mcp-ticketer 0.12.0__py3-none-any.whl → 2.0.1__py3-none-any.whl

mcp_ticketer/cli/main.py

@@ -10,24 +10,24 @@ from typing import Any
 import typer
 from dotenv import load_dotenv
 from rich.console import Console
-from rich.table import Table
 
 # Import adapters module to trigger registration
 import mcp_ticketer.adapters  # noqa: F401
 
 from ..__version__ import __version__
-from ..core import AdapterRegistry, Priority, TicketState
-from ..core.models import Comment, SearchQuery
-from ..queue import Queue, QueueStatus, WorkerManager
-from ..queue.health_monitor import HealthStatus, QueueHealthMonitor
-from ..queue.ticket_registry import TicketRegistry
+from ..core import AdapterRegistry
 from .configure import configure_wizard, set_adapter_config, show_current_config
 from .diagnostics import run_diagnostics
 from .discover import app as discover_app
+from .init_command import init
 from .instruction_commands import app as instruction_app
+from .mcp_server_commands import mcp_app
 from .migrate_config import migrate_config_command
 from .platform_commands import app as platform_app
+from .platform_installer import install, remove, uninstall
+from .project_update_commands import app as project_update_app
 from .queue_commands import app as queue_app
+from .setup_command import setup
 from .ticket_commands import app as ticket_app
 
 # Load environment variables from .env files
@@ -93,6 +93,7 @@ def load_config(project_dir: Path | None = None) -> dict:
     from user home directory or system-wide locations.
 
     Args:
+    ----
         project_dir: Optional project directory to load config from
 
     Resolution order:
@@ -100,6 +101,7 @@ def load_config(project_dir: Path | None = None) -> dict:
     2. Default to aitrackdown adapter
 
     Returns:
+    -------
         Configuration dictionary with adapter and config keys.
         Defaults to aitrackdown if no local config exists.
 
@@ -151,6 +153,7 @@ def _discover_from_env_files() -> str | None:
     """Discover adapter configuration from .env or .env.local files.
 
     Returns:
+    -------
         Adapter name if discovered, None otherwise
 
     """
@@ -196,6 +199,7 @@ def _save_adapter_to_config(adapter_name: str) -> None:
     """Save adapter configuration to config file.
 
     Args:
+    ----
         adapter_name: Name of the adapter to save as default
 
     """
@@ -246,9 +250,11 @@ def merge_config(updates: dict) -> dict:
     """Merge updates into existing config.
 
     Args:
+    ----
         updates: Configuration updates to merge
 
     Returns:
+    -------
         Updated configuration
 
     """
@@ -276,6 +282,7 @@ def get_adapter(
     """Get configured adapter instance.
 
     Args:
+    ----
         override_adapter: Override the default adapter type
         override_config: Override configuration for the adapter
 
@@ -303,7 +310,6 @@ def get_adapter(
         adapter_config = config["config"]
 
     # Add environment variables for authentication
-    import os
 
     if adapter_type == "linear":
         if not adapter_config.get("api_key"):
@@ -320,3220 +326,296 @@ def get_adapter(
     return AdapterRegistry.get_adapter(adapter_type, adapter_config)
 
 
-async def _validate_adapter_credentials(
-    adapter_type: str, config_file_path: Path
-) -> list[str]:
-    """Validate adapter credentials by performing real connectivity tests.
-
-    Args:
-        adapter_type: Type of adapter to validate
-        config_file_path: Path to config file
-
-    Returns:
-        List of validation issues (empty if valid)
-
-    """
-    import json
-
-    issues = []
-
-    try:
-        # Load config
-        with open(config_file_path) as f:
-            config = json.load(f)
-
-        adapter_config = config.get("adapters", {}).get(adapter_type, {})
-
-        if not adapter_config:
-            issues.append(f"No configuration found for {adapter_type}")
-            return issues
-
-        # Validate based on adapter type
-        if adapter_type == "linear":
-            api_key = adapter_config.get("api_key")
-
-            # Check API key format
-            if not api_key:
-                issues.append("Linear API key is missing")
-                return issues
-
-            if not api_key.startswith("lin_api_"):
-                issues.append(
-                    "Invalid Linear API key format (should start with 'lin_api_')"
-                )
-                return issues
-
-            # Test actual connectivity
-            try:
-                from ..adapters.linear import LinearAdapter
-
-                adapter = LinearAdapter(adapter_config)
-                # Try to list one ticket to verify connectivity
-                await adapter.list(limit=1)
-            except Exception as e:
-                error_msg = str(e)
-                if "401" in error_msg or "Unauthorized" in error_msg:
-                    issues.append(
-                        "Failed to authenticate with Linear API - invalid API key"
-                    )
-                elif "403" in error_msg or "Forbidden" in error_msg:
-                    issues.append("Linear API key lacks required permissions")
-                elif "team" in error_msg.lower():
-                    issues.append(f"Linear team configuration error: {error_msg}")
-                else:
-                    issues.append(f"Failed to connect to Linear API: {error_msg}")
-
-        elif adapter_type == "jira":
-            server = adapter_config.get("server")
-            email = adapter_config.get("email")
-            api_token = adapter_config.get("api_token")
-
-            # Check required fields
-            if not server:
-                issues.append("JIRA server URL is missing")
-            if not email:
-                issues.append("JIRA email is missing")
-            if not api_token:
-                issues.append("JIRA API token is missing")
-
-            if issues:
-                return issues
-
-            # Test actual connectivity
-            try:
-                from ..adapters.jira import JiraAdapter
-
-                adapter = JiraAdapter(adapter_config)
-                await adapter.list(limit=1)
-            except Exception as e:
-                error_msg = str(e)
-                if "401" in error_msg or "Unauthorized" in error_msg:
-                    issues.append(
-                        "Failed to authenticate with JIRA - invalid credentials"
-                    )
-                elif "403" in error_msg or "Forbidden" in error_msg:
-                    issues.append("JIRA credentials lack required permissions")
-                else:
-                    issues.append(f"Failed to connect to JIRA: {error_msg}")
-
-        elif adapter_type == "github":
-            token = adapter_config.get("token") or adapter_config.get("api_key")
-            owner = adapter_config.get("owner")
-            repo = adapter_config.get("repo")
-
-            # Check required fields
-            if not token:
-                issues.append("GitHub token is missing")
-            if not owner:
-                issues.append("GitHub owner is missing")
-            if not repo:
-                issues.append("GitHub repo is missing")
-
-            if issues:
-                return issues
-
-            # Test actual connectivity
-            try:
-                from ..adapters.github import GitHubAdapter
-
-                adapter = GitHubAdapter(adapter_config)
-                await adapter.list(limit=1)
-            except Exception as e:
-                error_msg = str(e)
-                if (
-                    "401" in error_msg
-                    or "Unauthorized" in error_msg
-                    or "Bad credentials" in error_msg
-                ):
-                    issues.append("Failed to authenticate with GitHub - invalid token")
-                elif "404" in error_msg or "Not Found" in error_msg:
-                    issues.append(f"GitHub repository not found: {owner}/{repo}")
-                elif "403" in error_msg or "Forbidden" in error_msg:
-                    issues.append("GitHub token lacks required permissions")
-                else:
-                    issues.append(f"Failed to connect to GitHub: {error_msg}")
-
-        elif adapter_type == "aitrackdown":
-            # AITrackdown doesn't require credentials, just check base_path is set
-            base_path = adapter_config.get("base_path")
-            if not base_path:
-                issues.append("AITrackdown base_path is missing")
-
-    except Exception as e:
-        issues.append(f"Validation error: {str(e)}")
-
-    return issues
-
-
-async def _validate_configuration_with_retry(
-    console: Console, adapter_type: str, config_file_path: Path, proj_path: Path
-) -> bool:
-    """Validate configuration with retry loop for corrections.
-
-    Args:
-        console: Rich console for output
-        adapter_type: Type of adapter configured
-        config_file_path: Path to config file
-        proj_path: Project path
-
-    Returns:
-        True if validation passed or user chose to continue, False if user chose to exit
-
-    """
-    max_retries = 3
-    retry_count = 0
-
-    while retry_count < max_retries:
-        console.print("\n[cyan]🔍 Validating configuration...[/cyan]")
-
-        # Run real adapter validation (suppress verbose output)
-        import io
-        import sys
-
-        # Capture output to suppress verbose diagnostics output
-        old_stdout = sys.stdout
-        old_stderr = sys.stderr
-        sys.stdout = io.StringIO()
-        sys.stderr = io.StringIO()
-
-        try:
-            # Perform real adapter validation using diagnostics
-            validation_issues = await _validate_adapter_credentials(
-                adapter_type, config_file_path
-            )
-        finally:
-            # Restore stdout/stderr
-            sys.stdout = old_stdout
-            sys.stderr = old_stderr
-
-        # Check if there are issues
-        if not validation_issues:
-            console.print("[green]✓ Configuration validated successfully![/green]")
-            return True
-
-        # Display issues found
-        console.print("[yellow]⚠️  Configuration validation found issues:[/yellow]")
-        for issue in validation_issues:
-            console.print(f"  [red]❌[/red] {issue}")
-
-        # Offer user options
-        console.print("\n[bold]What would you like to do?[/bold]")
-        console.print("1. [cyan]Re-enter configuration values[/cyan] (fix issues)")
-        console.print("2. [yellow]Continue anyway[/yellow] (skip validation)")
-        console.print("3. [red]Exit[/red] (fix manually later)")
-
-        try:
-            choice = typer.prompt("\nSelect option (1-3)", type=int, default=1)
-        except typer.Abort:
-            console.print("[yellow]Cancelled.[/yellow]")
-            return False
-
-        if choice == 1:
-            # Re-enter configuration
-            # Check BEFORE increment to fix off-by-one error
-            if retry_count >= max_retries:
-                console.print(
-                    f"[red]Maximum retry attempts ({max_retries}) reached.[/red]"
-                )
-                console.print(
-                    "[yellow]Please fix configuration manually and run 'mcp-ticketer doctor'[/yellow]"
-                )
-                return False
-            retry_count += 1
-
-            console.print(
-                f"\n[cyan]Retry {retry_count}/{max_retries} - Re-entering configuration...[/cyan]"
-            )
-
-            # Reload current config to get values
-            import json
-
-            with open(config_file_path) as f:
-                current_config = json.load(f)
-
-            # Re-prompt for adapter-specific configuration
-            if adapter_type == "linear":
-                console.print("\n[bold]Linear Configuration[/bold]")
-                console.print(
-                    "[dim]Get your API key at: https://linear.app/settings/api[/dim]\n"
-                )
-
-                linear_api_key = typer.prompt(
-                    "Enter your Linear API key", hide_input=True
-                )
-
-                console.print("\n[bold]Linear Team Configuration[/bold]")
-                console.print("You can provide either:")
-                console.print(
-                    "  1. Team URL (e.g., https://linear.app/workspace/team/TEAMKEY/active)"
-                )
-                console.print("  2. Team key (e.g., 'ENG', 'DESIGN', 'PRODUCT')")
-                console.print("  3. Team ID (UUID)")
-                console.print(
-                    "[dim]Find team URL or key in: Linear → Your Team → Team Issues Page[/dim]\n"
-                )
-
-                team_input = typer.prompt("Team URL, key, or ID")
-
-                # Check if input is a URL
-                linear_team_id = None
-                linear_team_key = None
-
-                if team_input.startswith("https://linear.app/"):
-                    console.print("[cyan]Detected team URL, deriving team ID...[/cyan]")
-                    from .linear_commands import derive_team_from_url
-
-                    derived_team_id, error = await derive_team_from_url(
-                        linear_api_key, team_input
-                    )
-
-                    if derived_team_id:
-                        linear_team_id = derived_team_id
-                        console.print(
-                            "[green]✓[/green] Successfully derived team ID from URL"
-                        )
-                    else:
-                        console.print(f"[red]Error:[/red] {error}")
-                        console.print("Please provide team key or ID manually instead.")
-                        team_input = typer.prompt("Team key or ID")
-
-                        if len(team_input) > 20:  # Likely a UUID
-                            linear_team_id = team_input
-                        else:
-                            linear_team_key = team_input
-                else:
-                    # Input is team key or ID
-                    if len(team_input) > 20:  # Likely a UUID
-                        linear_team_id = team_input
-                    else:
-                        linear_team_key = team_input
-
-                # Update config
-                linear_config = {
-                    "api_key": linear_api_key,
-                    "type": "linear",
-                }
-                if linear_team_key:
-                    linear_config["team_key"] = linear_team_key
-                if linear_team_id:
-                    linear_config["team_id"] = linear_team_id
-
-                current_config["adapters"]["linear"] = linear_config
-
-            elif adapter_type == "jira":
-                console.print("\n[bold]JIRA Configuration[/bold]")
-                console.print("Enter your JIRA server details.\n")
-
-                server = typer.prompt(
-                    "JIRA server URL (e.g., https://company.atlassian.net)"
-                )
-                email = typer.prompt("Your JIRA email address")
-
-                console.print("\nYou need a JIRA API token.")
-                console.print(
-                    "[dim]Generate one at: https://id.atlassian.com/manage/api-tokens[/dim]\n"
-                )
-
-                token = typer.prompt("Enter your JIRA API token", hide_input=True)
-
-                project = typer.prompt(
-                    "Default JIRA project key (optional, press Enter to skip)",
-                    default="",
-                    show_default=False,
-                )
-
-                # Update config
-                jira_config = {
-                    "server": server,
-                    "email": email,
-                    "api_token": token,
-                    "type": "jira",
-                }
-                if project:
-                    jira_config["project_key"] = project
-
-                current_config["adapters"]["jira"] = jira_config
-
-            elif adapter_type == "github":
-                console.print("\n[bold]GitHub Configuration[/bold]")
-                console.print("Enter your GitHub repository details.\n")
-
-                owner = typer.prompt(
-                    "GitHub repository owner (username or organization)"
-                )
-                repo = typer.prompt("GitHub repository name")
-
-                console.print("\nYou need a GitHub Personal Access Token.")
-                console.print(
-                    "[dim]Create one at: https://github.com/settings/tokens/new[/dim]"
-                )
-                console.print(
-                    "[dim]Required scopes: repo (for private repos) or public_repo (for public repos)[/dim]\n"
-                )
-
-                token = typer.prompt(
-                    "Enter your GitHub Personal Access Token", hide_input=True
-                )
-
-                # Update config
-                current_config["adapters"]["github"] = {
-                    "owner": owner,
-                    "repo": repo,
-                    "token": token,
-                    "type": "github",
-                }
-
-            elif adapter_type == "aitrackdown":
-                # AITrackdown doesn't need credentials, but save config before returning
-                # Save updated configuration
-                with open(config_file_path, "w") as f:
-                    json.dump(current_config, f, indent=2)
-
-                console.print(
-                    "[yellow]AITrackdown doesn't require credentials. Continuing...[/yellow]"
-                )
-                console.print("[dim]✓ Configuration updated[/dim]")
-                return True
-
-            else:
-                console.print(f"[red]Unknown adapter type: {adapter_type}[/red]")
-                return False
-
-            # Save updated configuration
-            with open(config_file_path, "w") as f:
-                json.dump(current_config, f, indent=2)
-
-            console.print("[dim]✓ Configuration updated[/dim]")
-            # Loop will retry validation
-
-        elif choice == 2:
-            # Continue anyway
-            console.print(
-                "[yellow]⚠️  Continuing with potentially invalid configuration.[/yellow]"
-            )
-            console.print("[dim]You can validate later with: mcp-ticketer doctor[/dim]")
-            return True
-
-        elif choice == 3:
-            # Exit
-            console.print(
-                "[yellow]Configuration saved but not validated. Run 'mcp-ticketer doctor' to test.[/yellow]"
-            )
-            return False
-
-        else:
-            console.print(
-                f"[red]Invalid choice: {choice}. Please enter 1, 2, or 3.[/red]"
-            )
-            # Continue loop to ask again
-
-    return True
-
-
-def _prompt_for_adapter_selection(console: Console) -> str:
-    """Interactive prompt for adapter selection.
-
-    Args:
-        console: Rich console for output
-
-    Returns:
-        Selected adapter type
-
-    """
-    console.print("\n[bold blue]🚀 MCP Ticketer Setup[/bold blue]")
-    console.print("Choose which ticket system you want to connect to:\n")
-
-    # Define adapter options with descriptions
-    adapters = [
-        {
-            "name": "linear",
-            "title": "Linear",
-            "description": "Modern project management (linear.app)",
-            "requirements": "API key and team ID",
-        },
-        {
-            "name": "github",
-            "title": "GitHub Issues",
-            "description": "GitHub repository issues",
-            "requirements": "Personal access token, owner, and repo",
-        },
-        {
-            "name": "jira",
-            "title": "JIRA",
-            "description": "Atlassian JIRA project management",
-            "requirements": "Server URL, email, and API token",
-        },
-        {
-            "name": "aitrackdown",
-            "title": "Local Files (AITrackdown)",
-            "description": "Store tickets in local files (no external service)",
-            "requirements": "None - works offline",
-        },
-    ]
-
-    # Display options
-    for i, adapter in enumerate(adapters, 1):
-        console.print(f"[cyan]{i}.[/cyan] [bold]{adapter['title']}[/bold]")
-        console.print(f"   {adapter['description']}")
-        console.print(f"   [dim]Requirements: {adapter['requirements']}[/dim]\n")
-
-    # Get user selection
-    while True:
-        try:
-            choice = typer.prompt("Select adapter (1-4)", type=int, default=1)
-            if 1 <= choice <= len(adapters):
-                selected_adapter = adapters[choice - 1]
-                console.print(
-                    f"\n[green]✓ Selected: {selected_adapter['title']}[/green]"
-                )
-                return selected_adapter["name"]
-            else:
-                console.print(
-                    f"[red]Please enter a number between 1 and {len(adapters)}[/red]"
-                )
-        except (ValueError, typer.Abort):
-            console.print("[yellow]Setup cancelled.[/yellow]")
-            raise typer.Exit(0) from None
-
-
-@app.command()
-def setup(
-    project_path: str | None = typer.Option(
-        None, "--path", help="Project path (default: current directory)"
-    ),
-    skip_platforms: bool = typer.Option(
-        False,
-        "--skip-platforms",
-        help="Skip platform installation (only initialize adapter)",
-    ),
-    force_reinit: bool = typer.Option(
-        False,
-        "--force-reinit",
-        help="Force re-initialization even if config exists",
-    ),
-) -> None:
-    """Smart setup command - combines init + platform installation.
-
-    This command intelligently detects your current setup state and only
-    performs necessary configuration. It's the recommended way to get started.
-
-    Detection & Smart Actions:
-    - First run: Full setup (init + platform installation)
-    - Existing config: Skip init, offer platform installation
-    - Detects changes: Offers to update configurations
-    - Respects existing: Won't overwrite without confirmation
-
-    Examples:
-        # Smart setup (recommended for first-time setup)
-        mcp-ticketer setup
-
-        # Setup for different project
-        mcp-ticketer setup --path /path/to/project
-
-        # Re-initialize configuration
-        mcp-ticketer setup --force-reinit
-
-        # Only init adapter, skip platform installation
-        mcp-ticketer setup --skip-platforms
-
-    Note: For advanced configuration, use 'init' and 'install' separately.
-
-    """
-    from .platform_detection import PlatformDetector
-
-    proj_path = Path(project_path) if project_path else Path.cwd()
-    config_path = proj_path / ".mcp-ticketer" / "config.json"
-
-    console.print("[bold cyan]🚀 MCP Ticketer Smart Setup[/bold cyan]\n")
-
-    # Step 1: Detect existing configuration
-    config_exists = config_path.exists()
-    config_valid = False
-    current_adapter = None
-
-    if config_exists and not force_reinit:
-        try:
-            with open(config_path) as f:
-                config = json.load(f)
-                current_adapter = config.get("default_adapter")
-                config_valid = bool(current_adapter and config.get("adapters"))
-        except (json.JSONDecodeError, OSError):
-            config_valid = False
-
-    if config_valid:
-        console.print("[green]✓[/green] Configuration detected")
-        console.print(f"[dim]  Adapter: {current_adapter}[/dim]")
-        console.print(f"[dim]  Location: {config_path}[/dim]\n")
-
-        # Offer to reconfigure
-        if not typer.confirm(
-            "Configuration already exists. Keep existing settings?", default=True
-        ):
-            console.print("[cyan]Re-initializing configuration...[/cyan]\n")
-            force_reinit = True
-            config_valid = False
-    else:
-        if config_exists:
-            console.print(
-                "[yellow]⚠[/yellow]  Configuration file exists but is invalid\n"
-            )
-        else:
-            console.print("[yellow]⚠[/yellow]  No configuration found\n")
-
-    # Step 2: Initialize adapter configuration if needed
-    if not config_valid or force_reinit:
-        console.print("[bold]Step 1/2: Adapter Configuration[/bold]\n")
-
-        # Run init command non-interactively through function call
-        # We'll use the discover and prompt flow from init
-        from ..core.env_discovery import discover_config
-
-        discovered = discover_config(proj_path)
-        adapter_type = None
-
-        # Try auto-discovery
-        if discovered and discovered.adapters:
-            primary = discovered.get_primary_adapter()
-            if primary:
-                adapter_type = primary.adapter_type
-                console.print(f"[green]✓ Auto-detected {adapter_type} adapter[/green]")
-                console.print(f"[dim]  Source: {primary.found_in}[/dim]")
-                console.print(f"[dim]  Confidence: {primary.confidence:.0%}[/dim]\n")
-
-                if not typer.confirm(
-                    f"Use detected {adapter_type} adapter?", default=True
-                ):
-                    adapter_type = None
-
-        # If no adapter detected, prompt for selection
-        if not adapter_type:
-            adapter_type = _prompt_for_adapter_selection(console)
-
-        # Now run the full init with the selected adapter
-        console.print(f"\n[cyan]Initializing {adapter_type} adapter...[/cyan]\n")
-
-        # Call init programmatically
-        init(
-            adapter=adapter_type,
-            project_path=str(proj_path),
-            global_config=False,
-        )
-
-        console.print("\n[green]✓ Adapter configuration complete[/green]\n")
-    else:
-        console.print("[green]✓ Step 1/2: Adapter already configured[/green]\n")
-
-    # Step 3: Platform installation
-    if skip_platforms:
-        console.print(
-            "[yellow]⚠[/yellow]  Skipping platform installation (--skip-platforms)\n"
-        )
-        _show_setup_complete_message(console, proj_path)
-        return
-
-    console.print("[bold]Step 2/2: Platform Installation[/bold]\n")
-
-    # Detect available platforms
-    detector = PlatformDetector()
-    detected = detector.detect_all(project_path=proj_path)
-
-    if not detected:
-        console.print("[yellow]No AI platforms detected on this system.[/yellow]")
-        console.print(
-            "\n[dim]Supported platforms: Claude Code, Claude Desktop, Gemini, Codex, Auggie[/dim]"
-        )
-        console.print(
-            "[dim]Install these platforms to use them with mcp-ticketer.[/dim]\n"
-        )
-        _show_setup_complete_message(console, proj_path)
-        return
-
-    # Filter to only installed platforms
-    installed = [p for p in detected if p.is_installed]
-
-    if not installed:
-        console.print(
-            "[yellow]AI platforms detected but have configuration issues.[/yellow]"
-        )
-        console.print(
-            "\n[dim]Run 'mcp-ticketer install --auto-detect' for details.[/dim]\n"
-        )
-        _show_setup_complete_message(console, proj_path)
-        return
-
-    # Show detected platforms
-    console.print(f"[green]✓[/green] Detected {len(installed)} platform(s):\n")
-    for plat in installed:
-        console.print(f"  • {plat.display_name} ({plat.scope})")
-
-    console.print()
-
-    # Check if mcp-ticketer is already configured for these platforms
-    already_configured = _check_existing_platform_configs(installed, proj_path)
-
-    if already_configured:
-        console.print(
-            f"[green]✓[/green] mcp-ticketer already configured for {len(already_configured)} platform(s)\n"
-        )
-        for plat_name in already_configured:
-            console.print(f"  • {plat_name}")
-        console.print()
-
-        if not typer.confirm("Update platform configurations anyway?", default=False):
-            console.print("[yellow]Skipping platform installation[/yellow]\n")
-            _show_setup_complete_message(console, proj_path)
-            return
-
-    # Offer to install for all or select specific
-    console.print("[bold]Platform Installation Options:[/bold]")
-    console.print("1. Install for all detected platforms")
-    console.print("2. Select specific platform")
-    console.print("3. Skip platform installation")
-
-    try:
-        choice = typer.prompt("\nSelect option (1-3)", type=int, default=1)
-    except typer.Abort:
-        console.print("[yellow]Setup cancelled[/yellow]")
-        raise typer.Exit(0) from None
-
-    if choice == 3:
-        console.print("[yellow]Skipping platform installation[/yellow]\n")
-        _show_setup_complete_message(console, proj_path)
-        return
-
-    # Import configuration functions
-    from .auggie_configure import configure_auggie_mcp
-    from .codex_configure import configure_codex_mcp
-    from .gemini_configure import configure_gemini_mcp
-    from .mcp_configure import configure_claude_mcp
-
-    platform_mapping = {
-        "claude-code": lambda: configure_claude_mcp(global_config=False, force=True),
-        "claude-desktop": lambda: configure_claude_mcp(global_config=True, force=True),
-        "auggie": lambda: configure_auggie_mcp(force=True),
-        "gemini": lambda: configure_gemini_mcp(scope="project", force=True),
-        "codex": lambda: configure_codex_mcp(force=True),
-    }
-
-    platforms_to_install = []
-
-    if choice == 1:
-        # Install for all
-        platforms_to_install = installed
-    elif choice == 2:
-        # Select specific platform
-        console.print("\n[bold]Select platform:[/bold]")
-        for idx, plat in enumerate(installed, 1):
-            console.print(f"  {idx}. {plat.display_name} ({plat.scope})")
-
-        try:
-            plat_choice = typer.prompt("\nSelect platform number", type=int)
-            if 1 <= plat_choice <= len(installed):
-                platforms_to_install = [installed[plat_choice - 1]]
-            else:
-                console.print("[red]Invalid selection[/red]")
-                raise typer.Exit(1) from None
-        except typer.Abort:
-            console.print("[yellow]Setup cancelled[/yellow]")
-            raise typer.Exit(0) from None
-
-    # Install for selected platforms
-    console.print()
-    success_count = 0
-    failed = []
-
-    for plat in platforms_to_install:
-        config_func = platform_mapping.get(plat.name)
-        if not config_func:
-            console.print(f"[yellow]⚠[/yellow]  No installer for {plat.display_name}")
-            continue
-
-        try:
-            console.print(f"[cyan]Installing for {plat.display_name}...[/cyan]")
-            config_func()
-            console.print(f"[green]✓[/green] {plat.display_name} configured\n")
-            success_count += 1
-        except Exception as e:
-            console.print(
-                f"[red]✗[/red] Failed to configure {plat.display_name}: {e}\n"
-            )
-            failed.append(plat.display_name)
-
-    # Summary
-    console.print(
-        f"[bold]Platform Installation:[/bold] {success_count}/{len(platforms_to_install)} succeeded"
-    )
-    if failed:
-        console.print(f"[red]Failed:[/red] {', '.join(failed)}")
-
-    console.print()
-    _show_setup_complete_message(console, proj_path)
-
-
-def _check_existing_platform_configs(platforms: list, proj_path: Path) -> list[str]:
-    """Check if mcp-ticketer is already configured for given platforms.
-
-    Args:
-        platforms: List of DetectedPlatform objects
-        proj_path: Project path
-
-    Returns:
-        List of platform display names that are already configured
-
-    """
-    configured = []
-
-    for plat in platforms:
-        try:
-            if plat.name == "claude-code":
-                config_path = Path.home() / ".claude.json"
-                if config_path.exists():
-                    with open(config_path) as f:
-                        config = json.load(f)
-                        projects = config.get("projects", {})
-                        proj_key = str(proj_path)
-                        if proj_key in projects:
-                            mcp_servers = projects[proj_key].get("mcpServers", {})
-                            if "mcp-ticketer" in mcp_servers:
-                                configured.append(plat.display_name)
-
-            elif plat.name == "claude-desktop":
-                if plat.config_path.exists():
-                    with open(plat.config_path) as f:
-                        config = json.load(f)
-                        if "mcp-ticketer" in config.get("mcpServers", {}):
-                            configured.append(plat.display_name)
-
-            elif plat.name in ["auggie", "codex", "gemini"]:
-                if plat.config_path.exists():
-                    # Check if mcp-ticketer is configured
-                    # Implementation depends on each platform's config format
-                    # For now, just check if config exists (simplified)
-                    pass
-
-        except (json.JSONDecodeError, OSError):
-            pass
-
-    return configured
-
-
-def _show_setup_complete_message(console: Console, proj_path: Path) -> None:
-    """Show setup complete message with next steps.
-
-    Args:
-        console: Rich console for output
-        proj_path: Project path
-
-    """
-    console.print("[bold green]🎉 Setup Complete![/bold green]\n")
-
-    console.print("[bold]Quick Start:[/bold]")
-    console.print("1. Create a test ticket:")
-    console.print("   [cyan]mcp-ticketer create 'My first ticket'[/cyan]\n")
-
-    console.print("2. List tickets:")
-    console.print("   [cyan]mcp-ticketer list[/cyan]\n")
-
-    console.print("[bold]Useful Commands:[/bold]")
-    console.print("  [cyan]mcp-ticketer doctor[/cyan]        - Validate configuration")
-    console.print("  [cyan]mcp-ticketer install <platform>[/cyan] - Add more platforms")
-    console.print("  [cyan]mcp-ticketer --help[/cyan]        - See all commands\n")
-
-    console.print(
-        f"[dim]Configuration: {proj_path / '.mcp-ticketer' / 'config.json'}[/dim]"
-    )
-
-
-@app.command()
-def init(
-    adapter: str | None = typer.Option(
-        None,
-        "--adapter",
-        "-a",
-        help="Adapter type to use (interactive prompt if not specified)",
-    ),
-    project_path: str | None = typer.Option(
-        None, "--path", help="Project path (default: current directory)"
-    ),
-    global_config: bool = typer.Option(
-        False,
-        "--global",
-        "-g",
-        help="Save to global config instead of project-specific",
-    ),
-    base_path: str | None = typer.Option(
-        None,
-        "--base-path",
-        "-p",
-        help="Base path for ticket storage (AITrackdown only)",
-    ),
-    api_key: str | None = typer.Option(
-        None, "--api-key", help="API key for Linear or API token for JIRA"
-    ),
-    team_id: str | None = typer.Option(
-        None, "--team-id", help="Linear team ID (required for Linear adapter)"
-    ),
-    jira_server: str | None = typer.Option(
-        None,
-        "--jira-server",
-        help="JIRA server URL (e.g., https://company.atlassian.net)",
-    ),
-    jira_email: str | None = typer.Option(
-        None, "--jira-email", help="JIRA user email for authentication"
-    ),
-    jira_project: str | None = typer.Option(
-        None, "--jira-project", help="Default JIRA project key"
-    ),
-    github_owner: str | None = typer.Option(
-        None, "--github-owner", help="GitHub repository owner"
-    ),
-    github_repo: str | None = typer.Option(
-        None, "--github-repo", help="GitHub repository name"
-    ),
-    github_token: str | None = typer.Option(
-        None, "--github-token", help="GitHub Personal Access Token"
-    ),
-) -> None:
-    """Initialize adapter configuration only (without platform installation).
-
-    This command sets up adapter configuration with interactive prompts.
-    It auto-detects adapter configuration from .env files or prompts for
-    interactive setup if no configuration is found.
-
-    Creates .mcp-ticketer/config.json in the current directory.
-
-    RECOMMENDED: Use 'mcp-ticketer setup' instead for a complete setup
-    experience that includes both adapter configuration and platform
-    installation in one command.
-
-    The init command automatically validates your configuration after setup:
-    - If validation passes, setup completes
-    - If issues are detected, you can re-enter credentials, continue anyway, or exit
-    - You get up to 3 retry attempts to fix configuration issues
-    - You can always re-validate later with 'mcp-ticketer doctor'
-
-    Examples:
-        # For first-time setup, use 'setup' instead (recommended)
-        mcp-ticketer setup
-
-        # Initialize adapter only (advanced usage)
-        mcp-ticketer init
-
-        # Force specific adapter
-        mcp-ticketer init --adapter linear
-
-        # Initialize for different project
-        mcp-ticketer init --path /path/to/project
-
-    """
-    from pathlib import Path
-
-    from ..core.env_discovery import discover_config
-
-    # Determine project path
-    proj_path = Path(project_path) if project_path else Path.cwd()
-
-    # Check if already initialized (unless using --global)
-    if not global_config:
-        config_path = proj_path / ".mcp-ticketer" / "config.json"
-
-        if config_path.exists():
-            if not typer.confirm(
-                f"Configuration already exists at {config_path}. Overwrite?",
-                default=False,
-            ):
-                console.print("[yellow]Initialization cancelled.[/yellow]")
-                raise typer.Exit(0) from None
-
-    # 1. Try auto-discovery if no adapter specified
-    discovered = None
-    adapter_type = adapter
-
-    if not adapter_type:
-        console.print(
-            "[cyan]🔍 Auto-discovering configuration from .env files...[/cyan]"
-        )
-
-        # First try our improved .env configuration loader
-        from ..mcp.server.main import _load_env_configuration
-
-        env_config = _load_env_configuration()
-
-        if env_config:
-            adapter_type = env_config["adapter_type"]
-            console.print(
-                f"[green]✓ Detected {adapter_type} adapter from environment files[/green]"
-            )
-
-            # Show what was discovered
-            console.print("\n[dim]Configuration found in: .env files[/dim]")
-            console.print("[dim]Confidence: 100%[/dim]")
-
-            # Ask user to confirm auto-detected adapter
-            if not typer.confirm(
-                f"Use detected {adapter_type} adapter?",
-                default=True,
-            ):
-                adapter_type = None  # Will trigger interactive selection
-        else:
-            # Fallback to old discovery system for backward compatibility
-            discovered = discover_config(proj_path)
-
-            if discovered and discovered.adapters:
-                primary = discovered.get_primary_adapter()
-                if primary:
-                    adapter_type = primary.adapter_type
-                    console.print(
-                        f"[green]✓ Detected {adapter_type} adapter from environment files[/green]"
-                    )
-
-                    # Show what was discovered
-                    console.print(
-                        f"\n[dim]Configuration found in: {primary.found_in}[/dim]"
-                    )
-                    console.print(f"[dim]Confidence: {primary.confidence:.0%}[/dim]")
-
-                    # Ask user to confirm auto-detected adapter
-                    if not typer.confirm(
-                        f"Use detected {adapter_type} adapter?",
-                        default=True,
-                    ):
-                        adapter_type = None  # Will trigger interactive selection
-                else:
-                    adapter_type = None  # Will trigger interactive selection
-            else:
-                adapter_type = None  # Will trigger interactive selection
-
-        # If no adapter determined, show interactive selection
-        if not adapter_type:
-            adapter_type = _prompt_for_adapter_selection(console)
-
-    # 2. Create configuration based on adapter type
-    config = {"default_adapter": adapter_type, "adapters": {}}
-
-    # 3. If discovered and matches adapter_type, use discovered config
-    if discovered and adapter_type != "aitrackdown":
-        discovered_adapter = discovered.get_adapter_by_type(adapter_type)
-        if discovered_adapter:
-            adapter_config = discovered_adapter.config.copy()
-            # Ensure the config has the correct 'type' field
-            adapter_config["type"] = adapter_type
-            # Remove 'adapter' field if present (legacy)
-            adapter_config.pop("adapter", None)
-            config["adapters"][adapter_type] = adapter_config
-
-    # 4. Handle manual configuration for specific adapters
-    if adapter_type == "aitrackdown":
-        config["adapters"]["aitrackdown"] = {
-            "type": "aitrackdown",
-            "base_path": base_path or ".aitrackdown",
-        }
-
-    elif adapter_type == "linear":
-        # If not auto-discovered, build from CLI params or prompt
-        if adapter_type not in config["adapters"]:
-            # API Key
-            linear_api_key = api_key or os.getenv("LINEAR_API_KEY")
-            if not linear_api_key:
-                console.print("\n[bold]Linear Configuration[/bold]")
-                console.print("You need a Linear API key to connect to Linear.")
-                console.print(
-                    "[dim]Get your API key at: https://linear.app/settings/api[/dim]\n"
-                )
-
-                linear_api_key = typer.prompt(
-                    "Enter your Linear API key", hide_input=True
-                )
-
-            # Team ID or Team Key or Team URL
-            # Try environment variables first
-            linear_team_key = os.getenv("LINEAR_TEAM_KEY")
-            linear_team_id = team_id or os.getenv("LINEAR_TEAM_ID")
-
-            if not linear_team_key and not linear_team_id:
-                console.print("\n[bold]Linear Team Configuration[/bold]")
-                console.print("You can provide either:")
-                console.print(
-                    "  1. Team URL (e.g., https://linear.app/workspace/team/TEAMKEY/active)"
-                )
-                console.print("  2. Team key (e.g., 'ENG', 'DESIGN', 'PRODUCT')")
-                console.print("  3. Team ID (UUID)")
-                console.print(
-                    "[dim]Find team URL or key in: Linear → Your Team → Team Issues Page[/dim]\n"
-                )
-
-                team_input = typer.prompt("Team URL, key, or ID")
-
-                # Check if input is a URL
-                if team_input.startswith("https://linear.app/"):
-                    console.print("[cyan]Detected team URL, deriving team ID...[/cyan]")
-                    import asyncio
-
-                    from .linear_commands import derive_team_from_url
-
-                    derived_team_id, error = asyncio.run(
-                        derive_team_from_url(linear_api_key, team_input)
-                    )
-
-                    if derived_team_id:
-                        linear_team_id = derived_team_id
-                        console.print(
-                            "[green]✓[/green] Successfully derived team ID from URL"
-                        )
-                    else:
-                        console.print(f"[red]Error:[/red] {error}")
-                        console.print("Please provide team key or ID manually instead.")
-                        team_input = typer.prompt("Team key or ID")
-
-                        # Store as either team_key or team_id based on format
-                        if len(team_input) > 20:  # Likely a UUID
-                            linear_team_id = team_input
-                        else:
-                            linear_team_key = team_input
-                else:
-                    # Input is team key or ID
-                    if len(team_input) > 20:  # Likely a UUID
-                        linear_team_id = team_input
-                    else:
-                        linear_team_key = team_input
-
-            # Validate required fields (following JIRA pattern)
-            if not linear_api_key:
-                console.print("[red]Error:[/red] Linear API key is required")
-                raise typer.Exit(1) from None
-
-            if not linear_team_id and not linear_team_key:
-                console.print(
-                    "[red]Error:[/red] Linear requires either team ID or team key"
-                )
-                raise typer.Exit(1) from None
-
-            # Build configuration
-            linear_config = {
-                "api_key": linear_api_key,
-                "type": "linear",
-            }
-
-            # Save whichever was provided
-            if linear_team_key:
-                linear_config["team_key"] = linear_team_key
-            if linear_team_id:
-                linear_config["team_id"] = linear_team_id
-
-            config["adapters"]["linear"] = linear_config
-
-    elif adapter_type == "jira":
-        # If not auto-discovered, build from CLI params or prompt
-        if adapter_type not in config["adapters"]:
-            server = jira_server or os.getenv("JIRA_SERVER")
-            email = jira_email or os.getenv("JIRA_EMAIL")
-            token = api_key or os.getenv("JIRA_API_TOKEN")
-            project = jira_project or os.getenv("JIRA_PROJECT_KEY")
-
-            # Interactive prompts for missing values
-            if not server:
-                console.print("\n[bold]JIRA Configuration[/bold]")
-                console.print("Enter your JIRA server details.\n")
-
-                server = typer.prompt(
-                    "JIRA server URL (e.g., https://company.atlassian.net)"
-                )
-
-            if not email:
-                email = typer.prompt("Your JIRA email address")
-
-            if not token:
-                console.print("\nYou need a JIRA API token.")
-                console.print(
-                    "[dim]Generate one at: https://id.atlassian.com/manage/api-tokens[/dim]\n"
-                )
-
-                token = typer.prompt("Enter your JIRA API token", hide_input=True)
-
-            if not project:
-                project = typer.prompt(
-                    "Default JIRA project key (optional, press Enter to skip)",
-                    default="",
-                    show_default=False,
-                )
-
-            # Validate required fields
-            if not server:
-                console.print("[red]Error:[/red] JIRA server URL is required")
-                raise typer.Exit(1) from None
-
-            if not email:
-                console.print("[red]Error:[/red] JIRA email is required")
-                raise typer.Exit(1) from None
-
-            if not token:
-                console.print("[red]Error:[/red] JIRA API token is required")
-                raise typer.Exit(1) from None
-
-            jira_config = {
-                "server": server,
-                "email": email,
-                "api_token": token,
-                "type": "jira",
-            }
-
-            if project:
-                jira_config["project_key"] = project
-
-            config["adapters"]["jira"] = jira_config
-
-    elif adapter_type == "github":
-        # If not auto-discovered, build from CLI params or prompt
-        if adapter_type not in config["adapters"]:
-            owner = github_owner or os.getenv("GITHUB_OWNER")
-            repo = github_repo or os.getenv("GITHUB_REPO")
-            token = github_token or os.getenv("GITHUB_TOKEN")
-
-            # Interactive prompts for missing values
-            if not owner:
-                console.print("\n[bold]GitHub Configuration[/bold]")
-                console.print("Enter your GitHub repository details.\n")
-
-                owner = typer.prompt(
-                    "GitHub repository owner (username or organization)"
-                )
-
-            if not repo:
-                repo = typer.prompt("GitHub repository name")
-
-            if not token:
-                console.print("\nYou need a GitHub Personal Access Token.")
-                console.print(
-                    "[dim]Create one at: https://github.com/settings/tokens/new[/dim]"
-                )
-                console.print(
-                    "[dim]Required scopes: repo (for private repos) or public_repo (for public repos)[/dim]\n"
-                )
-
-                token = typer.prompt(
-                    "Enter your GitHub Personal Access Token", hide_input=True
-                )
-
-            # Validate required fields
-            if not owner:
-                console.print("[red]Error:[/red] GitHub repository owner is required")
-                raise typer.Exit(1) from None
-
-            if not repo:
-                console.print("[red]Error:[/red] GitHub repository name is required")
-                raise typer.Exit(1) from None
-
-            if not token:
-                console.print(
-                    "[red]Error:[/red] GitHub Personal Access Token is required"
-                )
-                raise typer.Exit(1) from None
-
-            config["adapters"]["github"] = {
-                "owner": owner,
-                "repo": repo,
-                "token": token,
-                "type": "github",
-            }
-
-    # 5. Save to project-local config (global config deprecated for security)
-    # Always save to ./.mcp-ticketer/config.json (PROJECT-SPECIFIC)
-    config_file_path = proj_path / ".mcp-ticketer" / "config.json"
-    config_file_path.parent.mkdir(parents=True, exist_ok=True)
-
-    with open(config_file_path, "w") as f:
-        json.dump(config, f, indent=2)
-
-    if global_config:
-        console.print(
-            "[yellow]Note: Global config deprecated for security. Saved to project config instead.[/yellow]"
-        )
-
-    console.print(f"[green]✓ Initialized with {adapter_type} adapter[/green]")
-    console.print(f"[dim]Project configuration saved to {config_file_path}[/dim]")
-
-    # Add .mcp-ticketer to .gitignore if not already there
-    gitignore_path = proj_path / ".gitignore"
-    if gitignore_path.exists():
-        gitignore_content = gitignore_path.read_text()
-        if ".mcp-ticketer" not in gitignore_content:
-            with open(gitignore_path, "a") as f:
-                f.write("\n# MCP Ticketer\n.mcp-ticketer/\n")
-            console.print("[dim]✓ Added .mcp-ticketer/ to .gitignore[/dim]")
-    else:
-        # Create .gitignore if it doesn't exist
-        with open(gitignore_path, "w") as f:
-            f.write("# MCP Ticketer\n.mcp-ticketer/\n")
-        console.print("[dim]✓ Created .gitignore with .mcp-ticketer/[/dim]")
-
-    # Validate configuration with loop for corrections
-    import asyncio
-
-    if not asyncio.run(
-        _validate_configuration_with_retry(
-            console, adapter_type, config_file_path, proj_path
-        )
-    ):
-        # User chose to exit without valid configuration
-        raise typer.Exit(1) from None
-
-    # Show next steps
-    _show_next_steps(console, adapter_type, config_file_path)
-
-
-def _show_next_steps(
-    console: Console, adapter_type: str, config_file_path: Path
-) -> None:
-    """Show helpful next steps after initialization.
-
-    Args:
-        console: Rich console for output
-        adapter_type: Type of adapter that was configured
-        config_file_path: Path to the configuration file
-
-    """
-    console.print("\n[bold green]🎉 Setup Complete![/bold green]")
-    console.print(f"MCP Ticketer is now configured to use {adapter_type.title()}.\n")
-
-    console.print("[bold]Next Steps:[/bold]")
-    console.print("1. [cyan]Create a test ticket:[/cyan]")
-    console.print("   mcp-ticketer create 'Test ticket from MCP Ticketer'")
-
-    if adapter_type != "aitrackdown":
-        console.print(
-            f"\n2. [cyan]Verify the ticket appears in {adapter_type.title()}[/cyan]"
-        )
-        if adapter_type == "linear":
-            console.print("   Check your Linear workspace for the new ticket")
-        elif adapter_type == "github":
-            console.print("   Check your GitHub repository's Issues tab")
-        elif adapter_type == "jira":
-            console.print("   Check your JIRA project for the new ticket")
-    else:
-        console.print("\n2. [cyan]Check local ticket storage:[/cyan]")
-        console.print("   ls .aitrackdown/")
-
-    console.print("\n3. [cyan]Install MCP for AI clients (optional):[/cyan]")
-    console.print("   mcp-ticketer install claude-code     # For Claude Code")
-    console.print("   mcp-ticketer install claude-desktop  # For Claude Desktop")
-    console.print("   mcp-ticketer install auggie          # For Auggie")
-    console.print("   mcp-ticketer install gemini          # For Gemini CLI")
-
-    console.print(f"\n[dim]Configuration saved to: {config_file_path}[/dim]")
-    console.print(
-        "[dim]Run 'mcp-ticketer doctor' to re-validate configuration anytime[/dim]"
-    )
-    console.print("[dim]Run 'mcp-ticketer --help' for more commands[/dim]")
-
-
-@app.command("set")
-def set_config(
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", "-a", help="Set default adapter"
-    ),
-    team_key: str | None = typer.Option(
-        None, "--team-key", help="Linear team key (e.g., BTA)"
-    ),
-    team_id: str | None = typer.Option(None, "--team-id", help="Linear team ID"),
-    owner: str | None = typer.Option(None, "--owner", help="GitHub repository owner"),
-    repo: str | None = typer.Option(None, "--repo", help="GitHub repository name"),
-    server: str | None = typer.Option(None, "--server", help="JIRA server URL"),
-    project: str | None = typer.Option(None, "--project", help="JIRA project key"),
-    base_path: str | None = typer.Option(
-        None, "--base-path", help="AITrackdown base path"
-    ),
-) -> None:
-    """Set default adapter and adapter-specific configuration.
-
-    When called without arguments, shows current configuration.
-    """
-    if not any([adapter, team_key, team_id, owner, repo, server, project, base_path]):
-        # Show current configuration
-        config = load_config()
-        console.print("[bold]Current Configuration:[/bold]")
-        console.print(
-            f"Default adapter: [cyan]{config.get('default_adapter', 'aitrackdown')}[/cyan]"
-        )
-
-        adapters_config = config.get("adapters", {})
-        if adapters_config:
-            console.print("\n[bold]Adapter Settings:[/bold]")
-            for adapter_name, adapter_config in adapters_config.items():
-                console.print(f"\n[cyan]{adapter_name}:[/cyan]")
-                for key, value in adapter_config.items():
-                    # Don't display sensitive values like tokens
-                    if (
-                        "token" in key.lower()
-                        or "key" in key.lower()
-                        and "team" not in key.lower()
-                    ):
-                        value = "***" if value else "not set"
-                    console.print(f"  {key}: {value}")
-        return
-
-    updates = {}
-
-    # Set default adapter
-    if adapter:
-        updates["default_adapter"] = adapter.value
-        console.print(f"[green]✓[/green] Default adapter set to: {adapter.value}")
-
-    # Build adapter-specific configuration
-    adapter_configs = {}
-
-    # Linear configuration
-    if team_key or team_id:
-        linear_config = {}
-        if team_key:
-            linear_config["team_key"] = team_key
-        if team_id:
-            linear_config["team_id"] = team_id
-        adapter_configs["linear"] = linear_config
-        console.print("[green]✓[/green] Linear settings updated")
-
-    # GitHub configuration
-    if owner or repo:
-        github_config = {}
-        if owner:
-            github_config["owner"] = owner
-        if repo:
-            github_config["repo"] = repo
-        adapter_configs["github"] = github_config
-        console.print("[green]✓[/green] GitHub settings updated")
-
-    # JIRA configuration
-    if server or project:
-        jira_config = {}
-        if server:
-            jira_config["server"] = server
-        if project:
-            jira_config["project_key"] = project
-        adapter_configs["jira"] = jira_config
-        console.print("[green]✓[/green] JIRA settings updated")
-
-    # AITrackdown configuration
-    if base_path:
-        adapter_configs["aitrackdown"] = {"base_path": base_path}
-        console.print("[green]✓[/green] AITrackdown settings updated")
-
-    if adapter_configs:
-        updates["adapters"] = adapter_configs
-
-    # Merge and save configuration
-    if updates:
-        config = merge_config(updates)
-        save_config(config)
-        console.print(f"[dim]Configuration saved to {CONFIG_FILE}[/dim]")
-
-
-@app.command("configure")
-def configure_command(
-    show: bool = typer.Option(False, "--show", help="Show current configuration"),
-    adapter: str | None = typer.Option(
-        None, "--adapter", help="Set default adapter type"
-    ),
-    api_key: str | None = typer.Option(None, "--api-key", help="Set API key/token"),
-    project_id: str | None = typer.Option(None, "--project-id", help="Set project ID"),
-    team_id: str | None = typer.Option(None, "--team-id", help="Set team ID (Linear)"),
-    global_scope: bool = typer.Option(
-        False,
-        "--global",
-        "-g",
-        help="Save to global config instead of project-specific",
-    ),
-) -> None:
-    """Configure MCP Ticketer integration.
-
-    Run without arguments to launch interactive wizard.
-    Use --show to display current configuration.
-    Use options to set specific values directly.
-    """
-    # Show configuration
-    if show:
-        show_current_config()
-        return
-
-    # Direct configuration
-    if any([adapter, api_key, project_id, team_id]):
-        set_adapter_config(
-            adapter=adapter,
-            api_key=api_key,
-            project_id=project_id,
-            team_id=team_id,
-            global_scope=global_scope,
-        )
-        return
-
-    # Run interactive wizard
-    configure_wizard()
-
-
-@app.command("migrate-config")
-def migrate_config(
-    dry_run: bool = typer.Option(
-        False, "--dry-run", help="Show what would be done without making changes"
-    ),
-) -> None:
-    """Migrate configuration from old format to new format.
-
-    This command will:
-    1. Detect old configuration format
-    2. Convert to new schema
-    3. Backup old config
-    4. Apply new config
-    """
-    migrate_config_command(dry_run=dry_run)
-
-
-@app.command("queue-status", deprecated=True, hidden=True)
-def old_queue_status_command() -> None:
-    """Show queue and worker status.
-
-    DEPRECATED: Use 'mcp-ticketer queue status' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer queue status' instead.[/yellow]\n"
-    )
-
-    queue = Queue()
-    manager = WorkerManager()
-
-    # Get queue stats
-    stats = queue.get_stats()
-    pending = stats.get(QueueStatus.PENDING.value, 0)
-
-    # Show queue status
-    console.print("[bold]Queue Status:[/bold]")
-    console.print(f"  Pending: {pending}")
-    console.print(f"  Processing: {stats.get(QueueStatus.PROCESSING.value, 0)}")
-    console.print(f"  Completed: {stats.get(QueueStatus.COMPLETED.value, 0)}")
-    console.print(f"  Failed: {stats.get(QueueStatus.FAILED.value, 0)}")
-
-    # Show worker status
-    worker_status = manager.get_status()
-    if worker_status["running"]:
-        console.print(
-            f"\n[green]● Worker is running[/green] (PID: {worker_status.get('pid')})"
-        )
-    else:
-        console.print("\n[red]○ Worker is not running[/red]")
-        if pending > 0:
-            console.print(
-                "[yellow]Note: There are pending items. Start worker with 'mcp-ticketer queue worker start'[/yellow]"
-            )
-
-
-@app.command("queue-health", deprecated=True, hidden=True)
-def old_queue_health_command(
-    auto_repair: bool = typer.Option(
-        False, "--auto-repair", help="Attempt automatic repair of issues"
-    ),
-    verbose: bool = typer.Option(
-        False, "--verbose", "-v", help="Show detailed health information"
-    ),
-) -> None:
-    """Check queue system health and detect issues immediately.
-
-    DEPRECATED: Use 'mcp-ticketer queue health' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer queue health' instead.[/yellow]\n"
-    )
-    health_monitor = QueueHealthMonitor()
-    health = health_monitor.check_health()
-
-    # Display overall status
-    status_color = {
-        HealthStatus.HEALTHY: "green",
-        HealthStatus.WARNING: "yellow",
-        HealthStatus.CRITICAL: "red",
-        HealthStatus.FAILED: "red",
-    }
-
-    status_icon = {
-        HealthStatus.HEALTHY: "✓",
-        HealthStatus.WARNING: "⚠️",
-        HealthStatus.CRITICAL: "🚨",
-        HealthStatus.FAILED: "❌",
-    }
-
-    color = status_color.get(health["status"], "white")
-    icon = status_icon.get(health["status"], "?")
-
-    console.print(f"[{color}]{icon} Queue Health: {health['status'].upper()}[/{color}]")
-    console.print(f"Last checked: {health['timestamp']}")
-
-    # Display alerts
-    if health["alerts"]:
-        console.print("\n[bold]Issues Found:[/bold]")
-        for alert in health["alerts"]:
-            alert_color = status_color.get(alert["level"], "white")
-            console.print(f"[{alert_color}]  • {alert['message']}[/{alert_color}]")
-
-            if verbose and alert.get("details"):
-                for key, value in alert["details"].items():
-                    console.print(f"    {key}: {value}")
-    else:
-        console.print("\n[green]✓ No issues detected[/green]")
-
-    # Auto-repair if requested
-    if auto_repair and health["status"] in [
-        HealthStatus.CRITICAL,
-        HealthStatus.WARNING,
-    ]:
-        console.print("\n[yellow]Attempting automatic repair...[/yellow]")
-        repair_result = health_monitor.auto_repair()
-
-        if repair_result["actions_taken"]:
-            console.print("[green]Repair actions taken:[/green]")
-            for action in repair_result["actions_taken"]:
-                console.print(f"[green]  ✓ {action}[/green]")
-
-            # Re-check health
-            console.print("\n[yellow]Re-checking health after repair...[/yellow]")
-            new_health = health_monitor.check_health()
-            new_color = status_color.get(new_health["status"], "white")
-            new_icon = status_icon.get(new_health["status"], "?")
-            console.print(
-                f"[{new_color}]{new_icon} Updated Health: {new_health['status'].upper()}[/{new_color}]"
-            )
-        else:
-            console.print("[yellow]No repair actions available[/yellow]")
-
-    # Exit with appropriate code
-    if health["status"] == HealthStatus.CRITICAL:
-        raise typer.Exit(1) from None
-    elif health["status"] == HealthStatus.WARNING:
-        raise typer.Exit(2) from None
-
-
-@app.command(deprecated=True, hidden=True)
-def create(
-    title: str = typer.Argument(..., help="Ticket title"),
-    description: str | None = typer.Option(
-        None, "--description", "-d", help="Ticket description"
-    ),
-    priority: Priority = typer.Option(
-        Priority.MEDIUM, "--priority", "-p", help="Priority level"
-    ),
-    tags: list[str] | None = typer.Option(
-        None, "--tag", "-t", help="Tags (can be specified multiple times)"
-    ),
-    assignee: str | None = typer.Option(
-        None, "--assignee", "-a", help="Assignee username"
-    ),
-    project: str | None = typer.Option(
-        None,
-        "--project",
-        help="Parent project/epic ID (synonym for --epic)",
-    ),
-    epic: str | None = typer.Option(
-        None,
-        "--epic",
-        help="Parent epic/project ID (synonym for --project)",
-    ),
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", help="Override default adapter"
-    ),
-) -> None:
-    """Create a new ticket with comprehensive health checks.
-
-    DEPRECATED: Use 'mcp-ticketer ticket create' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer ticket create' instead.[/yellow]\n"
-    )
-
-    # IMMEDIATE HEALTH CHECK - Critical for reliability
-    health_monitor = QueueHealthMonitor()
-    health = health_monitor.check_health()
-
-    # Display health status
-    if health["status"] == HealthStatus.CRITICAL:
-        console.print("[red]🚨 CRITICAL: Queue system has serious issues![/red]")
-        for alert in health["alerts"]:
-            if alert["level"] == "critical":
-                console.print(f"[red]  • {alert['message']}[/red]")
-
-        # Attempt auto-repair
-        console.print("[yellow]Attempting automatic repair...[/yellow]")
-        repair_result = health_monitor.auto_repair()
-
-        if repair_result["actions_taken"]:
-            for action in repair_result["actions_taken"]:
-                console.print(f"[yellow]  ✓ {action}[/yellow]")
-
-            # Re-check health after repair
-            health = health_monitor.check_health()
-            if health["status"] == HealthStatus.CRITICAL:
-                console.print(
-                    "[red]❌ Auto-repair failed. Manual intervention required.[/red]"
-                )
-                console.print(
-                    "[red]Cannot safely create ticket. Please check system status.[/red]"
-                )
-                raise typer.Exit(1) from None
-            else:
-                console.print(
-                    "[green]✓ Auto-repair successful. Proceeding with ticket creation.[/green]"
-                )
-        else:
-            console.print(
-                "[red]❌ No repair actions available. Manual intervention required.[/red]"
-            )
-            raise typer.Exit(1) from None
-
-    elif health["status"] == HealthStatus.WARNING:
-        console.print("[yellow]⚠️  Warning: Queue system has minor issues[/yellow]")
-        for alert in health["alerts"]:
-            if alert["level"] == "warning":
-                console.print(f"[yellow]  • {alert['message']}[/yellow]")
-        console.print("[yellow]Proceeding with ticket creation...[/yellow]")
-
-    # Get the adapter name with priority: 1) argument, 2) config, 3) .env files, 4) default
-    if adapter:
-        # Priority 1: Command-line argument - save to config for future use
-        adapter_name = adapter.value
-        _save_adapter_to_config(adapter_name)
-    else:
-        # Priority 2: Check existing config
-        config = load_config()
-        adapter_name = config.get("default_adapter")
-
-        if not adapter_name or adapter_name == "aitrackdown":
-            # Priority 3: Check .env files and save if found
-            env_adapter = _discover_from_env_files()
-            if env_adapter:
-                adapter_name = env_adapter
-                _save_adapter_to_config(adapter_name)
-            else:
-                # Priority 4: Default
-                adapter_name = "aitrackdown"
-
-    # Resolve project/epic synonym - prefer whichever is provided
-    parent_epic_id = project or epic
-
-    # Create task data
-    # Import Priority for type checking
-    from ..core.models import Priority as PriorityEnum
-
-    task_data = {
-        "title": title,
-        "description": description,
-        "priority": priority.value if isinstance(priority, PriorityEnum) else priority,
-        "tags": tags or [],
-        "assignee": assignee,
-        "parent_epic": parent_epic_id,
-    }
-
-    # WORKAROUND: Use direct operation for Linear adapter to bypass worker subprocess issue
-    if adapter_name == "linear":
-        console.print(
-            "[yellow]⚠️[/yellow]  Using direct operation for Linear adapter (bypassing queue)"
-        )
-        try:
-            # Load configuration and create adapter directly
-            config = load_config()
-            adapter_config = config.get("adapters", {}).get(adapter_name, {})
-
-            # Import and create adapter
-            from ..core.registry import AdapterRegistry
-
-            adapter = AdapterRegistry.get_adapter(adapter_name, adapter_config)
-
-            # Create task directly
-            from ..core.models import Priority, Task
-
-            task = Task(
-                title=task_data["title"],
-                description=task_data.get("description"),
-                priority=(
-                    Priority(task_data["priority"])
-                    if task_data.get("priority")
-                    else Priority.MEDIUM
-                ),
-                tags=task_data.get("tags", []),
-                assignee=task_data.get("assignee"),
-                parent_epic=task_data.get("parent_epic"),
-            )
-
-            # Create ticket synchronously
-            import asyncio
-
-            result = asyncio.run(adapter.create(task))
-
-            console.print(f"[green]✓[/green] Ticket created successfully: {result.id}")
-            console.print(f"  Title: {result.title}")
-            console.print(f"  Priority: {result.priority}")
-            console.print(f"  State: {result.state}")
-            # Get URL from metadata if available
-            if (
-                result.metadata
-                and "linear" in result.metadata
-                and "url" in result.metadata["linear"]
-            ):
-                console.print(f"  URL: {result.metadata['linear']['url']}")
-
-            return result.id
-
-        except Exception as e:
-            console.print(f"[red]❌[/red] Failed to create ticket: {e}")
-            raise
-
-    # Use queue for other adapters
-    queue = Queue()
-    queue_id = queue.add(
-        ticket_data=task_data,
-        adapter=adapter_name,
-        operation="create",
-        project_dir=str(Path.cwd()),  # Explicitly pass current project directory
-    )
-
-    # Register in ticket registry for tracking
-    registry = TicketRegistry()
-    registry.register_ticket_operation(
-        queue_id, adapter_name, "create", title, task_data
-    )
-
-    console.print(f"[green]✓[/green] Queued ticket creation: {queue_id}")
-    console.print(f"  Title: {title}")
-    console.print(f"  Priority: {priority}")
-    console.print(f"  Adapter: {adapter_name}")
-    console.print("[dim]Use 'mcp-ticketer check {queue_id}' to check progress[/dim]")
-
-    # Start worker if needed with immediate feedback
-    manager = WorkerManager()
-    worker_started = manager.start_if_needed()
-
-    if worker_started:
-        console.print("[dim]Worker started to process request[/dim]")
-
-        # Give immediate feedback on processing
-        import time
-
-        time.sleep(1)  # Brief pause to let worker start
-
-        # Check if item is being processed
-        item = queue.get_item(queue_id)
-        if item and item.status == QueueStatus.PROCESSING:
-            console.print("[green]✓ Item is being processed by worker[/green]")
-        elif item and item.status == QueueStatus.PENDING:
-            console.print("[yellow]⏳ Item is queued for processing[/yellow]")
-        else:
-            console.print(
-                "[red]⚠️  Item status unclear - check with 'mcp-ticketer check {queue_id}'[/red]"
-            )
-    else:
-        # Worker didn't start - this is a problem
-        pending_count = queue.get_pending_count()
-        if pending_count > 1:  # More than just this item
-            console.print(
-                f"[red]❌ Worker failed to start with {pending_count} pending items![/red]"
-            )
-            console.print(
-                "[red]This is a critical issue. Try 'mcp-ticketer queue worker start' manually.[/red]"
-            )
-        else:
-            console.print(
-                "[yellow]Worker not started (no other pending items)[/yellow]"
-            )
-
-
-@app.command("list", deprecated=True, hidden=True)
-def list_tickets(
-    state: TicketState | None = typer.Option(
-        None, "--state", "-s", help="Filter by state"
-    ),
-    priority: Priority | None = typer.Option(
-        None, "--priority", "-p", help="Filter by priority"
-    ),
-    limit: int = typer.Option(10, "--limit", "-l", help="Maximum number of tickets"),
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", help="Override default adapter"
-    ),
-) -> None:
-    """List tickets with optional filters.
-
-    DEPRECATED: Use 'mcp-ticketer ticket list' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer ticket list' instead.[/yellow]\n"
-    )
-
-    async def _list() -> None:
-        adapter_instance = get_adapter(
-            override_adapter=adapter.value if adapter else None
-        )
-        filters = {}
-        if state:
-            filters["state"] = state
-        if priority:
-            filters["priority"] = priority
-        return await adapter_instance.list(limit=limit, filters=filters)
-
-    tickets = asyncio.run(_list())
-
-    if not tickets:
-        console.print("[yellow]No tickets found[/yellow]")
-        return
-
-    # Create table
-    table = Table(title="Tickets")
-    table.add_column("ID", style="cyan", no_wrap=True)
-    table.add_column("Title", style="white")
-    table.add_column("State", style="green")
-    table.add_column("Priority", style="yellow")
-    table.add_column("Assignee", style="blue")
-
-    for ticket in tickets:
-        # Handle assignee field - Epic doesn't have assignee, Task does
-        assignee = getattr(ticket, "assignee", None) or "-"
-
-        table.add_row(
-            ticket.id or "N/A",
-            ticket.title,
-            ticket.state,
-            ticket.priority,
-            assignee,
-        )
-
-    console.print(table)
-
-
-@app.command(deprecated=True, hidden=True)
-def show(
-    ticket_id: str = typer.Argument(..., help="Ticket ID"),
-    comments: bool = typer.Option(False, "--comments", "-c", help="Show comments"),
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", help="Override default adapter"
-    ),
-) -> None:
-    """Show detailed ticket information.
-
-    DEPRECATED: Use 'mcp-ticketer ticket show' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer ticket show' instead.[/yellow]\n"
-    )
-
-    async def _show() -> None:
-        adapter_instance = get_adapter(
-            override_adapter=adapter.value if adapter else None
-        )
-        ticket = await adapter_instance.read(ticket_id)
-        ticket_comments = None
-        if comments and ticket:
-            ticket_comments = await adapter_instance.get_comments(ticket_id)
-        return ticket, ticket_comments
-
-    ticket, ticket_comments = asyncio.run(_show())
-
-    if not ticket:
-        console.print(f"[red]✗[/red] Ticket not found: {ticket_id}")
-        raise typer.Exit(1) from None
-
-    # Display ticket details
-    console.print(f"\n[bold]Ticket: {ticket.id}[/bold]")
-    console.print(f"Title: {ticket.title}")
-    console.print(f"State: [green]{ticket.state}[/green]")
-    console.print(f"Priority: [yellow]{ticket.priority}[/yellow]")
-
-    if ticket.description:
-        console.print("\n[dim]Description:[/dim]")
-        console.print(ticket.description)
-
-    if ticket.tags:
-        console.print(f"\nTags: {', '.join(ticket.tags)}")
-
-    if ticket.assignee:
-        console.print(f"Assignee: {ticket.assignee}")
-
-    # Display comments if requested
-    if ticket_comments:
-        console.print(f"\n[bold]Comments ({len(ticket_comments)}):[/bold]")
-        for comment in ticket_comments:
-            console.print(f"\n[dim]{comment.created_at} - {comment.author}:[/dim]")
-            console.print(comment.content)
-
-
-@app.command(deprecated=True, hidden=True)
-def comment(
-    ticket_id: str = typer.Argument(..., help="Ticket ID"),
-    content: str = typer.Argument(..., help="Comment content"),
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", help="Override default adapter"
-    ),
-) -> None:
-    """Add a comment to a ticket.
-
-    DEPRECATED: Use 'mcp-ticketer ticket comment' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer ticket comment' instead.[/yellow]\n"
-    )
-
-    async def _comment() -> None:
-        adapter_instance = get_adapter(
-            override_adapter=adapter.value if adapter else None
-        )
-
-        # Create comment
-        comment = Comment(
-            ticket_id=ticket_id,
-            content=content,
-            author="cli-user",  # Could be made configurable
-        )
-
-        result = await adapter_instance.add_comment(comment)
-        return result
-
-    try:
-        result = asyncio.run(_comment())
-        console.print("[green]✓[/green] Comment added successfully")
-        if result.id:
-            console.print(f"Comment ID: {result.id}")
-        console.print(f"Content: {content}")
-    except Exception as e:
-        console.print(f"[red]✗[/red] Failed to add comment: {e}")
-        raise typer.Exit(1) from e
-
-
-@app.command(deprecated=True, hidden=True)
-def update(
-    ticket_id: str = typer.Argument(..., help="Ticket ID"),
-    title: str | None = typer.Option(None, "--title", help="New title"),
-    description: str | None = typer.Option(
-        None, "--description", "-d", help="New description"
-    ),
-    priority: Priority | None = typer.Option(
-        None, "--priority", "-p", help="New priority"
-    ),
-    assignee: str | None = typer.Option(None, "--assignee", "-a", help="New assignee"),
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", help="Override default adapter"
-    ),
-) -> None:
-    """Update ticket fields.
-
-    DEPRECATED: Use 'mcp-ticketer ticket update' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer ticket update' instead.[/yellow]\n"
-    )
-    updates = {}
-    if title:
-        updates["title"] = title
-    if description:
-        updates["description"] = description
-    if priority:
-        updates["priority"] = (
-            priority.value if isinstance(priority, Priority) else priority
-        )
-    if assignee:
-        updates["assignee"] = assignee
-
-    if not updates:
-        console.print("[yellow]No updates specified[/yellow]")
-        raise typer.Exit(1) from None
-
-    # Get the adapter name
-    config = load_config()
-    adapter_name = (
-        adapter.value if adapter else config.get("default_adapter", "aitrackdown")
-    )
-
-    # Add ticket_id to updates
-    updates["ticket_id"] = ticket_id
-
-    # Add to queue with explicit project directory
-    queue = Queue()
-    queue_id = queue.add(
-        ticket_data=updates,
-        adapter=adapter_name,
-        operation="update",
-        project_dir=str(Path.cwd()),  # Explicitly pass current project directory
-    )
-
-    console.print(f"[green]✓[/green] Queued ticket update: {queue_id}")
-    for key, value in updates.items():
-        if key != "ticket_id":
-            console.print(f"  {key}: {value}")
-    console.print("[dim]Use 'mcp-ticketer status {queue_id}' to check progress[/dim]")
-
-    # Start worker if needed
-    manager = WorkerManager()
-    if manager.start_if_needed():
-        console.print("[dim]Worker started to process request[/dim]")
-
-
-@app.command(deprecated=True, hidden=True)
-def transition(
-    ticket_id: str = typer.Argument(..., help="Ticket ID"),
-    state_positional: TicketState | None = typer.Argument(
-        None, help="Target state (positional - deprecated, use --state instead)"
-    ),
-    state: TicketState | None = typer.Option(
-        None, "--state", "-s", help="Target state (recommended)"
-    ),
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", help="Override default adapter"
-    ),
-) -> None:
-    """Change ticket state with validation.
-
-    DEPRECATED: Use 'mcp-ticketer ticket transition' instead.
-
-    Examples:
-        # Recommended syntax with flag:
-        mcp-ticketer ticket transition BTA-215 --state done
-        mcp-ticketer ticket transition BTA-215 -s in_progress
-
-        # Legacy positional syntax (still supported):
-        mcp-ticketer ticket transition BTA-215 done
-
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer ticket transition' instead.[/yellow]\n"
-    )
-
-    # Determine which state to use (prefer flag over positional)
-    target_state = state if state is not None else state_positional
-
-    if target_state is None:
-        console.print("[red]Error: State is required[/red]")
-        console.print(
-            "Use either:\n"
-            "  - Flag syntax (recommended): mcp-ticketer transition TICKET-ID --state STATE\n"
-            "  - Positional syntax: mcp-ticketer transition TICKET-ID STATE"
-        )
-        raise typer.Exit(1) from None
-
-    # Get the adapter name
-    config = load_config()
-    adapter_name = (
-        adapter.value if adapter else config.get("default_adapter", "aitrackdown")
-    )
-
-    # Add to queue with explicit project directory
-    queue = Queue()
-    queue_id = queue.add(
-        ticket_data={
-            "ticket_id": ticket_id,
-            "state": (
-                target_state.value if hasattr(target_state, "value") else target_state
-            ),
-        },
-        adapter=adapter_name,
-        operation="transition",
-        project_dir=str(Path.cwd()),  # Explicitly pass current project directory
-    )
-
-    console.print(f"[green]✓[/green] Queued state transition: {queue_id}")
-    console.print(f"  Ticket: {ticket_id} → {target_state}")
-    console.print("[dim]Use 'mcp-ticketer status {queue_id}' to check progress[/dim]")
-
-    # Start worker if needed
-    manager = WorkerManager()
-    if manager.start_if_needed():
-        console.print("[dim]Worker started to process request[/dim]")
-
-
-@app.command(deprecated=True, hidden=True)
-def search(
-    query: str | None = typer.Argument(None, help="Search query"),
-    state: TicketState | None = typer.Option(None, "--state", "-s"),
-    priority: Priority | None = typer.Option(None, "--priority", "-p"),
-    assignee: str | None = typer.Option(None, "--assignee", "-a"),
-    limit: int = typer.Option(10, "--limit", "-l"),
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", help="Override default adapter"
-    ),
-) -> None:
-    """Search tickets with advanced query.
-
-    DEPRECATED: Use 'mcp-ticketer ticket search' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer ticket search' instead.[/yellow]\n"
-    )
-
-    async def _search() -> None:
-        adapter_instance = get_adapter(
-            override_adapter=adapter.value if adapter else None
-        )
-        search_query = SearchQuery(
-            query=query,
-            state=state,
-            priority=priority,
-            assignee=assignee,
-            limit=limit,
-        )
-        return await adapter_instance.search(search_query)
-
-    tickets = asyncio.run(_search())
-
-    if not tickets:
-        console.print("[yellow]No tickets found matching query[/yellow]")
-        return
-
-    # Display results
-    console.print(f"\n[bold]Found {len(tickets)} ticket(s)[/bold]\n")
-
-    for ticket in tickets:
-        console.print(f"[cyan]{ticket.id}[/cyan]: {ticket.title}")
-        console.print(f"  State: {ticket.state} | Priority: {ticket.priority}")
-        if ticket.assignee:
-            console.print(f"  Assignee: {ticket.assignee}")
-        console.print()
-
-
-# Add ticket command group to main app
-app.add_typer(ticket_app, name="ticket")
-
-# Add platform command group to main app
-app.add_typer(platform_app, name="platform")
-
-# Add queue command to main app
-app.add_typer(queue_app, name="queue")
-
-# Add discover command to main app
-app.add_typer(discover_app, name="discover")
-
-# Add instructions command to main app
-app.add_typer(instruction_app, name="instructions")
-
-
-# Add diagnostics command
-@app.command("doctor")
-def doctor_command(
-    output_file: str | None = typer.Option(
-        None, "--output", "-o", help="Save full report to file"
-    ),
-    json_output: bool = typer.Option(
-        False, "--json", help="Output report in JSON format"
-    ),
-    simple: bool = typer.Option(
-        False, "--simple", help="Use simple diagnostics (no heavy dependencies)"
-    ),
-) -> None:
-    """Run comprehensive system diagnostics and health check (alias: diagnose)."""
-    if simple:
-        from .simple_health import simple_diagnose
-
-        report = simple_diagnose()
-        if output_file:
-            import json
-
-            with open(output_file, "w") as f:
-                json.dump(report, f, indent=2)
-            console.print(f"\n📄 Report saved to: {output_file}")
-        if json_output:
-            import json
-
-            console.print("\n" + json.dumps(report, indent=2))
-        if report["issues"]:
-            raise typer.Exit(1) from None
-    else:
-        try:
-            asyncio.run(
-                run_diagnostics(output_file=output_file, json_output=json_output)
-            )
-        except typer.Exit:
-            # typer.Exit is expected - don't fall back to simple diagnostics
-            raise
-        except Exception as e:
-            console.print(f"⚠️  Full diagnostics failed: {e}")
-            console.print("🔄 Falling back to simple diagnostics...")
-            from .simple_health import simple_diagnose
-
-            report = simple_diagnose()
-            if report["issues"]:
-                raise typer.Exit(1) from None
-
-
-@app.command("diagnose", hidden=True)
-def diagnose_alias(
-    output_file: str | None = typer.Option(
-        None, "--output", "-o", help="Save full report to file"
-    ),
-    json_output: bool = typer.Option(
-        False, "--json", help="Output report in JSON format"
-    ),
-    simple: bool = typer.Option(
-        False, "--simple", help="Use simple diagnostics (no heavy dependencies)"
-    ),
-) -> None:
-    """Run comprehensive system diagnostics and health check (alias for doctor)."""
-    # Call the doctor_command function with the same parameters
-    doctor_command(output_file=output_file, json_output=json_output, simple=simple)
-
-
-@app.command("status")
-def status_command() -> None:
-    """Quick health check - shows system status summary (alias: health)."""
-    from .simple_health import simple_health_check
-
-    result = simple_health_check()
-    if result != 0:
-        raise typer.Exit(result) from None
-
-
-@app.command("health")
-def health_alias() -> None:
-    """Quick health check - shows system status summary (alias for status)."""
-    from .simple_health import simple_health_check
-
-    result = simple_health_check()
-    if result != 0:
-        raise typer.Exit(result) from None
-
-
-# Create MCP configuration command group
-mcp_app = typer.Typer(
-    name="mcp",
-    help="Configure MCP integration for AI clients (Claude, Gemini, Codex, Auggie)",
-    add_completion=False,
-    invoke_without_command=True,
-)
-
-
-@mcp_app.callback()
-def mcp_callback(
-    ctx: typer.Context,
-    project_path: str | None = typer.Option(
-        None, "--path", "-p", help="Project directory path (default: current directory)"
-    ),
-) -> None:
-    """MCP command group - runs MCP server if no subcommand provided.
-
-    Examples:
-        mcp-ticketer mcp              # Start server in current directory
-        mcp-ticketer mcp --path /dir  # Start server in specific directory
-        mcp-ticketer mcp -p /dir      # Start server (short form)
-        mcp-ticketer mcp status       # Check MCP status
-        mcp-ticketer mcp serve        # Explicitly start server
-
-    """
-    if ctx.invoked_subcommand is None:
-        # No subcommand provided, run the serve command
-        # Change to project directory if provided
-        if project_path:
-            import os
-
-            os.chdir(project_path)
-        # Invoke the serve command through context
-        ctx.invoke(mcp_serve, adapter=None, base_path=None)
-
-
-@app.command()
-def install(
-    platform: str | None = typer.Argument(
-        None,
-        help="Platform to install (claude-code, claude-desktop, gemini, codex, auggie)",
-    ),
-    auto_detect: bool = typer.Option(
-        False,
-        "--auto-detect",
-        "-d",
-        help="Auto-detect and show all installed AI platforms",
-    ),
-    install_all: bool = typer.Option(
-        False,
-        "--all",
-        help="Install for all detected platforms",
-    ),
-    adapter: str | None = typer.Option(
-        None,
-        "--adapter",
-        "-a",
-        help="Adapter type to use (interactive prompt if not specified)",
-    ),
-    project_path: str | None = typer.Option(
-        None, "--path", help="Project path (default: current directory)"
+@app.command("set")
+def set_config(
+    adapter: AdapterType | None = typer.Option(
+        None, "--adapter", "-a", help="Set default adapter"
     ),
-    global_config: bool = typer.Option(
-        False,
-        "--global",
-        "-g",
-        help="Save to global config instead of project-specific",
+    team_key: str | None = typer.Option(
+        None, "--team-key", help="Linear team key (e.g., BTA)"
     ),
+    team_id: str | None = typer.Option(None, "--team-id", help="Linear team ID"),
+    owner: str | None = typer.Option(None, "--owner", help="GitHub repository owner"),
+    repo: str | None = typer.Option(None, "--repo", help="GitHub repository name"),
+    server: str | None = typer.Option(None, "--server", help="JIRA server URL"),
+    project: str | None = typer.Option(None, "--project", help="JIRA project key"),
     base_path: str | None = typer.Option(
-        None,
-        "--base-path",
-        "-p",
-        help="Base path for ticket storage (AITrackdown only)",
-    ),
-    api_key: str | None = typer.Option(
-        None, "--api-key", help="API key for Linear or API token for JIRA"
-    ),
-    team_id: str | None = typer.Option(
-        None, "--team-id", help="Linear team ID (required for Linear adapter)"
-    ),
-    jira_server: str | None = typer.Option(
-        None,
-        "--jira-server",
-        help="JIRA server URL (e.g., https://company.atlassian.net)",
-    ),
-    jira_email: str | None = typer.Option(
-        None, "--jira-email", help="JIRA user email for authentication"
-    ),
-    jira_project: str | None = typer.Option(
-        None, "--jira-project", help="Default JIRA project key"
-    ),
-    github_owner: str | None = typer.Option(
-        None, "--github-owner", help="GitHub repository owner"
-    ),
-    github_repo: str | None = typer.Option(
-        None, "--github-repo", help="GitHub repository name"
-    ),
-    github_token: str | None = typer.Option(
-        None, "--github-token", help="GitHub Personal Access Token"
-    ),
-    dry_run: bool = typer.Option(
-        False,
-        "--dry-run",
-        help="Show what would be done without making changes (for platform installation)",
+        None, "--base-path", help="AITrackdown base path"
     ),
 ) -> None:
-    """Install MCP server configuration for AI platforms.
-
-    This command configures mcp-ticketer as an MCP server for various AI
-    platforms. It updates platform-specific configuration files to enable
-    mcp-ticketer integration.
-
-    RECOMMENDED: Use 'mcp-ticketer setup' for first-time setup, which
-    handles both adapter configuration and platform installation together.
-
-    Platform Installation:
-        # Auto-detect and prompt for platform selection
-        mcp-ticketer install
-
-        # Show all detected platforms
-        mcp-ticketer install --auto-detect
-
-        # Install for all detected platforms
-        mcp-ticketer install --all
-
-        # Install for specific platform
-        mcp-ticketer install claude-code     # Claude Code (project-level)
-        mcp-ticketer install claude-desktop  # Claude Desktop (global)
-        mcp-ticketer install gemini          # Gemini CLI
-        mcp-ticketer install codex           # Codex
-        mcp-ticketer install auggie          # Auggie
-
-    Legacy Usage (adapter setup, deprecated - use 'init' or 'setup' instead):
-        mcp-ticketer install --adapter linear  # Use 'init' or 'setup' instead
+    """Set default adapter and adapter-specific configuration.
 
+    When called without arguments, shows current configuration.
     """
-    from .platform_detection import PlatformDetector, get_platform_by_name
-
-    detector = PlatformDetector()
-
-    # Handle auto-detect flag (just show detected platforms and exit)
-    if auto_detect:
-        detected = detector.detect_all(
-            project_path=Path(project_path) if project_path else Path.cwd()
-        )
-
-        if not detected:
-            console.print("[yellow]No AI platforms detected.[/yellow]")
-            console.print("\n[bold]Supported platforms:[/bold]")
-            console.print("  • Claude Code - Project-level configuration")
-            console.print("  • Claude Desktop - Global GUI application")
-            console.print("  • Auggie - CLI tool with global config")
-            console.print("  • Codex - CLI tool with global config")
-            console.print("  • Gemini - CLI tool with project/global config")
-            console.print(
-                "\n[dim]Install these platforms to use them with mcp-ticketer.[/dim]"
-            )
-            return
-
-        console.print("[bold]Detected AI platforms:[/bold]\n")
-        table = Table(show_header=True, header_style="bold cyan")
-        table.add_column("Platform", style="green")
-        table.add_column("Status", style="yellow")
-        table.add_column("Scope", style="blue")
-        table.add_column("Config Path", style="dim")
-
-        for plat in detected:
-            status = "✓ Installed" if plat.is_installed else "⚠ Config Issue"
-            table.add_row(plat.display_name, status, plat.scope, str(plat.config_path))
-
-        console.print(table)
-        console.print(
-            "\n[dim]Run 'mcp-ticketer install <platform>' to configure a specific platform[/dim]"
-        )
-        console.print(
-            "[dim]Run 'mcp-ticketer install --all' to configure all detected platforms[/dim]"
-        )
-        return
-
-    # Handle --all flag (install for all detected platforms)
-    if install_all:
-        detected = detector.detect_all(
-            project_path=Path(project_path) if project_path else Path.cwd()
-        )
-
-        if not detected:
-            console.print("[yellow]No AI platforms detected.[/yellow]")
-            console.print(
-                "Run 'mcp-ticketer install --auto-detect' to see supported platforms."
-            )
-            return
-
-        # Handle dry-run mode - show what would be installed without actually installing
-        if dry_run:
-            console.print(
-                "\n[yellow]DRY RUN - The following platforms would be configured:[/yellow]\n"
-            )
-
-            installable_count = 0
-            for plat in detected:
-                if plat.is_installed:
-                    console.print(f"  ✓ {plat.display_name} ({plat.scope})")
-                    installable_count += 1
-                else:
-                    console.print(
-                        f"  ⚠ {plat.display_name} ({plat.scope}) - would be skipped (configuration issue)"
-                    )
-
-            console.print(
-                f"\n[dim]Would configure {installable_count} platform(s)[/dim]"
-            )
-            return
-
-        console.print(
-            f"[bold]Installing for {len(detected)} detected platform(s)...[/bold]\n"
-        )
-
-        # Import configuration functions
-        from .auggie_configure import configure_auggie_mcp
-        from .codex_configure import configure_codex_mcp
-        from .gemini_configure import configure_gemini_mcp
-        from .mcp_configure import configure_claude_mcp
-
-        # Map platform names to configuration functions
-        platform_mapping = {
-            "claude-code": lambda: configure_claude_mcp(
-                global_config=False, force=True
-            ),
-            "claude-desktop": lambda: configure_claude_mcp(
-                global_config=True, force=True
-            ),
-            "auggie": lambda: configure_auggie_mcp(force=True),
-            "gemini": lambda: configure_gemini_mcp(scope="project", force=True),
-            "codex": lambda: configure_codex_mcp(force=True),
-        }
-
-        success_count = 0
-        failed = []
-
-        for plat in detected:
-            if not plat.is_installed:
-                console.print(
-                    f"[yellow]⚠[/yellow]  Skipping {plat.display_name} (configuration issue)"
-                )
-                continue
-
-            config_func = platform_mapping.get(plat.name)
-            if not config_func:
-                console.print(
-                    f"[yellow]⚠[/yellow]  No installer for {plat.display_name}"
-                )
-                continue
-
-            try:
-                console.print(f"[cyan]Installing for {plat.display_name}...[/cyan]")
-                config_func()
-                success_count += 1
-            except Exception as e:
-                console.print(
-                    f"[red]✗[/red]  Failed to install for {plat.display_name}: {e}"
-                )
-                failed.append(plat.display_name)
-
-        console.print(
-            f"\n[bold]Installation complete:[/bold] {success_count} succeeded"
-        )
-        if failed:
-            console.print(f"[red]Failed:[/red] {', '.join(failed)}")
-        return
-
-    # If no platform argument and no adapter flag, auto-detect and prompt
-    if platform is None and adapter is None:
-        detected = detector.detect_all(
-            project_path=Path(project_path) if project_path else Path.cwd()
-        )
-
-        # Filter to only installed platforms
-        installed = [p for p in detected if p.is_installed]
-
-        if not installed:
-            console.print("[yellow]No AI platforms detected.[/yellow]")
-            console.print("\n[bold]To see supported platforms:[/bold]")
-            console.print("  mcp-ticketer install --auto-detect")
-            console.print("\n[bold]Or run legacy adapter setup:[/bold]")
-            console.print("  mcp-ticketer install --adapter <adapter-type>")
-            return
-
-        # Show detected platforms and prompt for selection
-        console.print("[bold]Detected AI platforms:[/bold]\n")
-        for idx, plat in enumerate(installed, 1):
-            console.print(f"  {idx}. {plat.display_name} ({plat.scope})")
-
+    if not any([adapter, team_key, team_id, owner, repo, server, project, base_path]):
+        # Show current configuration
+        config = load_config()
+        console.print("[bold]Current Configuration:[/bold]")
         console.print(
-            "\n[dim]Enter the number of the platform to configure, or 'q' to quit:[/dim]"
-        )
-        choice = typer.prompt("Select platform")
-
-        if choice.lower() == "q":
-            console.print("Installation cancelled.")
-            return
-
-        try:
-            idx = int(choice) - 1
-            if idx < 0 or idx >= len(installed):
-                console.print("[red]Invalid selection.[/red]")
-                raise typer.Exit(1) from None
-            platform = installed[idx].name
-        except ValueError as e:
-            console.print("[red]Invalid input. Please enter a number.[/red]")
-            raise typer.Exit(1) from e
-
-    # If platform argument is provided, handle MCP platform installation (NEW SYNTAX)
-    if platform is not None:
-        # Validate that the platform is actually installed
-        platform_info = get_platform_by_name(
-            platform, project_path=Path(project_path) if project_path else Path.cwd()
+            f"Default adapter: [cyan]{config.get('default_adapter', 'aitrackdown')}[/cyan]"
         )
 
-        if platform_info and not platform_info.is_installed:
-            console.print(
-                f"[yellow]⚠[/yellow]  {platform_info.display_name} was detected but has a configuration issue."
-            )
-            console.print(f"[dim]Config path: {platform_info.config_path}[/dim]\n")
-
-            proceed = typer.confirm(
-                "Do you want to proceed with installation anyway?", default=False
-            )
-            if not proceed:
-                console.print("Installation cancelled.")
-                return
-
-        elif not platform_info:
-            # Platform not detected at all - warn but allow proceeding
-            console.print(
-                f"[yellow]⚠[/yellow]  Platform '{platform}' not detected on this system."
-            )
-            console.print(
-                "[dim]Run 'mcp-ticketer install --auto-detect' to see detected platforms.[/dim]\n"
-            )
-
-            proceed = typer.confirm(
-                "Do you want to proceed with installation anyway?", default=False
-            )
-            if not proceed:
-                console.print("Installation cancelled.")
-                return
-
-        # Import configuration functions
-        from .auggie_configure import configure_auggie_mcp
-        from .codex_configure import configure_codex_mcp
-        from .gemini_configure import configure_gemini_mcp
-        from .mcp_configure import configure_claude_mcp
-
-        # Map platform names to configuration functions
-        platform_mapping = {
-            "claude-code": {
-                "func": lambda: configure_claude_mcp(global_config=False, force=True),
-                "name": "Claude Code",
-            },
-            "claude-desktop": {
-                "func": lambda: configure_claude_mcp(global_config=True, force=True),
-                "name": "Claude Desktop",
-            },
-            "auggie": {
-                "func": lambda: configure_auggie_mcp(force=True),
-                "name": "Auggie",
-            },
-            "gemini": {
-                "func": lambda: configure_gemini_mcp(scope="project", force=True),
-                "name": "Gemini CLI",
-            },
-            "codex": {
-                "func": lambda: configure_codex_mcp(force=True),
-                "name": "Codex",
-            },
-        }
-
-        if platform not in platform_mapping:
-            console.print(f"[red]Unknown platform: {platform}[/red]")
-            console.print("\n[bold]Available platforms:[/bold]")
-            for p in platform_mapping.keys():
-                console.print(f"  • {p}")
-            raise typer.Exit(1) from None
-
-        config = platform_mapping[platform]
-
-        if dry_run:
-            console.print(f"[cyan]DRY RUN - Would install for {config['name']}[/cyan]")
-            return
-
-        try:
-            config["func"]()
-        except Exception as e:
-            console.print(f"[red]Installation failed: {e}[/red]")
-            raise typer.Exit(1) from e
-        return
-
-    # Otherwise, delegate to init for adapter initialization (LEGACY BEHAVIOR)
-    # This makes 'install' and 'init' synonymous when called without platform argument
-    init(
-        adapter=adapter,
-        project_path=project_path,
-        global_config=global_config,
-        base_path=base_path,
-        api_key=api_key,
-        team_id=team_id,
-        jira_server=jira_server,
-        jira_email=jira_email,
-        jira_project=jira_project,
-        github_owner=github_owner,
-        github_repo=github_repo,
-        github_token=github_token,
-    )
-
-
-@app.command()
-def remove(
-    platform: str | None = typer.Argument(
-        None,
-        help="Platform to remove (claude-code, claude-desktop, auggie, gemini, codex)",
-    ),
-    dry_run: bool = typer.Option(
-        False, "--dry-run", help="Show what would be done without making changes"
-    ),
-) -> None:
-    """Remove mcp-ticketer from AI platforms.
-
-    Without arguments, shows help and available platforms.
-    With a platform argument, removes MCP configuration for that platform.
-
-    Examples:
-        # Remove from Claude Code (project-level)
-        mcp-ticketer remove claude-code
-
-        # Remove from Claude Desktop (global)
-        mcp-ticketer remove claude-desktop
-
-        # Remove from Auggie
-        mcp-ticketer remove auggie
-
-        # Dry run to preview changes
-        mcp-ticketer remove claude-code --dry-run
-
-    """
-    # If no platform specified, show help message
-    if platform is None:
-        console.print("[bold]Remove mcp-ticketer from AI platforms[/bold]\n")
-        console.print("Usage: mcp-ticketer remove <platform>\n")
-        console.print("[bold]Available platforms:[/bold]")
-        console.print("  • claude-code     - Claude Code (project-level)")
-        console.print("  • claude-desktop  - Claude Desktop (global)")
-        console.print("  • auggie          - Auggie (global)")
-        console.print("  • gemini          - Gemini CLI (project-level by default)")
-        console.print("  • codex           - Codex (global)")
+        adapters_config = config.get("adapters", {})
+        if adapters_config:
+            console.print("\n[bold]Adapter Settings:[/bold]")
+            for adapter_name, adapter_config in adapters_config.items():
+                console.print(f"\n[cyan]{adapter_name}:[/cyan]")
+                for key, value in adapter_config.items():
+                    # Don't display sensitive values like tokens
+                    if (
+                        "token" in key.lower()
+                        or "key" in key.lower()
+                        and "team" not in key.lower()
+                    ):
+                        value = "***" if value else "not set"
+                    console.print(f"  {key}: {value}")
         return
 
-    # Import removal functions
-    from .auggie_configure import remove_auggie_mcp
-    from .codex_configure import remove_codex_mcp
-    from .gemini_configure import remove_gemini_mcp
-    from .mcp_configure import remove_claude_mcp
-
-    # Map platform names to removal functions
-    platform_mapping = {
-        "claude-code": {
-            "func": lambda: remove_claude_mcp(global_config=False, dry_run=dry_run),
-            "name": "Claude Code",
-        },
-        "claude-desktop": {
-            "func": lambda: remove_claude_mcp(global_config=True, dry_run=dry_run),
-            "name": "Claude Desktop",
-        },
-        "auggie": {
-            "func": lambda: remove_auggie_mcp(dry_run=dry_run),
-            "name": "Auggie",
-        },
-        "gemini": {
-            "func": lambda: remove_gemini_mcp(scope="project", dry_run=dry_run),
-            "name": "Gemini CLI",
-        },
-        "codex": {
-            "func": lambda: remove_codex_mcp(dry_run=dry_run),
-            "name": "Codex",
-        },
-    }
-
-    if platform not in platform_mapping:
-        console.print(f"[red]Unknown platform: {platform}[/red]")
-        console.print("\n[bold]Available platforms:[/bold]")
-        for p in platform_mapping.keys():
-            console.print(f"  • {p}")
-        raise typer.Exit(1) from None
-
-    config = platform_mapping[platform]
-
-    try:
-        config["func"]()
-    except Exception as e:
-        console.print(f"[red]Removal failed: {e}[/red]")
-        raise typer.Exit(1) from e
-
-
-@app.command()
-def uninstall(
-    platform: str | None = typer.Argument(
-        None,
-        help="Platform to uninstall (claude-code, claude-desktop, auggie, gemini, codex)",
-    ),
-    dry_run: bool = typer.Option(
-        False, "--dry-run", help="Show what would be done without making changes"
-    ),
-) -> None:
-    """Uninstall mcp-ticketer from AI platforms (alias for remove).
-
-    This is an alias for the 'remove' command.
-
-    Without arguments, shows help and available platforms.
-    With a platform argument, removes MCP configuration for that platform.
-
-    Examples:
-        # Uninstall from Claude Code (project-level)
-        mcp-ticketer uninstall claude-code
-
-        # Uninstall from Claude Desktop (global)
-        mcp-ticketer uninstall claude-desktop
-
-        # Uninstall from Auggie
-        mcp-ticketer uninstall auggie
+    updates = {}
 
-        # Dry run to preview changes
-        mcp-ticketer uninstall claude-code --dry-run
+    # Set default adapter
+    if adapter:
+        updates["default_adapter"] = adapter.value
+        console.print(f"[green]✓[/green] Default adapter set to: {adapter.value}")
 
-    """
-    # Call the remove command with the same parameters
-    remove(platform=platform, dry_run=dry_run)
+    # Build adapter-specific configuration
+    adapter_configs = {}
 
+    # Linear configuration
+    if team_key or team_id:
+        linear_config = {}
+        if team_key:
+            linear_config["team_key"] = team_key
+        if team_id:
+            linear_config["team_id"] = team_id
+        adapter_configs["linear"] = linear_config
+        console.print("[green]✓[/green] Linear settings updated")
 
-@app.command(deprecated=True, hidden=True)
-def check(queue_id: str = typer.Argument(..., help="Queue ID to check")) -> None:
-    """Check status of a queued operation.
+    # GitHub configuration
+    if owner or repo:
+        github_config = {}
+        if owner:
+            github_config["owner"] = owner
+        if repo:
+            github_config["repo"] = repo
+        adapter_configs["github"] = github_config
+        console.print("[green]✓[/green] GitHub settings updated")
 
-    DEPRECATED: Use 'mcp-ticketer ticket check' instead.
-    """
-    console.print(
-        "[yellow]⚠️  This command is deprecated. Use 'mcp-ticketer ticket check' instead.[/yellow]\n"
-    )
-    queue = Queue()
-    item = queue.get_item(queue_id)
-
-    if not item:
-        console.print(f"[red]Queue item not found: {queue_id}[/red]")
-        raise typer.Exit(1) from None
-
-    # Display status
-    console.print(f"\n[bold]Queue Item: {item.id}[/bold]")
-    console.print(f"Operation: {item.operation}")
-    console.print(f"Adapter: {item.adapter}")
-
-    # Status with color
-    if item.status == QueueStatus.COMPLETED:
-        console.print(f"Status: [green]{item.status}[/green]")
-    elif item.status == QueueStatus.FAILED:
-        console.print(f"Status: [red]{item.status}[/red]")
-    elif item.status == QueueStatus.PROCESSING:
-        console.print(f"Status: [yellow]{item.status}[/yellow]")
-    else:
-        console.print(f"Status: {item.status}")
+    # JIRA configuration
+    if server or project:
+        jira_config = {}
+        if server:
+            jira_config["server"] = server
+        if project:
+            jira_config["project_key"] = project
+        adapter_configs["jira"] = jira_config
+        console.print("[green]✓[/green] JIRA settings updated")
 
-    # Timestamps
-    console.print(f"Created: {item.created_at.strftime('%Y-%m-%d %H:%M:%S')}")
-    if item.processed_at:
-        console.print(f"Processed: {item.processed_at.strftime('%Y-%m-%d %H:%M:%S')}")
+    # AITrackdown configuration
+    if base_path:
+        adapter_configs["aitrackdown"] = {"base_path": base_path}
+        console.print("[green]✓[/green] AITrackdown settings updated")
 
-    # Error or result
-    if item.error_message:
-        console.print(f"\n[red]Error:[/red] {item.error_message}")
-    elif item.result:
-        console.print("\n[green]Result:[/green]")
-        for key, value in item.result.items():
-            console.print(f"  {key}: {value}")
+    if adapter_configs:
+        updates["adapters"] = adapter_configs
 
-    if item.retry_count > 0:
-        console.print(f"\nRetry Count: {item.retry_count}")
+    # Merge and save configuration
+    if updates:
+        config = merge_config(updates)
+        save_config(config)
+        console.print(f"[dim]Configuration saved to {CONFIG_FILE}[/dim]")
 
 
-@mcp_app.command(name="serve")
-def mcp_serve(
-    adapter: AdapterType | None = typer.Option(
-        None, "--adapter", "-a", help="Override default adapter type"
+@app.command("configure")
+def configure_command(
+    show: bool = typer.Option(False, "--show", help="Show current configuration"),
+    adapter: str | None = typer.Option(
+        None, "--adapter", help="Set default adapter type"
     ),
-    base_path: str | None = typer.Option(
-        None, "--base-path", help="Base path for AITrackdown adapter"
+    api_key: str | None = typer.Option(None, "--api-key", help="Set API key/token"),
+    project_id: str | None = typer.Option(None, "--project-id", help="Set project ID"),
+    team_id: str | None = typer.Option(None, "--team-id", help="Set team ID (Linear)"),
+    global_scope: bool = typer.Option(
+        False,
+        "--global",
+        "-g",
+        help="Save to global config instead of project-specific",
     ),
 ) -> None:
-    """Start MCP server for JSON-RPC communication over stdio.
-
-    This command is used by Claude Code/Desktop when connecting to the MCP server.
-    You typically don't need to run this manually - use 'mcp-ticketer install add' to configure.
-
-    Configuration Resolution:
-    - When MCP server starts, it uses the current working directory (cwd)
-    - The cwd is set by Claude Code/Desktop from the 'cwd' field in .mcp/config.json
-    - Configuration is loaded with this priority:
-      1. Project-specific: .mcp-ticketer/config.json in cwd
-      2. Global: ~/.mcp-ticketer/config.json
-      3. Default: aitrackdown adapter with .aitrackdown base path
-    """
-    from ..mcp.server.server_sdk import configure_adapter
-    from ..mcp.server.server_sdk import main as sdk_main
-
-    # Load configuration (respects project-specific config in cwd)
-    config = load_config()
-
-    # Determine adapter type with priority: CLI arg > config > .env files > default
-    if adapter:
-        # Priority 1: Command line argument
-        adapter_type = adapter.value
-        # Get base config from config file
-        adapters_config = config.get("adapters", {})
-        adapter_config = adapters_config.get(adapter_type, {})
-    else:
-        # Priority 2: Configuration file (project-specific)
-        adapter_type = config.get("default_adapter")
-        if adapter_type:
-            adapters_config = config.get("adapters", {})
-            adapter_config = adapters_config.get(adapter_type, {})
-        else:
-            # Priority 3: .env files (auto-detection fallback)
-            from ..mcp.server.main import _load_env_configuration
-
-            env_config = _load_env_configuration()
-            if env_config:
-                adapter_type = env_config["adapter_type"]
-                adapter_config = env_config["adapter_config"]
-            else:
-                # Priority 4: Default fallback
-                adapter_type = "aitrackdown"
-                adapters_config = config.get("adapters", {})
-                adapter_config = adapters_config.get(adapter_type, {})
-
-    # Override with command line options if provided (highest priority)
-    if base_path and adapter_type == "aitrackdown":
-        adapter_config["base_path"] = base_path
-
-    # Fallback to legacy config format
-    if not adapter_config and "config" in config:
-        adapter_config = config["config"]
+    """Configure MCP Ticketer integration.
 
-    # MCP server uses stdio for JSON-RPC, so we can't print to stdout
-    # Only print to stderr to avoid interfering with the protocol
-    import sys
+    Run without arguments to launch interactive wizard.
+    Use --show to display current configuration.
+    Use options to set specific values directly.
+    """
+    # Show configuration
+    if show:
+        show_current_config()
+        return
 
-    if sys.stderr.isatty():
-        # Only print if stderr is a terminal (not redirected)
-        console.file = sys.stderr
-        console.print(
-            f"[green]Starting MCP SDK server[/green] with {adapter_type} adapter"
-        )
-        console.print(
-            "[dim]Server running on stdio. Send JSON-RPC requests via stdin.[/dim]"
+    # Direct configuration
+    if any([adapter, api_key, project_id, team_id]):
+        set_adapter_config(
+            adapter=adapter,
+            api_key=api_key,
+            project_id=project_id,
+            team_id=team_id,
+            global_scope=global_scope,
         )
+        return
 
-    # Configure adapter and run SDK server
-    try:
-        configure_adapter(adapter_type, adapter_config)
-        sdk_main()
-    except KeyboardInterrupt:
-        # Send this to stderr
-        if sys.stderr.isatty():
-            console.print("\n[yellow]Server stopped by user[/yellow]")
-        sys.exit(0)
-    except Exception as e:
-        # Log error to stderr
-        sys.stderr.write(f"MCP server error: {e}\n")
-        sys.exit(1)
+    # Run interactive wizard
+    configure_wizard()
 
 
-@mcp_app.command(name="claude")
-def mcp_claude(
-    global_config: bool = typer.Option(
+@app.command("config")
+def config_alias(
+    show: bool = typer.Option(False, "--show", help="Show current configuration"),
+    adapter: str | None = typer.Option(
+        None, "--adapter", help="Set default adapter type"
+    ),
+    api_key: str | None = typer.Option(None, "--api-key", help="Set API key/token"),
+    project_id: str | None = typer.Option(None, "--project-id", help="Set project ID"),
+    team_id: str | None = typer.Option(None, "--team-id", help="Set team ID (Linear)"),
+    global_scope: bool = typer.Option(
         False,
         "--global",
         "-g",
-        help="Configure Claude Desktop instead of project-level",
-    ),
-    force: bool = typer.Option(
-        False, "--force", "-f", help="Overwrite existing configuration"
+        help="Save to global config instead of project-specific",
     ),
 ) -> None:
-    """Configure Claude Code to use mcp-ticketer MCP server.
-
-    Reads configuration from .mcp-ticketer/config.json and updates
-    Claude Code's MCP settings accordingly.
-
-    By default, configures project-level (.mcp/config.json).
-    Use --global to configure Claude Desktop instead.
-
-    Examples:
-        # Configure for current project (default)
-        mcp-ticketer mcp claude
-
-        # Configure Claude Desktop globally
-        mcp-ticketer mcp claude --global
-
-        # Force overwrite existing configuration
-        mcp-ticketer mcp claude --force
+    """Alias for configure command - shorter syntax."""
+    configure_command(show, adapter, api_key, project_id, team_id, global_scope)
 
-    """
-    from ..cli.mcp_configure import configure_claude_mcp
-
-    try:
-        configure_claude_mcp(global_config=global_config, force=force)
-    except Exception as e:
-        console.print(f"[red]✗ Configuration failed:[/red] {e}")
-        raise typer.Exit(1) from e
 
-
-@mcp_app.command(name="gemini")
-def mcp_gemini(
-    scope: str = typer.Option(
-        "project",
-        "--scope",
-        "-s",
-        help="Configuration scope: 'project' (default) or 'user'",
-    ),
-    force: bool = typer.Option(
-        False, "--force", "-f", help="Overwrite existing configuration"
+@app.command("migrate-config")
+def migrate_config(
+    dry_run: bool = typer.Option(
+        False, "--dry-run", help="Show what would be done without making changes"
     ),
 ) -> None:
-    """Configure Gemini CLI to use mcp-ticketer MCP server.
-
-    Reads configuration from .mcp-ticketer/config.json and creates
-    Gemini CLI settings file with mcp-ticketer configuration.
-
-    By default, configures project-level (.gemini/settings.json).
-    Use --scope user to configure user-level (~/.gemini/settings.json).
-
-    Examples:
-        # Configure for current project (default)
-        mcp-ticketer mcp gemini
-
-        # Configure at user level
-        mcp-ticketer mcp gemini --scope user
-
-        # Force overwrite existing configuration
-        mcp-ticketer mcp gemini --force
+    """Migrate configuration from old format to new format.
 
+    This command will:
+    1. Detect old configuration format
+    2. Convert to new schema
+    3. Backup old config
+    4. Apply new config
     """
-    from ..cli.gemini_configure import configure_gemini_mcp
-
-    # Validate scope parameter
-    if scope not in ["project", "user"]:
-        console.print(
-            f"[red]✗ Invalid scope:[/red] '{scope}'. Must be 'project' or 'user'"
-        )
-        raise typer.Exit(1) from None
+    migrate_config_command(dry_run=dry_run)
 
-    try:
-        configure_gemini_mcp(scope=scope, force=force)  # type: ignore
-    except Exception as e:
-        console.print(f"[red]✗ Configuration failed:[/red] {e}")
-        raise typer.Exit(1) from e
 
+# Add ticket command group to main app
+app.add_typer(ticket_app, name="ticket")
 
-@mcp_app.command(name="codex")
-def mcp_codex(
-    force: bool = typer.Option(
-        False, "--force", "-f", help="Overwrite existing configuration"
-    ),
-) -> None:
-    """Configure Codex CLI to use mcp-ticketer MCP server.
+# Add platform command group to main app
+app.add_typer(platform_app, name="platform")
 
-    Reads configuration from .mcp-ticketer/config.json and creates
-    Codex CLI config.toml with mcp-ticketer configuration.
+# Add queue command to main app
+app.add_typer(queue_app, name="queue")
 
-    IMPORTANT: Codex CLI ONLY supports global configuration at ~/.codex/config.toml.
-    There is no project-level configuration support. After configuration,
-    you must restart Codex CLI for changes to take effect.
+# Add discover command to main app
+app.add_typer(discover_app, name="discover")
 
-    Examples:
-        # Configure Codex CLI globally
-        mcp-ticketer mcp codex
+# Add instructions command to main app
+app.add_typer(instruction_app, name="instructions")
 
-        # Force overwrite existing configuration
-        mcp-ticketer mcp codex --force
+# Add project-update command group to main app
+app.add_typer(project_update_app, name="project-update")
 
-    """
-    from ..cli.codex_configure import configure_codex_mcp
+# Add setup and init commands to main app
+app.command()(setup)
+app.command()(init)
 
-    try:
-        configure_codex_mcp(force=force)
-    except Exception as e:
-        console.print(f"[red]✗ Configuration failed:[/red] {e}")
-        raise typer.Exit(1) from e
+# Add platform installer commands to main app
+app.command()(install)
+app.command()(remove)
+app.command()(uninstall)
 
 
-@mcp_app.command(name="auggie")
-def mcp_auggie(
-    force: bool = typer.Option(
-        False, "--force", "-f", help="Overwrite existing configuration"
+# Add diagnostics command
+@app.command("doctor")
+def doctor_command(
+    output_file: str | None = typer.Option(
+        None, "--output", "-o", help="Save full report to file"
+    ),
+    json_output: bool = typer.Option(
+        False, "--json", help="Output report in JSON format"
+    ),
+    simple: bool = typer.Option(
+        False, "--simple", help="Use simple diagnostics (no heavy dependencies)"
     ),
 ) -> None:
-    """Configure Auggie CLI to use mcp-ticketer MCP server.
-
-    Reads configuration from .mcp-ticketer/config.json and creates
-    Auggie CLI settings.json with mcp-ticketer configuration.
-
-    IMPORTANT: Auggie CLI ONLY supports global configuration at ~/.augment/settings.json.
-    There is no project-level configuration support. After configuration,
-    you must restart Auggie CLI for changes to take effect.
-
-    Examples:
-        # Configure Auggie CLI globally
-        mcp-ticketer mcp auggie
-
-        # Force overwrite existing configuration
-        mcp-ticketer mcp auggie --force
-
-    """
-    from ..cli.auggie_configure import configure_auggie_mcp
-
-    try:
-        configure_auggie_mcp(force=force)
-    except Exception as e:
-        console.print(f"[red]✗ Configuration failed:[/red] {e}")
-        raise typer.Exit(1) from e
-
-
-@mcp_app.command(name="status")
-def mcp_status() -> None:
-    """Check MCP server status.
-
-    Shows whether the MCP server is configured and running for various platforms.
-
-    Examples:
-        mcp-ticketer mcp status
-
-    """
-    import json
-    from pathlib import Path
+    """Run comprehensive system diagnostics and health check (alias: diagnose)."""
+    if simple:
+        from .simple_health import simple_diagnose
 
-    console.print("[bold]MCP Server Status[/bold]\n")
+        report = simple_diagnose()
+        if output_file:
+            import json
 
-    # Check project-level configuration
-    project_config = Path.cwd() / ".mcp-ticketer" / "config.json"
-    if project_config.exists():
-        console.print(f"[green]✓[/green] Project config found: {project_config}")
-        try:
-            with open(project_config) as f:
-                config = json.load(f)
-                adapter = config.get("default_adapter", "aitrackdown")
-                console.print(f"  Default adapter: [cyan]{adapter}[/cyan]")
-        except Exception as e:
-            console.print(f"  [yellow]Warning: Could not read config: {e}[/yellow]")
-    else:
-        console.print("[yellow]○[/yellow] No project config found")
+            with open(output_file, "w") as f:
+                json.dump(report, f, indent=2)
+            console.print(f"\n📄 Report saved to: {output_file}")
+        if json_output:
+            import json
 
-    # Check Claude Code configuration
-    claude_code_config = Path.cwd() / ".mcp" / "config.json"
-    if claude_code_config.exists():
-        console.print(
-            f"\n[green]✓[/green] Claude Code configured: {claude_code_config}"
-        )
+            console.print("\n" + json.dumps(report, indent=2))
+        if report["issues"]:
+            raise typer.Exit(1) from None
     else:
-        console.print("\n[yellow]○[/yellow] Claude Code not configured")
-
-    # Check Claude Desktop configuration
-    claude_desktop_config = (
-        Path.home()
-        / "Library"
-        / "Application Support"
-        / "Claude"
-        / "claude_desktop_config.json"
-    )
-    if claude_desktop_config.exists():
         try:
-            with open(claude_desktop_config) as f:
-                config = json.load(f)
-                if "mcpServers" in config and "mcp-ticketer" in config["mcpServers"]:
-                    console.print(
-                        f"[green]✓[/green] Claude Desktop configured: {claude_desktop_config}"
-                    )
-                else:
-                    console.print(
-                        "[yellow]○[/yellow] Claude Desktop config exists but mcp-ticketer not found"
-                    )
-        except Exception:
-            console.print(
-                "[yellow]○[/yellow] Claude Desktop config exists but could not be read"
+            asyncio.run(
+                run_diagnostics(output_file=output_file, json_output=json_output)
             )
-    else:
-        console.print("[yellow]○[/yellow] Claude Desktop not configured")
+        except typer.Exit:
+            # typer.Exit is expected - don't fall back to simple diagnostics
+            raise
+        except Exception as e:
+            console.print(f"⚠️  Full diagnostics failed: {e}")
+            console.print("🔄 Falling back to simple diagnostics...")
+            from .simple_health import simple_diagnose
 
-    # Check Gemini configuration
-    gemini_project_config = Path.cwd() / ".gemini" / "settings.json"
-    gemini_user_config = Path.home() / ".gemini" / "settings.json"
-    if gemini_project_config.exists():
-        console.print(
-            f"\n[green]✓[/green] Gemini (project) configured: {gemini_project_config}"
-        )
-    elif gemini_user_config.exists():
-        console.print(
-            f"\n[green]✓[/green] Gemini (user) configured: {gemini_user_config}"
-        )
-    else:
-        console.print("\n[yellow]○[/yellow] Gemini not configured")
+            report = simple_diagnose()
+            if report["issues"]:
+                raise typer.Exit(1) from None
 
-    # Check Codex configuration
-    codex_config = Path.home() / ".codex" / "config.toml"
-    if codex_config.exists():
-        console.print(f"[green]✓[/green] Codex configured: {codex_config}")
-    else:
-        console.print("[yellow]○[/yellow] Codex not configured")
 
-    # Check Auggie configuration
-    auggie_config = Path.home() / ".augment" / "settings.json"
-    if auggie_config.exists():
-        console.print(f"[green]✓[/green] Auggie configured: {auggie_config}")
-    else:
-        console.print("[yellow]○[/yellow] Auggie not configured")
+@app.command("diagnose", hidden=True)
+def diagnose_alias(
+    output_file: str | None = typer.Option(
+        None, "--output", "-o", help="Save full report to file"
+    ),
+    json_output: bool = typer.Option(
+        False, "--json", help="Output report in JSON format"
+    ),
+    simple: bool = typer.Option(
+        False, "--simple", help="Use simple diagnostics (no heavy dependencies)"
+    ),
+) -> None:
+    """Run comprehensive system diagnostics and health check (alias for doctor)."""
+    # Call the doctor_command function with the same parameters
+    doctor_command(output_file=output_file, json_output=json_output, simple=simple)
 
-    console.print(
-        "\n[dim]Run 'mcp-ticketer install <platform>' to configure a platform[/dim]"
-    )
 
+@app.command("status")
+def status_command() -> None:
+    """Quick health check - shows system status summary (alias: health)."""
+    from .simple_health import simple_health_check
 
-@mcp_app.command(name="stop")
-def mcp_stop() -> None:
-    """Stop MCP server (placeholder - MCP runs on-demand via stdio).
+    result = simple_health_check()
+    if result != 0:
+        raise typer.Exit(result) from None
 
-    Note: The MCP server runs on-demand when AI clients connect via stdio.
-    It doesn't run as a persistent background service, so there's nothing to stop.
-    This command is provided for consistency but has no effect.
 
-    Examples:
-        mcp-ticketer mcp stop
+@app.command("health")
+def health_alias() -> None:
+    """Quick health check - shows system status summary (alias for status)."""
+    from .simple_health import simple_health_check
 
-    """
-    console.print(
-        "[yellow]ℹ[/yellow]  MCP server runs on-demand via stdio (not as a background service)"
-    )
-    console.print("There is no persistent server process to stop.")
-    console.print(
-        "\n[dim]The server starts automatically when AI clients connect and stops when they disconnect.[/dim]"
-    )
+    result = simple_health_check()
+    if result != 0:
+        raise typer.Exit(result) from None
 
 
 # Add command groups to main app (must be after all subcommands are defined)