,
+)
+
+# Import functions from refactored install module
+from .install import _install_to_platform, detect_all_platforms
+
+# Platforms to exclude from auto-setup (user can still manually install)
+EXCLUDED_PLATFORMS_FROM_SETUP = {Platform.CLAUDE_DESKTOP}
+
+# Create console for rich output
+console = Console()
+
+# Create setup app
+setup_app = create_enhanced_typer(
+    help="""🚀 Smart zero-config setup for mcp-vector-search
+
+[bold cyan]What it does:[/bold cyan]
+  ✅ Auto-detects your project's languages and file types
+  ✅ Initializes semantic search with optimal settings
+  ✅ Indexes your entire codebase
+  ✅ Configures ALL installed MCP platforms
+  ✅ Sets up automatic file watching
+  ✅ No configuration needed - just run it!
+
+[bold cyan]Perfect for:[/bold cyan]
+  • Getting started quickly in any project
+  • Team onboarding (commit .mcp.json to repo)
+  • Setting up multiple MCP platforms at once
+  • Letting AI tools handle the configuration
+
+[dim]💡 This is the recommended way to set up mcp-vector-search[/dim]
+""",
+    invoke_without_command=True,
+    no_args_is_help=False,
+)
+
+
+# ==============================================================================
+# Helper Functions
+# ==============================================================================
+
+
+def check_claude_cli_available() -> bool:
+    """Check if Claude CLI is available.
+
+    Returns:
+        True if claude CLI is installed and accessible
+    """
+    return shutil.which("claude") is not None
+
+
+def check_uv_available() -> bool:
+    """Check if uv is available.
+
+    Returns:
+        True if uv is installed and accessible
+    """
+    return shutil.which("uv") is not None
+
+
+def register_with_claude_cli(
+    project_root: Path,
+    server_name: str = "mcp-vector-search",
+    enable_watch: bool = True,
+    verbose: bool = False,
+) -> bool:
+    """Register MCP server with Claude CLI using native 'claude mcp add' command.
+
+    Args:
+        project_root: Project root directory
+        server_name: Name for the MCP server entry (default: "mcp-vector-search")
+        enable_watch: Enable file watching
+        verbose: Show verbose output
+
+    Returns:
+        True if registration was successful, False otherwise
+    """
+    try:
+        # Check if mcp-vector-search command is available first
+        # This ensures we work with pipx/homebrew installations, not just uv
+        if not shutil.which("mcp-vector-search"):
+            if verbose:
+                print_warning(
+                    "  ⚠️  mcp-vector-search command not in PATH, will use manual JSON configuration"
+                )
+            return False
+
+        # First, try to remove existing server (safe to ignore if doesn't exist)
+        # This ensures clean registration when server already exists
+        remove_cmd = ["claude", "mcp", "remove", server_name]
+
+        if verbose:
+            print_info("  Checking for existing MCP server registration...")
+
+        subprocess.run(
+            remove_cmd,
+            capture_output=True,
+            text=True,
+            timeout=10,
+        )
+        # Ignore result - it's OK if server doesn't exist
+
+        # Build the add command using mcp-vector-search CLI
+        # This works for all installation methods: pipx, homebrew, and uv
+        # Claude Code sets CWD to the project directory, so no path needed
+        # claude mcp add --transport stdio mcp-vector-search \
+        #   --env MCP_ENABLE_FILE_WATCHING=true \
+        #   -- mcp-vector-search mcp
+        cmd = [
+            "claude",
+            "mcp",
+            "add",
+            "--transport",
+            "stdio",
+            server_name,
+            "--env",
+            f"MCP_ENABLE_FILE_WATCHING={'true' if enable_watch else 'false'}",
+            "--",
+            "mcp-vector-search",
+            "mcp",
+        ]
+
+        if verbose:
+            print_info(f"  Running: {' '.join(cmd)}")
+
+        # Run the add command
+        result = subprocess.run(
+            cmd,
+            capture_output=True,
+            text=True,
+            timeout=30,
+        )
+
+        if result.returncode == 0:
+            print_success("  ✅ Registered with Claude CLI")
+            if verbose:
+                print_info("     Command: claude mcp add mcp")
+            return True
+        else:
+            if verbose:
+                print_warning(f"  ⚠️  Claude CLI registration failed: {result.stderr}")
+            return False
+
+    except subprocess.TimeoutExpired:
+        logger.warning("Claude CLI registration timed out")
+        if verbose:
+            print_warning("  ⚠️  Claude CLI command timed out")
+        return False
+    except Exception as e:
+        logger.warning(f"Claude CLI registration failed: {e}")
+        if verbose:
+            print_warning(f"  ⚠️  Claude CLI error: {e}")
+        return False
+
+
+def scan_project_file_extensions(
+    project_root: Path,
+    timeout: float = 2.0,
+) -> list[str] | None:
+    """Scan project for unique file extensions with timeout.
+
+    This function quickly scans the project to find which file extensions are
+    actually in use, allowing for more targeted indexing. If the scan takes too
+    long (e.g., very large codebase), it times out and returns None to use defaults.
+
+    Args:
+        project_root: Project root directory to scan
+        timeout: Maximum time in seconds to spend scanning (default: 2.0)
+
+    Returns:
+        Sorted list of file extensions found (e.g., ['.py', '.js', '.md'])
+        or None if scan timed out or failed
+    """
+    extensions: set[str] = set()
+    start_time = time.time()
+    file_count = 0
+
+    try:
+        # Create project manager to get gitignore patterns
+        project_manager = ProjectManager(project_root)
+
+        for path in project_root.rglob("*"):
+            # Check timeout
+            if time.time() - start_time > timeout:
+                logger.debug(
+                    f"File extension scan timed out after {timeout}s "
+                    f"({file_count} files scanned)"
+                )
+                return None
+
+            # Skip directories
+            if not path.is_file():
+                continue
+
+            # Skip ignored paths
+            if project_manager._should_ignore_path(path, is_directory=False):
+                continue
+
+            # Get extension
+            ext = path.suffix
+            if ext:
+                # Only include extensions we know about (in language mappings)
+                language = get_language_from_extension(ext)
+                if language != "text" or ext in [".txt", ".md", ".rst"]:
+                    extensions.add(ext)
+
+            file_count += 1
+
+        elapsed = time.time() - start_time
+        logger.debug(
+            f"File extension scan completed in {elapsed:.2f}s "
+            f"({file_count} files, {len(extensions)} extensions found)"
+        )
+
+        return sorted(extensions) if extensions else None
+
+    except Exception as e:
+        logger.debug(f"File extension scan failed: {e}")
+        return None
+
+
+def select_optimal_embedding_model(languages: list[str]) -> str:
+    """Select the best embedding model based on detected languages.
+
+    Args:
+        languages: List of detected language names
+
+    Returns:
+        Name of optimal embedding model
+    """
+    # For code-heavy projects, use code-optimized model
+    if languages:
+        code_languages = {"python", "javascript", "typescript", "java", "go", "rust"}
+        detected_set = {lang.lower() for lang in languages}
+
+        if detected_set & code_languages:
+            return DEFAULT_EMBEDDING_MODELS["code"]
+
+    # Default to general-purpose model
+    return DEFAULT_EMBEDDING_MODELS["code"]
+
+
+def _obfuscate_api_key(api_key: str) -> str:
+    """Obfuscate API key for display.
+
+    Shows first 6 characters + "..." + last 4 characters.
+    For short keys (<10 chars), shows "****...1234".
+
+    Args:
+        api_key: API key to obfuscate
+
+    Returns:
+        Obfuscated string like "sk-or-...abc1234" or "****...1234"
+    """
+    if not api_key:
+        return "****"
+
+    if len(api_key) < 10:
+        # Short key - show masked prefix
+        return f"****...{api_key[-4:]}"
+
+    # Full key - show first 6 + last 4
+    return f"{api_key[:6]}...{api_key[-4:]}"
+
+
+def setup_llm_api_keys(project_root: Path, interactive: bool = True) -> bool:
+    """Check and optionally set up LLM API keys (OpenAI or OpenRouter) for chat command.
+
+    This function checks for API keys in environment and config file.
+    In interactive mode, prompts user to configure either provider.
+
+    Args:
+        project_root: Project root directory
+        interactive: Whether to prompt for API key input
+
+    Returns:
+        True if at least one API key is configured, False otherwise
+    """
+    from ...core.config_utils import (
+        delete_openai_api_key,
+        delete_openrouter_api_key,
+        get_config_file_path,
+        get_openai_api_key,
+        get_openrouter_api_key,
+        get_preferred_llm_provider,
+        save_openai_api_key,
+        save_openrouter_api_key,
+        save_preferred_llm_provider,
+    )
+
+    config_dir = project_root / ".mcp-vector-search"
+
+    # Check if API keys are already available
+    openai_key = get_openai_api_key(config_dir)
+    openrouter_key = get_openrouter_api_key(config_dir)
+    preferred_provider = get_preferred_llm_provider(config_dir)
+
+    openai_from_env = bool(os.environ.get("OPENAI_API_KEY"))
+    openrouter_from_env = bool(os.environ.get("OPENROUTER_API_KEY"))
+
+    has_any_key = bool(openai_key or openrouter_key)
+
+    # Non-interactive mode: just report status
+    if not interactive:
+        if has_any_key:
+            print_success("   ✅ LLM API key(s) found")
+            if openai_key:
+                source = (
+                    "Environment variable"
+                    if openai_from_env
+                    else f"Config file ({get_config_file_path(config_dir)})"
+                )
+                print_info(f"      OpenAI: ends with {openai_key[-4:]} ({source})")
+            if openrouter_key:
+                source = (
+                    "Environment variable"
+                    if openrouter_from_env
+                    else f"Config file ({get_config_file_path(config_dir)})"
+                )
+                print_info(
+                    f"      OpenRouter: ends with {openrouter_key[-4:]} ({source})"
+                )
+            if preferred_provider:
+                print_info(f"      Preferred provider: {preferred_provider}")
+            print_info("      Chat command is ready to use!")
+            return True
+        else:
+            print_info("   ℹ️  No LLM API keys found")
+            print_info("")
+            print_info(
+                "   The 'chat' command uses AI to answer questions about your code."
+            )
+            print_info("")
+            print_info("   [bold cyan]To enable the chat command:[/bold cyan]")
+            print_info("   [cyan]Option A - OpenAI (recommended):[/cyan]")
+            print_info(
+                "   1. Get a key: [cyan]https://platform.openai.com/api-keys[/cyan]"
+            )
+            print_info("   2. [yellow]export OPENAI_API_KEY='your-key'[/yellow]")
+            print_info("")
+            print_info("   [cyan]Option B - OpenRouter:[/cyan]")
+            print_info("   1. Get a key: [cyan]https://openrouter.ai/keys[/cyan]")
+            print_info("   2. [yellow]export OPENROUTER_API_KEY='your-key'[/yellow]")
+            print_info("")
+            print_info("   Or run: [yellow]mcp-vector-search setup[/yellow]")
+            print_info("")
+            print_info(
+                "   [dim]💡 You can skip this for now - search still works![/dim]"
+            )
+            return False
+
+    # Interactive mode - prompt for API key setup
+    print_info("")
+    print_info("   [bold cyan]LLM API Key Setup[/bold cyan]")
+    print_info("")
+    print_info("   The 'chat' command uses AI to answer questions about your code.")
+    print_info("   You can use OpenAI or OpenRouter (or both).")
+    print_info("")
+
+    # Show current status
+    if openai_key or openrouter_key:
+        print_info("   [bold]Current Configuration:[/bold]")
+        if openai_key:
+            obfuscated = _obfuscate_api_key(openai_key)
+            source = "environment variable" if openai_from_env else "config file"
+            print_info(f"   • OpenAI: {obfuscated} [dim]({source})[/dim]")
+        else:
+            print_info("   • OpenAI: [dim]not configured[/dim]")
+
+        if openrouter_key:
+            obfuscated = _obfuscate_api_key(openrouter_key)
+            source = "environment variable" if openrouter_from_env else "config file"
+            print_info(f"   • OpenRouter: {obfuscated} [dim]({source})[/dim]")
+        else:
+            print_info("   • OpenRouter: [dim]not configured[/dim]")
+
+        if preferred_provider:
+            print_info(f"   • Preferred: [cyan]{preferred_provider}[/cyan]")
+        print_info("")
+
+    print_info("   [bold cyan]Options:[/bold cyan]")
+    print_info("   1. Configure OpenAI (recommended, fast & cheap)")
+    print_info("   2. Configure OpenRouter")
+    print_info("   3. Set preferred provider")
+    print_info("   4. Skip / Keep current")
+    print_info("")
+
+    try:
+        from ..output import console
+
+        choice = console.input("   [yellow]Select option (1-4): [/yellow]").strip()
+
+        if choice == "1":
+            # Configure OpenAI
+            return _setup_single_provider(
+                provider="openai",
+                existing_key=openai_key,
+                is_from_env=openai_from_env,
+                config_dir=config_dir,
+                save_func=save_openai_api_key,
+                delete_func=delete_openai_api_key,
+                get_key_url="https://platform.openai.com/api-keys",
+            )
+
+        elif choice == "2":
+            # Configure OpenRouter
+            return _setup_single_provider(
+                provider="openrouter",
+                existing_key=openrouter_key,
+                is_from_env=openrouter_from_env,
+                config_dir=config_dir,
+                save_func=save_openrouter_api_key,
+                delete_func=delete_openrouter_api_key,
+                get_key_url="https://openrouter.ai/keys",
+            )
+
+        elif choice == "3":
+            # Set preferred provider
+            if not has_any_key:
+                print_warning("   ⚠️  Configure at least one API key first")
+                return False
+
+            print_info("")
+            print_info("   [bold]Select preferred provider:[/bold]")
+            providers = []
+            if openai_key:
+                providers.append("openai")
+                print_info("   1. OpenAI")
+            if openrouter_key:
+                providers.append("openrouter")
+                idx = len(providers)
+                print_info(f"   {idx}. OpenRouter")
+
+            pref_choice = console.input(
+                f"\n   [yellow]Select (1-{len(providers)}): [/yellow]"
+            ).strip()
+
+            try:
+                idx = int(pref_choice) - 1
+                if 0 <= idx < len(providers):
+                    selected_provider = providers[idx]
+                    save_preferred_llm_provider(selected_provider, config_dir)
+                    print_success(
+                        f"   ✅ Preferred provider set to: {selected_provider}"
+                    )
+                    return True
+                else:
+                    print_warning("   ⚠️  Invalid selection")
+                    return has_any_key
+            except ValueError:
+                print_warning("   ⚠️  Invalid input")
+                return has_any_key
+
+        elif choice == "4" or not choice:
+            # Skip / Keep current
+            if has_any_key:
+                print_info("   ⏭️  Keeping existing configuration")
+                return True
+            else:
+                print_info("   ⏭️  Skipped LLM API key setup")
+                return False
+
+        else:
+            print_warning("   ⚠️  Invalid option")
+            return has_any_key
+
+    except KeyboardInterrupt:
+        print_info("\n   ⏭️  API key setup cancelled")
+        return has_any_key
+    except Exception as e:
+        logger.error(f"Error during API key setup: {e}")
+        print_error(f"   ❌ Error: {e}")
+        return has_any_key
+
+
+def _setup_single_provider(
+    provider: str,
+    existing_key: str | None,
+    is_from_env: bool,
+    config_dir: Path,
+    save_func,
+    delete_func,
+    get_key_url: str,
+) -> bool:
+    """Helper function to set up a single LLM provider.
+
+    Args:
+        provider: Provider name ('openai' or 'openrouter')
+        existing_key: Existing API key if any
+        is_from_env: Whether existing key is from environment
+        config_dir: Config directory path
+        save_func: Function to save API key
+        delete_func: Function to delete API key
+        get_key_url: URL to get API key
+
+    Returns:
+        True if provider is configured, False otherwise
+    """
+    from ..output import console
+
+    provider_display = provider.capitalize()
+
+    print_info("")
+    print_info(f"   [bold cyan]{provider_display} API Key Setup[/bold cyan]")
+    print_info("")
+
+    if not existing_key:
+        print_info(f"   Get a key: [cyan]{get_key_url}[/cyan]")
+        print_info("")
+
+    # Show current status
+    if existing_key:
+        obfuscated = _obfuscate_api_key(existing_key)
+        source = "environment variable" if is_from_env else "config file"
+        print_info(f"   Current: {obfuscated} [dim]({source})[/dim]")
+        if is_from_env:
+            print_info("   [dim]Note: Environment variable takes precedence[/dim]")
+        print_info("")
+
+    print_info("   [dim]Options:[/dim]")
+    if existing_key:
+        print_info("   [dim]• Press Enter to keep existing key[/dim]")
+    else:
+        print_info("   [dim]• Press Enter to skip[/dim]")
+    print_info("   [dim]• Enter new key to update[/dim]")
+    if existing_key and not is_from_env:
+        print_info("   [dim]• Type 'clear' to remove from config[/dim]")
+    print_info("")
+
+    try:
+        if existing_key:
+            obfuscated = _obfuscate_api_key(existing_key)
+            prompt_text = (
+                f"   [yellow]{provider_display} API key [{obfuscated}]: [/yellow]"
+            )
+        else:
+            prompt_text = (
+                f"   [yellow]{provider_display} API key (Enter to skip): [/yellow]"
+            )
+
+        user_input = console.input(prompt_text).strip()
+
+        # Handle different inputs
+        if not user_input:
+            # Empty input - keep existing or skip
+            if existing_key:
+                print_info("   ⏭️  Keeping existing API key")
+                return True
+            else:
+                print_info("   ⏭️  Skipped")
+                return False
+
+        elif user_input.lower() in ("clear", "delete", "remove"):
+            # Clear the API key
+            if not existing_key:
+                print_warning("   ⚠️  No API key to clear")
+                return False
+
+            if is_from_env:
+                print_warning("   ⚠️  Cannot clear environment variable from config")
+                return True
+
+            # Delete from config file
+            try:
+                deleted = delete_func(config_dir)
+                if deleted:
+                    print_success("   ✅ API key removed from config")
+                    return False
+                else:
+                    print_warning("   ⚠️  API key not found in config")
+                    return False
+            except Exception as e:
+                print_error(f"   ❌ Failed to delete API key: {e}")
+                return False
+
+        else:
+            # New API key provided
+            try:
+                save_func(user_input, config_dir)
+                from ...core.config_utils import get_config_file_path
+
+                config_path = get_config_file_path(config_dir)
+                print_success(f"   ✅ API key saved to {config_path}")
+                print_info(f"      Last 4 characters: {user_input[-4:]}")
+
+                if is_from_env:
+                    print_warning("")
+                    print_warning(
+                        "   ⚠️  Note: Environment variable will still take precedence"
+                    )
+
+                return True
+            except Exception as e:
+                print_error(f"   ❌ Failed to save API key: {e}")
+                return False
+
+    except KeyboardInterrupt:
+        print_info("\n   ⏭️  Setup cancelled")
+        return bool(existing_key)
+    except Exception as e:
+        logger.error(f"Error during {provider} setup: {e}")
+        print_error(f"   ❌ Error: {e}")
+        return bool(existing_key)
+
+
+def setup_openrouter_api_key(project_root: Path, interactive: bool = True) -> bool:
+    """Check and optionally set up OpenRouter API key for chat command.
+
+    This function checks for API key in environment and config file.
+    In interactive mode, always prompts user with existing value as default.
+
+    Args:
+        project_root: Project root directory
+        interactive: Whether to prompt for API key input
+
+    Returns:
+        True if API key is configured, False otherwise
+    """
+    from ...core.config_utils import (
+        delete_openrouter_api_key,
+        get_config_file_path,
+        get_openrouter_api_key,
+        save_openrouter_api_key,
+    )
+
+    config_dir = project_root / ".mcp-vector-search"
+
+    # Check if API key is already available
+    existing_api_key = get_openrouter_api_key(config_dir)
+    is_from_env = bool(os.environ.get("OPENROUTER_API_KEY"))
+
+    # Show current status
+    if existing_api_key and not interactive:
+        # Non-interactive: just report status
+        print_success(
+            f"   ✅ OpenRouter API key found (ends with {existing_api_key[-4:]})"
+        )
+
+        # Check where it came from
+        if is_from_env:
+            print_info("      Source: Environment variable")
+        else:
+            config_path = get_config_file_path(config_dir)
+            print_info(f"      Source: Config file ({config_path})")
+
+        print_info("      Chat command is ready to use!")
+        return True
+
+    if not interactive:
+        # No key found and not interactive
+        print_info("   ℹ️  OpenRouter API key not found")
+        print_info("")
+        print_info("   The 'chat' command uses AI to answer questions about your code.")
+        print_info("   It requires an OpenRouter API key (free tier available).")
+        print_info("")
+        print_info("   [bold cyan]To enable the chat command:[/bold cyan]")
+        print_info("   1. Get a free API key: [cyan]https://openrouter.ai/keys[/cyan]")
+        print_info("   2. Option A - Environment variable (recommended for security):")
+        print_info("      [yellow]export OPENROUTER_API_KEY='your-key-here'[/yellow]")
+        print_info("   3. Option B - Save to local config (convenient):")
+        print_info("      [yellow]mcp-vector-search setup[/yellow]")
+        print_info("")
+        print_info("   [dim]💡 You can skip this for now - search still works![/dim]")
+        return False
+
+    # Interactive mode - always prompt with existing value as default
+    print_info("")
+    print_info("   [bold cyan]OpenRouter API Key Setup[/bold cyan]")
+    print_info("")
+    print_info("   The 'chat' command uses AI to answer questions about your code.")
+    print_info("   It requires an OpenRouter API key (free tier available).")
+    print_info("")
+
+    if not existing_api_key:
+        print_info("   Get a free API key: [cyan]https://openrouter.ai/keys[/cyan]")
+
+    # Show current status
+    if existing_api_key:
+        obfuscated = _obfuscate_api_key(existing_api_key)
+        if is_from_env:
+            print_info(
+                f"   Current: {obfuscated} [dim](from environment variable)[/dim]"
+            )
+            print_info(
+                "   [dim]Note: Environment variable takes precedence over config file[/dim]"
+            )
+        else:
+            print_info(f"   Current: {obfuscated} [dim](from config file)[/dim]")
+
+    print_info("")
+    print_info("   [dim]Options:[/dim]")
+    print_info(
+        "   [dim]• Press Enter to keep existing key (no change)[/dim]"
+        if existing_api_key
+        else "   [dim]• Press Enter to skip[/dim]"
+    )
+    print_info("   [dim]• Enter new key to update[/dim]")
+    if existing_api_key and not is_from_env:
+        print_info("   [dim]• Type 'clear' or 'delete' to remove from config[/dim]")
+    print_info("")
+
+    try:
+        # Prompt for API key with obfuscated default
+        from ..output import console
+
+        if existing_api_key:
+            obfuscated = _obfuscate_api_key(existing_api_key)
+            prompt_text = f"   [yellow]OpenRouter API key [{obfuscated}]: [/yellow]"
+        else:
+            prompt_text = (
+                "   [yellow]OpenRouter API key (press Enter to skip): [/yellow]"
+            )
+
+        user_input = console.input(prompt_text).strip()
+
+        # Handle different inputs
+        if not user_input:
+            # Empty input - keep existing or skip
+            if existing_api_key:
+                print_info("   ⏭️  Keeping existing API key (no change)")
+                return True
+            else:
+                print_info("   ⏭️  Skipped API key setup")
+                print_info("")
+                print_info("   [dim]You can set it up later by running:[/dim]")
+                print_info("   [cyan]mcp-vector-search setup[/cyan]")
+                return False
+
+        elif user_input.lower() in ("clear", "delete", "remove"):
+            # Clear the API key
+            if not existing_api_key:
+                print_warning("   ⚠️  No API key to clear")
+                return False
+
+            if is_from_env:
+                print_warning("   ⚠️  Cannot clear environment variable from config")
+                print_info(
+                    "   [dim]To remove, unset the OPENROUTER_API_KEY environment variable[/dim]"
+                )
+                return True
+
+            # Delete from config file
+            try:
+                deleted = delete_openrouter_api_key(config_dir)
+                if deleted:
+                    print_success("   ✅ API key removed from config")
+                    return False
+                else:
+                    print_warning("   ⚠️  API key not found in config")
+                    return False
+            except Exception as e:
+                print_error(f"   ❌ Failed to delete API key: {e}")
+                return False
+
+        else:
+            # New API key provided
+            try:
+                save_openrouter_api_key(user_input, config_dir)
+                config_path = get_config_file_path(config_dir)
+                print_success(f"   ✅ API key saved to {config_path}")
+                print_info(f"      Last 4 characters: {user_input[-4:]}")
+                print_info("      Chat command is now ready to use!")
+
+                if is_from_env:
+                    print_warning("")
+                    print_warning(
+                        "   ⚠️  Note: Environment variable will still take precedence"
+                    )
+                    print_warning(
+                        "      To use the config file key, unset OPENROUTER_API_KEY"
+                    )
+
+                return True
+            except Exception as e:
+                print_error(f"   ❌ Failed to save API key: {e}")
+                return False
+
+    except KeyboardInterrupt:
+        print_info("\n   ⏭️  API key setup cancelled")
+        return False
+    except Exception as e:
+        logger.error(f"Error during API key setup: {e}")
+        print_error(f"   ❌ Error: {e}")
+        return False
+
+
+# ==============================================================================
+# Main Setup Command
+# ==============================================================================
+
+
+@setup_app.callback()
+def main(
+    ctx: typer.Context,
+    force: bool = typer.Option(
+        False,
+        "--force",
+        "-f",
+        help="Force re-initialization if already set up",
+        rich_help_panel="⚙️  Options",
+    ),
+    verbose: bool = typer.Option(
+        False,
+        "--verbose",
+        "-v",
+        help="Show detailed progress information",
+        rich_help_panel="⚙️  Options",
+    ),
+    save_api_key: bool = typer.Option(
+        False,
+        "--save-api-key",
+        help="Interactively save OpenRouter API key to config",
+        rich_help_panel="🤖 Chat Options",
+    ),
+) -> None:
+    """🚀 Smart zero-config setup for mcp-vector-search.
+
+    Automatically detects your project type, languages, and installed MCP platforms,
+    then configures everything with sensible defaults. No user input required!
+
+    [bold cyan]Examples:[/bold cyan]
+
+    [green]Basic setup (recommended):[/green]
+        $ mcp-vector-search setup
+
+    [green]Force re-setup:[/green]
+        $ mcp-vector-search setup --force
+
+    [green]Verbose output for debugging:[/green]
+        $ mcp-vector-search setup --verbose
+
+    [dim]💡 Tip: This command is idempotent - safe to run multiple times[/dim]
+    """
+    # Only run main logic if no subcommand was invoked
+    if ctx.invoked_subcommand is not None:
+        return
+
+    try:
+        asyncio.run(_run_smart_setup(ctx, force, verbose, save_api_key))
+    except KeyboardInterrupt:
+        print_info("\nSetup interrupted by user")
+        raise typer.Exit(0)
+    except ProjectInitializationError as e:
+        print_error(f"Setup failed: {e}")
+        raise typer.Exit(1)
+    except Exception as e:
+        logger.error(f"Unexpected error during setup: {e}")
+        print_error(f"Setup failed: {e}")
+        raise typer.Exit(1)
+
+
+async def _run_smart_setup(
+    ctx: typer.Context, force: bool, verbose: bool, save_api_key: bool
+) -> None:
+    """Run the smart setup workflow."""
+    console.print(
+        Panel.fit(
+            "[bold cyan]🚀 Smart Setup for mcp-vector-search[/bold cyan]\n"
+            "[dim]Zero-config installation with auto-detection[/dim]",
+            border_style="cyan",
+        )
+    )
+
+    # Get project root from context or auto-detect
+    project_root = ctx.obj.get("project_root") or Path.cwd()
+
+    # ===========================================================================
+    # Phase 1: Detection & Analysis
+    # ===========================================================================
+    console.print("\n[bold blue]🔍 Detecting project...[/bold blue]")
+
+    project_manager = ProjectManager(project_root)
+
+    # Check if already initialized
+    already_initialized = project_manager.is_initialized()
+    if already_initialized and not force:
+        print_success("✅ Project already initialized")
+        print_info("   Skipping initialization, configuring MCP platforms...")
+    else:
+        if verbose:
+            print_info(f"   Project root: {project_root}")
+
+    # Detect languages (only if not already initialized, to avoid slow scan)
+    languages = []
+    if not already_initialized or force:
+        print_info("   Detecting languages...")
+        languages = project_manager.detect_languages()
+        if languages:
+            print_success(
+                f"   ✅ Found {len(languages)} language(s): {', '.join(languages)}"
+            )
+        else:
+            print_info("   No specific languages detected")
+
+    # Scan for file extensions with timeout
+    detected_extensions = None
+    if not already_initialized or force:
+        print_info("   Scanning file types...")
+        detected_extensions = scan_project_file_extensions(project_root, timeout=2.0)
+
+        if detected_extensions:
+            file_types_str = ", ".join(detected_extensions[:10])
+            if len(detected_extensions) > 10:
+                file_types_str += f" (+ {len(detected_extensions) - 10} more)"
+            print_success(f"   ✅ Detected {len(detected_extensions)} file type(s)")
+            if verbose:
+                print_info(f"      Extensions: {file_types_str}")
+        else:
+            print_info("   ⏱️  Scan timed out, using defaults")
+
+    # Detect installed MCP platforms
+    print_info("   Detecting MCP platforms...")
+    detected_platforms_list = detect_all_platforms()
+
+    if detected_platforms_list:
+        # Filter out excluded platforms for display
+        configurable_platforms = [
+            p
+            for p in detected_platforms_list
+            if p.platform not in EXCLUDED_PLATFORMS_FROM_SETUP
+        ]
+        excluded_platforms = [
+            p
+            for p in detected_platforms_list
+            if p.platform in EXCLUDED_PLATFORMS_FROM_SETUP
+        ]
+
+        if configurable_platforms:
+            platform_names = [p.platform.value for p in configurable_platforms]
+            print_success(
+                f"   ✅ Found {len(platform_names)} platform(s): {', '.join(platform_names)}"
+            )
+            if verbose:
+                for platform_info in configurable_platforms:
+                    print_info(
+                        f"      {platform_info.platform.value}: {platform_info.config_path}"
+                    )
+
+        # Note excluded platforms
+        if excluded_platforms:
+            excluded_names = [p.platform.value for p in excluded_platforms]
+            print_info(
+                f"   ℹ️  Skipping: {', '.join(excluded_names)} (use 'install mcp --platform' for manual install)"
+            )
+    else:
+        print_info("   No MCP platforms detected (will configure Claude Code)")
+
+    # ===========================================================================
+    # Phase 2: Smart Configuration
+    # ===========================================================================
+    if not already_initialized or force:
+        console.print("\n[bold blue]⚙️  Configuring...[/bold blue]")
+
+        # Choose file extensions
+        file_extensions = detected_extensions or DEFAULT_FILE_EXTENSIONS
+        if verbose:
+            print_info(f"   File extensions: {', '.join(file_extensions[:10])}...")
+
+        # Choose embedding model
+        embedding_model = select_optimal_embedding_model(languages)
+        print_success(f"   ✅ Embedding model: {embedding_model}")
+
+        # Other settings
+        similarity_threshold = 0.5
+        if verbose:
+            print_info(f"   Similarity threshold: {similarity_threshold}")
+            print_info("   Auto-indexing: enabled")
+            print_info("   File watching: enabled")
+
+    # ===========================================================================
+    # Phase 3: Initialization
+    # ===========================================================================
+    if not already_initialized or force:
+        console.print("\n[bold blue]🚀 Initializing...[/bold blue]")
+
+        project_manager.initialize(
+            file_extensions=file_extensions,
+            embedding_model=embedding_model,
+            similarity_threshold=similarity_threshold,
+            force=force,
+        )
+
+        print_success("✅ Vector database created")
+        print_success("✅ Configuration saved")
+
+    # ===========================================================================
+    # Phase 4: Indexing
+    # ===========================================================================
+    # Determine if indexing is needed:
+    # 1. Not already initialized (new setup)
+    # 2. Force flag is set
+    # 3. Index database doesn't exist
+    # 4. Index exists but is empty
+    # 5. Files have changed (incremental indexing will handle this)
+    needs_indexing = not already_initialized or force
+
+    if already_initialized and not force:
+        # Check if index exists and has content
+        index_db_path = project_root / ".mcp-vector-search" / "chroma.sqlite3"
+        if not index_db_path.exists():
+            print_info("   Index database not found, will create...")
+            needs_indexing = True
+        else:
+            # Check if index is empty or files have changed
+            # Run incremental indexing to catch any changes
+            print_info("   Checking for file changes...")
+            needs_indexing = True  # Always run incremental to catch changes
+
+    if needs_indexing:
+        console.print("\n[bold blue]🔍 Indexing codebase...[/bold blue]")
+
+        from .index import run_indexing
+
+        try:
+            start_time = time.time()
+            await run_indexing(
+                project_root=project_root,
+                force_reindex=force,
+                show_progress=True,
+            )
+            elapsed = time.time() - start_time
+            print_success(f"✅ Indexing completed in {elapsed:.1f}s")
+        except Exception as e:
+            print_error(f"❌ Indexing failed: {e}")
+            print_info("   You can run 'mcp-vector-search index' later")
+            # Continue with MCP setup even if indexing fails
+
+    # ===========================================================================
+    # Phase 5: MCP Integration
+    # ===========================================================================
+    console.print("\n[bold blue]🔗 Configuring MCP integrations...[/bold blue]")
+
+    configured_platforms = []
+    failed_platforms = []
+
+    # Check if Claude CLI is available for enhanced setup
+    claude_cli_available = check_claude_cli_available()
+    if verbose and claude_cli_available:
+        print_info("   ✅ Claude CLI detected, using native integration")
+
+    # Use detected platforms or default to empty list
+    # Filter out excluded platforms (e.g., Claude Desktop) - exclusion already noted in Phase 1
+    platforms_to_configure = [
+        p
+        for p in (detected_platforms_list or [])
+        if p.platform not in EXCLUDED_PLATFORMS_FROM_SETUP
+    ]
+
+    # Configure all detected platforms using new library
+    for platform_info in platforms_to_configure:
+        try:
+            success = _install_to_platform(platform_info, project_root)
+
+            if success:
+                configured_platforms.append(platform_info.platform.value)
+            else:
+                failed_platforms.append(platform_info.platform.value)
+
+        except Exception as e:
+            logger.warning(f"Failed to configure {platform_info.platform.value}: {e}")
+            print_warning(f"   ⚠️  {platform_info.platform.value}: {e}")
+            failed_platforms.append(platform_info.platform.value)
+
+    # Summary of MCP configuration
+    if configured_platforms:
+        print_success(f"✅ Configured {len(configured_platforms)} platform(s)")
+        if verbose:
+            for platform in configured_platforms:
+                print_info(f"   • {platform}")
+
+    if failed_platforms and verbose:
+        print_warning(f"⚠️  Failed to configure {len(failed_platforms)} platform(s)")
+        for platform in failed_platforms:
+            print_info(f"   • {platform}")
+
+    # ===========================================================================
+    # Phase 6: LLM API Key Setup (Optional)
+    # ===========================================================================
+    console.print("\n[bold blue]🤖 Chat Command Setup (Optional)...[/bold blue]")
+    # Always prompt interactively during setup - user can press Enter to skip/keep
+    # The save_api_key flag is now deprecated but kept for backward compatibility
+    llm_configured = setup_llm_api_keys(project_root=project_root, interactive=True)
+
+    # ===========================================================================
+    # Phase 7: Completion
+    # ===========================================================================
+    console.print("\n[bold green]🎉 Setup Complete![/bold green]")
+
+    # Show summary
+    summary_items = []
+    if not already_initialized or force:
+        summary_items.extend(
+            [
+                "Vector database initialized",
+                "Codebase indexed and searchable",
+            ]
+        )
+
+    summary_items.append(f"{len(configured_platforms)} MCP platform(s) configured")
+    summary_items.append("File watching enabled")
+    if llm_configured:
+        summary_items.append("LLM API configured for chat command")
+
+    console.print("\n[bold]What was set up:[/bold]")
+    for item in summary_items:
+        console.print(f"  ✅ {item}")
+
+    # Next steps
+    next_steps = [
+        "[cyan]mcp-vector-search search 'your query'[/cyan] - Search your code",
+        "[cyan]mcp-vector-search status[/cyan] - Check project status",
+    ]
+
+    if llm_configured:
+        next_steps.insert(
+            1, "[cyan]mcp-vector-search chat 'question'[/cyan] - Ask AI about your code"
+        )
+
+    if "claude-code" in configured_platforms:
+        next_steps.insert(0, "Open Claude Code in this directory to use MCP tools")
+
+    print_next_steps(next_steps, title="Ready to Use")
+
+    # Tips
+    if "claude-code" in configured_platforms:
+        console.print(
+            "\n[dim]💡 Tip: Commit .mcp.json to share configuration with your team[/dim]"
+        )
+
+
+if __name__ == "__main__":
+    setup_app()