markitect-main/markitect/cli.py

"""
CLI Entry Point and Basic Commands - Issue #12

This module provides the command-line interface for MarkiTect, allowing users
to interact with core functionality through terminal commands.

Commands:
- ingest: Process and store a markdown file
- status: Show processing status and metadata for a file
- list: List all stored files and their status

Integration with existing components:
- Uses DatabaseManager for file storage and retrieval
- Uses DocumentManager for high-performance document processing
- Maintains performance caching architecture
"""

import click
import os
import sys
import json
import yaml
from pathlib import Path
from typing import Optional, List, Tuple
from dataclasses import dataclass
from tabulate import tabulate
import builtins

from .database import DatabaseManager
from .legacy_compat import LegacyMode, emit_deprecation_warning, legacy_switch_option
from .__version__ import get_version_info, get_release_info
from .batch_processor import BatchProcessor, ProcessingMode, ErrorHandling, create_file_processor
from .config_manager import ConfigurationManager

# Import cost tracking commands
try:
    from .finance.cli import cost_commands
    COST_TRACKING_AVAILABLE = True
except ImportError:
    COST_TRACKING_AVAILABLE = False

# Import profile management commands
try:
    from .profile.commands import profile_commands
    PROFILE_MANAGEMENT_AVAILABLE = True
except ImportError:
    PROFILE_MANAGEMENT_AVAILABLE = False


def get_database_path(config):
    """Get database path from config."""
    return config.get('database_path', os.path.expanduser('~/.markitect/markitect.db'))


# Import legacy system components for advanced management
try:
    from .legacy import (
        LegacyRegistry, LegacyAgent, LegacyStatus, AgentConfig
    )
    LEGACY_SYSTEM_AVAILABLE = True
except ImportError:
    LEGACY_SYSTEM_AVAILABLE = False


def detect_execution_mode():
    """
    Detect whether we're running in interactive or automation mode.

    Returns:
        str: 'interactive' or 'automation'

    Detection logic:
    - Environment variable MARKITECT_MODE overrides detection
    - Interactive: TTY present, not in CI, not in pipe
    - Automation: CI environment, pipe/redirect, or explicit setting
    """
    # Explicit mode override
    mode = os.environ.get('MARKITECT_MODE', '').lower()
    if mode in ['interactive', 'automation']:
        return mode

    # Detect CI environments
    ci_indicators = [
        'CI', 'CONTINUOUS_INTEGRATION', 'GITHUB_ACTIONS',
        'GITLAB_CI', 'JENKINS_URL', 'BUILD_NUMBER'
    ]
    if any(os.environ.get(var) for var in ci_indicators):
        return 'automation'

    # Check if output is being piped or redirected
    if not sys.stdout.isatty():
        return 'automation'

    # Check if input is being piped
    if not sys.stdin.isatty():
        return 'automation'

    # Default to interactive for terminal usage
    return 'interactive'


def should_use_associated_files():
    """Determine if commands should use associated files behavior."""
    return detect_execution_mode() == 'interactive'
# DocumentManager removed - using CleanDocumentManager directly in commands
from .serializer import ASTSerializer
from .cache_service import CacheDirectoryService
from .ast_service import ASTService
from .schema_generator import SchemaGenerator
from .schema_validator import SchemaValidator
from .exceptions import FileNotFoundError, InvalidDepthError, SchemaValidationError, InvalidSchemaError


# Global options for CLI configuration
pass_config = click.make_pass_decorator(dict, ensure=True)


def get_default_format(available_formats=['table', 'json', 'yaml', 'simple'], fallback='simple'):
    """
    Get the default output format from environment variable or fallback.

    Supports MARKITECT_DEFAULT_FORMAT environment variable to customize
    the default output format across all commands.

    Args:
        available_formats: List of formats supported by the command
        fallback: Default format to use if env var not set or invalid

    Returns:
        Default format string
    """
    env_format = os.environ.get('MARKITECT_DEFAULT_FORMAT', '').lower()

    if env_format and env_format in available_formats:
        return env_format

    # If simple is available and no env override, use simple
    if 'simple' in available_formats:
        return 'simple'

    # Otherwise use the provided fallback
    return fallback


def format_output(data, output_format):
    """
    Format data according to specified output format.

    Args:
        data: Data to format
        output_format: Format type ('table', 'json', 'yaml')

    Returns:
        Formatted string output
    """
    if output_format == 'json':
        return json.dumps(data, indent=2, default=str)
    elif output_format == 'yaml':
        return yaml.dump(data, default_flow_style=False, allow_unicode=True)
    elif output_format == 'simple':
        # Simple format - just basic text output
        if isinstance(data, builtins.list):
            return '\n'.join(str(item) for item in data)
        elif isinstance(data, builtins.dict):
            return '\n'.join(f"{key}: {value}" for key, value in data.items())
        else:
            return str(data)
    elif output_format == 'table':
        try:
            # Check if it's a list type
            if isinstance(data, (builtins.list, builtins.tuple)):
                if data and isinstance(data[0], builtins.dict):
                    # List of dictionaries - format as table
                    headers = sorted(data[0].keys())
                    rows = []
                    for item in data:
                        row = []
                        for header in headers:
                            row.append(item.get(header, ''))
                        rows.append(row)
                    return tabulate(rows, headers=headers, tablefmt='grid')
                else:
                    # List of simple values
                    return tabulate([[item] for item in data], headers=['Value'], tablefmt='grid')
            elif isinstance(data, builtins.dict):
                # Single dictionary - format as key-value table
                rows = [[key, value] for key, value in data.items()]
                return tabulate(rows, headers=['Key', 'Value'], tablefmt='grid')
            else:
                # Fallback to string representation
                return str(data)
        except Exception as e:
            # Fallback to string if table formatting fails
            return f"Table formatting error: {e}\nData: {str(data)}"
    else:
        # Default to table format
        return format_output(data, 'table')


def print_version(ctx, param, value):
    """Callback to print version and exit."""
    if not value or ctx.resilient_parsing:
        return
    version_info = get_version_info()
    click.echo(version_info['full_version'])
    ctx.exit()

@click.group()
@click.option('--verbose', '-v', is_flag=True, help='Enable verbose output')
@click.option('--config', 'config_file', type=click.Path(exists=True), help='Configuration file path')
@click.option('--database', type=click.Path(), help='Database file path')
@click.option('--version', is_flag=True, expose_value=False, is_eager=True,
              callback=print_version, help='Show version and exit')
@pass_config
def cli(config, verbose, database, config_file):
    """
    MarkiTect - Advanced Markdown engine for structured content.

    Process markdown files with front matter support, AST caching,
    and relational metadata queries.

    Examples:
        markitect ingest document.md     # Process a markdown file
        markitect status document.md     # Check file status
        markitect list                   # List all stored files
    """
    # Store configuration in context
    config['verbose'] = verbose
    config['config_file'] = config_file

    # Determine database path
    if database:
        config['database_path'] = database
    else:
        # Default database location
        config['database_path'] = os.path.expanduser('~/.markitect/markitect.db')

    # Initialize database manager and ensure database exists
    try:
        db_manager = DatabaseManager(config['database_path'])
        db_manager.initialize_database()
        config['db_manager'] = db_manager

        if verbose:
            click.echo(f"Using database: {config['database_path']}", err=True)
    except Exception as e:
        click.echo(f"Error initializing database: {e}", err=True)
        sys.exit(1)


# Issue management commands removed - use dedicated 'issue' CLI or 'tddai' CLI instead

# Version and release information commands

@cli.command()
@click.option('--short', is_flag=True, help='Show only version number')
def version(short):
    """Show MarkiTect version information."""
    version_info = get_version_info()

    if short:
        click.echo(version_info['full_version'])
    else:
        click.echo("MarkiTect Version Information")
        click.echo("============================")
        click.echo(f"Version: {version_info['full_version']}")
        click.echo(f"Short Version: {version_info['short_version']}")

        if version_info.get('is_git_repo'):
            click.echo(f"Git Commit: {version_info.get('git_commit', 'N/A')}")
            click.echo(f"Git Branch: {version_info.get('git_branch', 'N/A')}")
            if version_info.get('git_tag'):
                click.echo(f"Git Tag: {version_info['git_tag']}")
            click.echo(f"Development Build: {'Yes' if version_info.get('is_dev') else 'No'}")
        else:
            click.echo("Git Repository: Not available")


@cli.command()
@click.option('--format', 'output_format', default='text',
              type=click.Choice(['text', 'json', 'yaml']),
              help='Output format (text, json, yaml)')
def release(output_format):
    """Show MarkiTect release information."""
    release_info = get_release_info()

    if output_format == 'json':
        import json
        click.echo(json.dumps(release_info, indent=2))
    elif output_format == 'yaml':
        import yaml
        click.echo(yaml.dump(release_info, default_flow_style=False))
    else:
        # Text format
        click.echo("MarkiTect Release Information")
        click.echo("============================")
        click.echo(f"Version: {release_info['full_version']}")
        click.echo(f"Release Type: {release_info['release_type']}")
        click.echo(f"Build From: {release_info['build_from']}")
        click.echo(f"Commit: {release_info['commit']}")
        click.echo(f"Clean Build: {'Yes' if release_info['clean_build'] else 'No'}")

        if release_info['is_git_repo']:
            click.echo(f"Git Repository: Available")
            if release_info['git_tag']:
                click.echo(f"Tagged Release: {release_info['git_tag']}")
        else:
            click.echo("Git Repository: Not available")



def _show_core_system_stats(config, format):
    """Display core MarkiTect system statistics and health information."""
    try:
        # Collect core system statistics
        stats = {}

        # Database Statistics
        try:
            db_manager = config.get('db_manager')
            if db_manager:
                # Get database file info
                db_path = config.get('database_path', 'Unknown')
                db_exists = Path(db_path).exists() if db_path != 'Unknown' else False

                if db_exists:
                    db_size = Path(db_path).stat().st_size
                    db_size_human = format_file_size(db_size)
                else:
                    db_size = 0
                    db_size_human = '0 B'

                # Get file counts from database using proper API
                try:
                    # Use execute_query method for database queries
                    total_files_result = db_manager.execute_query("SELECT COUNT(*) as count FROM markdown_files")
                    total_files = total_files_result[0]['count'] if total_files_result else 0

                    # Recent files (last 7 days)
                    recent_files_result = db_manager.execute_query("""
                        SELECT COUNT(*) as count FROM markdown_files
                        WHERE created_at >= datetime('now', '-7 days')
                    """)
                    recent_files = recent_files_result[0]['count'] if recent_files_result else 0

                    # Schema count (table might not exist)
                    try:
                        schema_count_result = db_manager.execute_query("SELECT COUNT(*) as count FROM schema_files")
                        schema_count = schema_count_result[0]['count'] if schema_count_result else 0
                    except Exception:
                        # schema_files table doesn't exist - this is okay
                        schema_count = 0

                    stats['database'] = {
                        'path': db_path,
                        'exists': db_exists,
                        'size_bytes': db_size,
                        'size_human': db_size_human,
                        'total_markdown_files': total_files,
                        'recent_files_7_days': recent_files,
                        'schema_files': schema_count,
                        'available': True
                    }
                except Exception as db_error:
                    stats['database'] = {
                        'path': db_path,
                        'exists': db_exists,
                        'size_bytes': db_size,
                        'size_human': db_size_human,
                        'available': False,
                        'error': str(db_error)
                    }
            else:
                stats['database'] = {
                    'available': False,
                    'message': 'Database manager not initialized'
                }
        except Exception as e:
            stats['database'] = {
                'available': False,
                'error': str(e)
            }

        # Cache Statistics
        try:
            from .cache_service import CacheDirectoryService
            cache_service = CacheDirectoryService()
            cache_stats = cache_service.get_cache_stats()

            stats['cache'] = {
                'directory': cache_stats.get('cache_directory', 'Unknown'),
                'total_files': cache_stats.get('total_files', 0),
                'size_bytes': cache_stats.get('cache_size_bytes', 0),
                'size_human': cache_stats.get('cache_size_human', '0 B'),
                'available': True
            }
        except Exception as e:
            stats['cache'] = {
                'available': False,
                'error': str(e)
            }

        # System Information
        stats['system'] = {
            'working_directory': os.getcwd(),
            'python_version': sys.version.split()[0],
            'config_file': config.get('config_file', 'None specified'),
            'verbose_mode': config.get('verbose', False),
            'execution_mode': detect_execution_mode()
        }

        # Subsystem Health Check
        subsystems = {
            'database': stats['database']['available'],
            'cache': stats['cache']['available'],
            'ast_service': True,  # Available if we got here
        }

        healthy_count = sum(subsystems.values())
        total_count = len(subsystems)

        stats['health'] = {
            'subsystems': subsystems,
            'healthy_subsystems': healthy_count,
            'total_subsystems': total_count,
            'health_percentage': round((healthy_count / total_count) * 100, 1),
            'overall_status': 'healthy' if healthy_count == total_count else 'degraded'
        }

        # Format output
        if format == 'json':
            click.echo(json.dumps(stats, indent=2))
        elif format == 'yaml':
            click.echo(yaml.dump(stats, default_flow_style=False))
        elif format == 'simple':
            # Simple key-value output
            if stats['database']['available']:
                db = stats['database']
                click.echo(f"database_files: {db['total_markdown_files']}")
                click.echo(f"database_size: {db['size_human']}")
                click.echo(f"database_recent_files: {db['recent_files_7_days']}")
            else:
                click.echo("database_available: False")

            if stats['cache']['available']:
                cache = stats['cache']
                click.echo(f"cache_files: {cache['total_files']}")
                click.echo(f"cache_size: {cache['size_human']}")
            else:
                click.echo("cache_available: False")

            health = stats['health']
            click.echo(f"system_health: {health['health_percentage']}%")
            click.echo(f"overall_status: {health['overall_status']}")
        else:  # table format (default)
            click.echo("📊 MarkiTect Core System Statistics")
            click.echo("=" * 50)

            # System Health Overview
            health = stats['health']
            health_icon = "✅" if health['overall_status'] == 'healthy' else "⚠️"
            click.echo(f"\n🏥 System Health: {health_icon} {health['overall_status'].title()} ({health['health_percentage']}%)")
            click.echo(f"   Healthy Subsystems: {health['healthy_subsystems']}/{health['total_subsystems']}")

            # Database section
            click.echo("\n🗄️  Database:")
            if stats['database']['available']:
                db = stats['database']
                click.echo(f"  Path: {db['path']}")
                click.echo(f"  Status: ✅ Available ({db['size_human']})")
                click.echo(f"  Markdown Files: {db['total_markdown_files']}")
                click.echo(f"  Schema Files: {db['schema_files']}")
                click.echo(f"  Recent Activity (7 days): {db['recent_files_7_days']} files")
            else:
                click.echo("  Status: ❌ Unavailable")
                if 'error' in stats['database']:
                    click.echo(f"  Error: {stats['database']['error']}")
                elif 'message' in stats['database']:
                    click.echo(f"  Note: {stats['database']['message']}")

            # Cache section
            click.echo("\n🗃️  Cache:")
            if stats['cache']['available']:
                cache = stats['cache']
                click.echo(f"  Directory: {cache['directory']}")
                click.echo(f"  Status: ✅ Available ({cache['size_human']})")
                click.echo(f"  Cached Files: {cache['total_files']}")
            else:
                click.echo("  Status: ❌ Unavailable")
                if 'error' in stats['cache']:
                    click.echo(f"  Error: {stats['cache']['error']}")

            # System section
            click.echo("\n🖥️  System Information:")
            sys_info = stats['system']
            click.echo(f"  Working Directory: {sys_info['working_directory']}")
            click.echo(f"  Python Version: {sys_info['python_version']}")
            click.echo(f"  Execution Mode: {sys_info['execution_mode']}")
            click.echo(f"  Config File: {sys_info['config_file']}")
            click.echo(f"  Verbose Mode: {sys_info['verbose_mode']}")

    except Exception as e:
        click.echo(f"Error gathering core system statistics: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)


@cli.command('stats')
@click.argument('file_path', type=str, required=False)
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
@pass_config
def stats(config, file_path, format):
    """
    Show core system statistics or file-specific information.

    When called with a file: Display file's processing status, metadata,
    and front matter content from the database.

    When called without a file: Show core MarkiTect system statistics
    including database status, processing metrics, and subsystem health.

    FILE_PATH: Optional path or name of the file to check

    Examples:
        markitect stats                         # Show core system statistics
        markitect stats README.md               # Show file-specific status
        markitect stats docs/guide.md --format json
    """
    try:
        # If no file provided, show core system statistics
        if not file_path:
            if config.get('verbose'):
                click.echo("Displaying core system statistics", err=True)

            _show_core_system_stats(config, format)
            return

        # File-specific status (existing behavior)
        if config['verbose']:
            click.echo(f"Checking status for: {file_path}")

        # Get file information from database
        db_manager = config['db_manager']
        file_info = db_manager.get_markdown_file(file_path)

        if file_info:
            click.echo(f"File: {file_info['filename']}")
            click.echo(f"Status: Processed")
            click.echo(f"Created: {file_info['created_at']}")

            if file_info['front_matter']:
                try:
                    front_matter = eval(file_info['front_matter'])  # Safe for our controlled data
                    if front_matter:
                        click.echo("Front Matter:")
                        for key, value in front_matter.items():
                            click.echo(f"  {key}: {value}")
                except (ValueError, TypeError, SyntaxError):
                    click.echo("Front Matter: (parsing error)")
            elif file_info['front_matter'] is None:
                pass  # No front matter to display

            if config['verbose']:
                content_preview = file_info['content'][:200] + "..." if len(file_info['content']) > 200 else file_info['content']
                click.echo(f"Content preview: {content_preview}")
        else:
            click.echo(f"File not found in database: {file_path}")
            click.echo("Use 'markitect ingest' to process the file first.")
            sys.exit(1)

    except Exception as e:
        click.echo(f"Error checking file status: {e}", err=True)
        if config['verbose']:
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)




@cli.command()
@click.argument('file_path', type=str)
@click.option('--add-section', type=str, help='Add section with title')
@click.option('--section-content', type=str, default='', help='Content for new section')
@click.option('--section-level', type=int, default=2, help='Heading level for new section (1-6)')
@click.option('--update-front-matter', type=str, help='Update front matter (format: key:value)')
@click.option('--output', '-o', type=click.Path(), help='Output file path (default: overwrite original in cache)')
@pass_config
def modify(config, file_path, add_section, section_content, section_level, update_front_matter, output):
    """
    Modify the content of a processed markdown file.

    Loads the file from cache, applies modifications, and updates the cache
    or outputs to a new file. Supports adding sections and updating front matter.

    FILE_PATH: Name of the file to modify

    Examples:
        markitect modify README.md --add-section "New Section" --section-content "New content"
        markitect modify doc.md --update-front-matter "status:updated"
        markitect modify doc.md --add-section "Notes" --output modified_doc.md
    """
    try:
        if config['verbose']:
            click.echo(f"Modifying file: {file_path}")

        db_manager = config['db_manager']

        # Get file information from database
        file_info = db_manager.get_markdown_file(file_path)
        if not file_info:
            click.echo(f"File not found in database: {file_path}", err=True)
            click.echo("Use 'markitect ingest' to process the file first.", err=True)
            sys.exit(1)

        # Load AST from cache
        cache_filename = f"{file_path}.ast.json"
        cache_path = Path('.ast_cache') / cache_filename

        if not cache_path.exists():
            click.echo(f"AST cache not found: {cache_path}", err=True)
            click.echo("Try re-ingesting the file to regenerate cache.", err=True)
            sys.exit(1)

        # Read AST from cache
        with open(cache_path, 'r', encoding='utf-8') as f:
            ast = json.load(f)

        # Parse front matter from database
        front_matter = {}
        if file_info.get('front_matter'):
            try:
                front_matter = eval(file_info['front_matter']) or {}
            except (ValueError, TypeError, SyntaxError):
                if config['verbose']:
                    click.echo("Warning: Could not parse existing front matter", err=True)

        # Prepare modifications
        modifications = {}
        changes_made = []

        # Handle add-section modification
        if add_section:
            modifications['add_section'] = {
                'title': add_section,
                'content': section_content,
                'level': section_level
            }
            changes_made.append(f"Added section: {add_section}")

        # Handle front matter updates
        if update_front_matter:
            try:
                if ':' in update_front_matter:
                    key, value = update_front_matter.split(':', 1)
                    key = key.strip()
                    value = value.strip()

                    # Try to parse value as appropriate type
                    if value.lower() in ['true', 'false']:
                        value = value.lower() == 'true'
                    elif value.isdigit():
                        value = int(value)
                    elif value.replace('.', '').isdigit():
                        value = float(value)

                    front_matter[key] = value
                    changes_made.append(f"Updated front matter: {key} = {value}")
                else:
                    click.echo("Invalid front matter format. Use 'key:value'", err=True)
                    sys.exit(1)
            except ValueError as e:
                click.echo(f"Error parsing front matter update: {e}", err=True)
                sys.exit(1)

        if not changes_made:
            click.echo("No modifications specified. Use --add-section or --update-front-matter", err=True)
            sys.exit(1)

        # Apply modifications to AST
        serializer = ASTSerializer()
        if modifications:
            ast = serializer.modify_ast_content(ast, modifications)

        # Serialize back to markdown
        markdown_content = serializer.serialize_to_markdown(ast, front_matter)

        # Handle output
        if output:
            # Write to specified output file
            output_path = Path(output)
            output_path.parent.mkdir(parents=True, exist_ok=True)
            with open(output_path, 'w', encoding='utf-8') as f:
                f.write(markdown_content)
            click.echo(f"✓ Modified file written to: {output_path}")
        else:
            # Update the cache and database with modifications
            with open(cache_path, 'w', encoding='utf-8') as f:
                json.dump(ast, f, indent=2, ensure_ascii=False)

            # Update database with new front matter
            if front_matter:
                # Note: This would require extending DatabaseManager to update front matter
                # For now, we'll just note the modification
                if config['verbose']:
                    click.echo("Note: Database front matter update not implemented yet", err=True)

            click.echo(f"✓ Modified file updated in cache: {file_path}")

        # Show changes made
        if config['verbose']:
            click.echo("Changes applied:", err=True)
            for change in changes_made:
                click.echo(f"  - {change}", err=True)

    except Exception as e:
        click.echo(f"Error modifying file: {e}", err=True)
        if config['verbose']:
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)




@cli.command('db-query')
@click.argument('sql', type=str)
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']), default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
@pass_config
def db_query(config, sql, format):
    """
    Execute SQL query against the database.

    Execute read-only SQL queries to explore and analyze document metadata.
    Only SELECT and WITH statements are allowed for security.

    SQL: SQL query to execute (SELECT statements only)

    Examples:
        markitect db-query "SELECT filename, created_at FROM markdown_files"
        markitect db-query "SELECT COUNT(*) as total FROM markdown_files" --format json
        markitect db-query "SELECT * FROM markdown_files WHERE filename LIKE '%.md'" --format yaml
    """
    try:
        if config['verbose']:
            click.echo(f"Executing query: {sql}", err=True)

        db_manager = config['db_manager']

        # Execute the query
        results = db_manager.execute_query(sql)

        if not results:
            if format == 'json':
                click.echo('[]')
            elif format == 'yaml':
                click.echo('[]')
            else:
                click.echo("No results found.")
            return

        # Format and display results
        formatted_output = format_output(results, format)
        click.echo(formatted_output)

        if config['verbose']:
            click.echo(f"Query returned {len(results)} result(s)", err=True)

    except ValueError as e:
        click.echo(f"Query error: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"Database error: {e}", err=True)
        if config['verbose']:
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)



@cli.command('db-schema')
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']), default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
@pass_config
def db_schema(config, format):
    """
    Show database schema and table structure.

    Display the structure of all tables in the database, including
    column names, types, and constraints.

    Examples:
        markitect db-schema
        markitect db-schema --format json
        markitect db-schema --format yaml
    """
    try:
        if config['verbose']:
            click.echo("Retrieving database schema...", err=True)

        db_manager = config['db_manager']

        # Get schema information
        schema_info = db_manager.get_schema()

        if not schema_info:
            click.echo("No tables found in database.")
            return

        # Format and display schema
        formatted_output = format_output(schema_info, format)
        click.echo(formatted_output)

        if config['verbose']:
            table_count = len(schema_info)
            click.echo(f"Schema contains {table_count} table(s)", err=True)

    except Exception as e:
        click.echo(f"Schema error: {e}", err=True)
        if config['verbose']:
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command()
@click.argument('file_path', type=str)
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']), default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
@pass_config
def metadata(config, file_path, format):
    """
    Display file metadata and front matter.

    DEPRECATED: Use 'db-data' instead. This command will be removed in a future version.

    Show detailed information about a specific file including its
    front matter, database metadata, and processing information.

    FILE_PATH: Name of the file to display metadata for

    Examples:
        markitect metadata README.md  (deprecated - use: markitect db-data README.md)
        markitect metadata docs/guide.md --format json  (deprecated - use: markitect db-data docs/guide.md --format json)
        markitect metadata config.md --format yaml  (deprecated - use: markitect db-data config.md --format yaml)
    """
    # Show deprecation warning (unless in legacy mode)
    if not LegacyMode.should_suppress_warnings():
        emit_deprecation_warning(
            "The 'metadata' command is deprecated. Please use 'db-data' instead. "
            "This command will be removed in a future version."
        )

    try:
        if config['verbose']:
            click.echo(f"Retrieving metadata for: {file_path}", err=True)

        db_manager = config['db_manager']

        # Get file information from database
        file_info = db_manager.get_markdown_file(file_path)

        if not file_info:
            click.echo(f"File not found in database: {file_path}", err=True)
            click.echo("Use 'markitect ingest' to process the file first.", err=True)
            sys.exit(1)

        # Parse front matter for better display
        if file_info.get('front_matter'):
            try:
                if isinstance(file_info['front_matter'], str):
                    file_info['front_matter'] = eval(file_info['front_matter'])
            except (ValueError, TypeError, SyntaxError):
                if config['verbose']:
                    click.echo("Warning: Could not parse front matter", err=True)

        # Format and display metadata
        formatted_output = format_output(file_info, format)
        click.echo(formatted_output)

        if config['verbose']:
            content_length = len(file_info.get('content', ''))
            click.echo(f"Content length: {content_length} characters", err=True)

    except Exception as e:
        click.echo(f"Metadata error: {e}", err=True)
        if config['verbose']:
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)




@cli.command('cache-stats')
@pass_config
def cache_stats(config):
    """
    Display cache statistics and effectiveness.

    Shows information about AST cache including directory path,
    total files cached, cache size, and performance metrics.

    Renamed from cache-info for consistency with subsystem naming convention.
    """
    try:
        cache_service = CacheDirectoryService()
        stats = cache_service.get_cache_stats()

        click.echo(f"Cache Directory: {stats['directory']}")
        click.echo(f"Total Files: {stats['total_files']}")
        click.echo(f"Cache Size: {stats['size_formatted']}")

    except Exception as e:
        click.echo(f"Cache info error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('cache-clean')
@pass_config
def cache_clean(config):
    """
    Clear cache and free memory.

    Removes all cached AST files from the cache directory
    to free up disk space and memory.
    """
    try:
        cache_service = CacheDirectoryService()
        result = cache_service.clean_cache()

        click.echo(result['message'])

        if not result['success'] and result.get('errors'):
            for error in result['errors']:
                click.echo(f"Warning: {error}", err=True)

        if not result['success']:
            sys.exit(1)

    except Exception as e:
        click.echo(f"Cache clean error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('cache-invalidate')
@click.argument('file_path', type=str)
@pass_config
def cache_invalidate(config, file_path):
    """
    Invalidate specific file cache.

    Removes the cached AST for a specific markdown file,
    forcing it to be re-parsed on next access.

    Args:
        file_path: Path to the file whose cache should be invalidated
    """
    try:
        cache_service = CacheDirectoryService()
        result = cache_service.invalidate_file_cache(file_path)

        click.echo(result['message'])

        if not result['success']:
            sys.exit(1)

    except Exception as e:
        click.echo(f"Cache invalidate error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('ast-show')
@click.argument('file_path', type=click.Path(exists=False))
@click.option('--format', '-f', type=click.Choice(['tree', 'json', 'compact']), default='tree', help='Display format')
@pass_config
def ast_show(config, file_path, format):
    """
    Display AST structure for file.

    Shows the Abstract Syntax Tree representation of a markdown file
    with various formatting options for analysis and debugging.

    FILE_PATH: Path to the markdown file to analyze

    Examples:
        markitect ast-show document.md
        markitect ast-show document.md --format json
        markitect ast-show document.md --format compact
    """
    try:
        if config.get('verbose'):
            click.echo(f"Analyzing AST structure for: {file_path}", err=True)

        ast_service = ASTService()
        result = ast_service.display_ast(Path(file_path), format)

        if result['success']:
            if result.get('message'):
                if config.get('verbose'):
                    click.echo(f"Info: {result['message']}", err=True)
            click.echo(result['output'])

            if config.get('verbose') and result.get('token_count'):
                click.echo(f"Total tokens: {result['token_count']}", err=True)
        else:
            click.echo(f"Error: {result['message']}", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"AST display error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('ast-query')
@click.argument('file_path', type=click.Path(exists=False))
@click.argument('jsonpath', type=str)
@click.option('--format', '-f', type=click.Choice(['json', 'compact']), default='json', help='Output format')
@pass_config
def ast_query(config, file_path, jsonpath, format):
    """
    Query AST using JSONPath.

    Execute JSONPath expressions against the AST structure of a markdown file
    to extract specific elements or patterns.

    FILE_PATH: Path to the markdown file to query
    JSONPATH: JSONPath expression to execute

    Examples:
        markitect ast-query doc.md '$.*.type'
        markitect ast-query doc.md '$..tag'
        markitect ast-query doc.md '$[:5]' --format compact
    """
    try:
        if config.get('verbose'):
            click.echo(f"Executing JSONPath query on: {file_path}", err=True)
            click.echo(f"Query: {jsonpath}", err=True)

        ast_service = ASTService()
        result = ast_service.query_ast(Path(file_path), jsonpath)

        if result['success']:
            if config.get('verbose'):
                click.echo(f"Query results: {result['count']} matches", err=True)

            if result['count'] == 0:
                click.echo("No matches found for query.")
            else:
                if format == 'compact':
                    for i, match in enumerate(result['matches']):
                        if isinstance(match, dict):
                            token_type = match.get('type', 'unknown')
                            content = match.get('content', match.get('tag', ''))[:30]
                            click.echo(f"[{i}] {token_type}: {content}")
                        else:
                            click.echo(f"[{i}] {match}")
                else:
                    import json
                    click.echo(json.dumps(result['matches'], indent=2, ensure_ascii=False))
        else:
            click.echo(f"Error: {result['message']}", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"AST query error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


def _show_ast_subsystem_stats(config, format):
    """Display AST subsystem statistics including cache and processing metrics."""
    try:
        # Import dependencies
        from .ast_cache import ASTCache
        from .cache_service import CacheDirectoryService

        # Collect AST subsystem statistics
        stats = {}

        # AST Cache information
        try:
            cache_service = CacheDirectoryService()
            cache_stats = cache_service.get_cache_stats()
            stats['ast_cache'] = {
                'directory': cache_stats.get('cache_directory', 'Unknown'),
                'total_files': cache_stats.get('total_files', 0),
                'cache_size_bytes': cache_stats.get('cache_size_bytes', 0),
                'cache_size_human': cache_stats.get('cache_size_human', '0 B'),
                'available': True
            }
        except Exception as e:
            stats['ast_cache'] = {
                'available': False,
                'error': str(e)
            }

        # Database statistics (files processed)
        try:
            db_manager = config.get('db_manager')
            if db_manager:
                # Get count of files in database (processed files)
                conn = db_manager.get_connection()
                cursor = conn.cursor()
                cursor.execute("SELECT COUNT(*) FROM markdown_files")
                total_files = cursor.fetchone()[0]

                # Get recent processing info
                cursor.execute("""
                    SELECT COUNT(*) FROM markdown_files
                    WHERE created_at >= datetime('now', '-7 days')
                """)
                recent_files = cursor.fetchone()[0]

                stats['processing'] = {
                    'total_files_processed': total_files,
                    'files_processed_last_7_days': recent_files,
                    'database_available': True
                }
            else:
                stats['processing'] = {
                    'database_available': False,
                    'message': 'Database not initialized'
                }
        except Exception as e:
            stats['processing'] = {
                'database_available': False,
                'error': str(e)
            }

        # System information
        stats['system'] = {
            'ast_service_available': True,  # If we got here, it's available
            'working_directory': os.getcwd(),
            'python_version': sys.version.split()[0]
        }

        # Format output
        if format == 'json':
            click.echo(json.dumps(stats, indent=2))
        elif format == 'yaml':
            click.echo(yaml.dump(stats, default_flow_style=False))
        elif format == 'simple':
            # Simple key-value output
            if stats['ast_cache']['available']:
                cache = stats['ast_cache']
                click.echo(f"ast_cache_directory: {cache['directory']}")
                click.echo(f"ast_cache_files: {cache['total_files']}")
                click.echo(f"ast_cache_size: {cache['cache_size_human']}")
            else:
                click.echo(f"ast_cache_available: False")

            if stats['processing']['database_available']:
                proc = stats['processing']
                click.echo(f"total_files_processed: {proc['total_files_processed']}")
                click.echo(f"recent_files_processed: {proc['files_processed_last_7_days']}")
            else:
                click.echo("database_available: False")

            sys_info = stats['system']
            click.echo(f"working_directory: {sys_info['working_directory']}")
            click.echo(f"python_version: {sys_info['python_version']}")
        else:  # table format (default)
            click.echo("📊 AST Subsystem Statistics")
            click.echo("=" * 50)

            # AST Cache section
            click.echo("\n🗃️  AST Cache:")
            if stats['ast_cache']['available']:
                cache = stats['ast_cache']
                click.echo(f"  Directory: {cache['directory']}")
                click.echo(f"  Cached Files: {cache['total_files']}")
                click.echo(f"  Cache Size: {cache['cache_size_human']}")
                if cache['total_files'] == 0:
                    click.echo("  Status: ⚠️  No files cached yet")
                else:
                    click.echo(f"  Status: ✅ Active")
            else:
                click.echo("  Status: ❌ Unavailable")
                if 'error' in stats['ast_cache']:
                    click.echo(f"  Error: {stats['ast_cache']['error']}")

            # Processing section
            click.echo("\n⚙️  Processing Metrics:")
            if stats['processing']['database_available']:
                proc = stats['processing']
                click.echo(f"  Total Files Processed: {proc['total_files_processed']}")
                click.echo(f"  Files Processed (Last 7 Days): {proc['files_processed_last_7_days']}")
                if proc['total_files_processed'] == 0:
                    click.echo("  Status: ⚠️  No files processed yet")
                else:
                    click.echo("  Status: ✅ Active")
            else:
                click.echo("  Status: ❌ Database unavailable")
                if 'error' in stats['processing']:
                    click.echo(f"  Error: {stats['processing']['error']}")
                elif 'message' in stats['processing']:
                    click.echo(f"  Note: {stats['processing']['message']}")

            # System section
            click.echo("\n🖥️  System Information:")
            sys_info = stats['system']
            click.echo(f"  AST Service: ✅ Available")
            click.echo(f"  Working Directory: {sys_info['working_directory']}")
            click.echo(f"  Python Version: {sys_info['python_version']}")

    except Exception as e:
        click.echo(f"Error gathering AST subsystem statistics: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)


@cli.command('ast-stats')
@click.argument('file_path', type=click.Path(exists=False), required=False)
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']), default='table', help='Output format')
@pass_config
def ast_stats(config, file_path, format):
    """
    Show AST statistics for files or AST subsystem information.

    When called with a file: Analyze markdown file structure and provide
    comprehensive statistics about document elements, organization, and content patterns.

    When called without a file: Show AST subsystem statistics including cache
    information, processing metrics, and system status.

    FILE_PATH: Optional path to the markdown file to analyze

    Examples:
        markitect ast-stats                    # Show AST subsystem statistics
        markitect ast-stats document.md        # Analyze specific file
        markitect ast-stats document.md --format json
    """
    try:
        # If no file provided, show AST subsystem statistics
        if not file_path:
            if config.get('verbose'):
                click.echo("Displaying AST subsystem statistics", err=True)

            _show_ast_subsystem_stats(config, format)
            return

        # File-specific analysis (existing behavior)
        if config.get('verbose'):
            click.echo(f"Calculating statistics for: {file_path}", err=True)

        ast_service = ASTService()
        result = ast_service.analyze_ast_statistics(Path(file_path))

        if result['success']:
            if config.get('verbose'):
                click.echo(f"Analysis complete for: {Path(file_path).name}", err=True)

            stats = result['statistics']
            if format == 'table':
                # Format statistics as readable table
                click.echo("Document Statistics:")
                click.echo("=" * 40)
                click.echo(f"Total AST tokens: {stats.get('total_tokens', 0)}")
                click.echo(f"Document structure: {stats.get('document_structure', 'unknown')}")
                click.echo()

                # Headings
                headings = stats.get('headings', {})
                click.echo(f"Headings: {headings.get('total', 0)}")
                for level, count in headings.get('by_level', {}).items():
                    click.echo(f"  {level.upper()}: {count}")

                click.echo(f"Paragraphs: {stats.get('paragraphs', 0)}")
                click.echo(f"Links: {stats.get('links', 0)}")

                # Lists
                lists = stats.get('lists', {})
                total_lists = lists.get('ordered', 0) + lists.get('unordered', 0)
                click.echo(f"Lists: {total_lists}")
                if total_lists > 0:
                    click.echo(f"  Ordered: {lists.get('ordered', 0)}")
                    click.echo(f"  Unordered: {lists.get('unordered', 0)}")

                click.echo(f"Code blocks: {stats.get('code_blocks', 0)}")
                click.echo(f"Inline code: {stats.get('inline_code', 0)}")
                click.echo(f"Blockquotes: {stats.get('blockquotes', 0)}")

                # Emphasis
                emphasis = stats.get('emphasis', {})
                click.echo(f"Strong text: {emphasis.get('strong', 0)}")
                click.echo(f"Italic text: {emphasis.get('italic', 0)}")

            elif format == 'json':
                import json
                click.echo(json.dumps(stats, indent=2, ensure_ascii=False))
            elif format == 'yaml':
                import yaml
                click.echo(yaml.dump(stats, default_flow_style=False, allow_unicode=True))
            elif format == 'simple':
                # Simple format - same as table but more concise
                click.echo("Document Statistics:")
                click.echo("=" * 40)
                click.echo(f"Total AST tokens: {stats.get('total_tokens', 0)}")
                click.echo(f"Document structure: {stats.get('document_structure', 'unknown')}")
                click.echo()
                # Headings
                headings = stats.get('headings', {})
                click.echo(f"Headings: {headings.get('total', 0)}")
                for level, count in headings.get('by_level', {}).items():
                    click.echo(f"  {level.upper()}: {count}")
                click.echo(f"Paragraphs: {stats.get('paragraphs', 0)}")
                click.echo(f"Links: {stats.get('links', 0)}")
                # Lists
                lists = stats.get('lists', {})
                total_lists = lists.get('ordered', 0) + lists.get('unordered', 0)
                click.echo(f"Lists: {total_lists}")
                if total_lists > 0:
                    click.echo(f"  Ordered: {lists.get('ordered', 0)}")
                    click.echo(f"  Unordered: {lists.get('unordered', 0)}")
                click.echo(f"Code blocks: {stats.get('code_blocks', 0)}")
                click.echo(f"Inline code: {stats.get('inline_code', 0)}")
                click.echo(f"Blockquotes: {stats.get('blockquotes', 0)}")
                # Emphasis
                emphasis = stats.get('emphasis', {})
                click.echo(f"Strong text: {emphasis.get('strong', 0)}")
                click.echo(f"Italic text: {emphasis.get('italic', 0)}")

        else:
            click.echo(f"Error: {result['message']}", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"AST statistics error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('schema-generate')
@click.argument('file_path', type=click.Path(exists=True, path_type=Path))
@click.option('--max-depth', '-d', type=int, help='Maximum heading depth to include in schema')
@click.option('--output', '-o', type=click.Path(path_type=Path), help='Output file path (default: stdout)')
@click.option('--outfile', type=click.Path(path_type=Path), help='Output file path (alias for --output)')
@click.option('--format', 'output_format', type=click.Choice(['json', 'yaml']), default='json', help='Output format')
@click.option('--mode', type=click.Choice(['outline']), help='Generation mode: outline for structure-focused schemas')
@click.option('--depth', type=int, help='Maximum depth for outline mode (similar to --max-depth)')
@click.option('--capture-heading-text', is_flag=True, help='Capture exact heading text as schema constraints')
@click.option('--include-content-instructions', is_flag=True, help='Include content field instructions for document generation')
@click.option('--instruction-type', type=click.Choice(['description', 'example', 'constraint', 'template']), default='description', help='Type of content instructions to generate')
@pass_config
def generate_schema(config, file_path, max_depth, output, outfile, output_format, mode, depth, capture_heading_text, include_content_instructions, instruction_type):
    """
    Generate a JSON schema from a markdown file's AST structure.

    FILE_PATH: Path to the markdown file to analyze

    Examples:
        markitect schema-generate document.md
        markitect schema-generate document.md --max-depth 2
        markitect schema-generate document.md --output schema.json

        # Outline mode for structure-focused schemas
        markitect schema-generate --mode outline document.md
        markitect schema-generate --mode outline --depth 3 --outfile schema.json document.md

        # Heading text capture for validation constraints
        markitect schema-generate --capture-heading-text document.md
        markitect schema-generate --mode outline --capture-heading-text --depth 2 document.md

        # Content instructions for document generation guidance
        markitect schema-generate --include-content-instructions document.md
        markitect schema-generate --include-content-instructions --instruction-type example document.md
        markitect schema-generate --mode outline --include-content-instructions --instruction-type template document.md

    Modes:
        Default: Standard schema generation with structural analysis
        Outline: Structure-focused schema with heading text capture and metaschema extensions

    Heading Text Capture:
        When --capture-heading-text is enabled, the schema will include exact heading text
        as enum constraints, enabling validation to enforce specific heading text requirements.

    Content Instructions:
        When --include-content-instructions is enabled, the schema will include guidance fields
        for document generation. Use --instruction-type to specify the type of instructions:
        - description: Descriptive guidance for content authors
        - example: Example-based content guidance
        - constraint: Content constraint specifications
        - template: Template-based content structure
    """
    try:
        # Handle parameter conflicts and defaults
        if outfile and output:
            click.echo("Error: Cannot specify both --output and --outfile", err=True)
            sys.exit(1)

        # Use outfile as output if specified
        final_output = outfile or output

        # Handle depth parameter for outline mode
        if mode == 'outline':
            if depth is not None and max_depth is not None:
                click.echo("Error: Cannot specify both --depth and --max-depth with outline mode", err=True)
                sys.exit(1)
            final_depth = depth if depth is not None else max_depth
        else:
            final_depth = max_depth

        # Validate depth parameter
        if final_depth is not None and final_depth < 1:
            click.echo("Invalid depth parameter: depth must be >= 1", err=True)
            sys.exit(1)

        # Initialize schema generator and associated files manager
        generator = SchemaGenerator()
        from .associated_files import AssociatedFilesManager
        associated_files = AssociatedFilesManager()

        # Generate schema with mode support
        schema = generator.generate_schema_from_file(
            file_path,
            max_depth=final_depth,
            mode=mode,
            outline_depth=depth if mode == 'outline' else None,
            capture_heading_text=capture_heading_text,
            include_content_instructions=include_content_instructions,
            instruction_type=instruction_type
        )

        # Format output
        if output_format == 'json':
            formatted_output = json.dumps(schema, indent=2, ensure_ascii=False)
        elif output_format == 'yaml':
            formatted_output = yaml.dump(schema, default_flow_style=False, allow_unicode=True)
        else:
            formatted_output = json.dumps(schema, indent=2, ensure_ascii=False)

        # Mode-based output logic
        if not final_output and should_use_associated_files():
            # Interactive mode: use associated file path
            from .associated_files import AssociatedFilesManager
            associated_files = AssociatedFilesManager()
            final_output = associated_files.get_associated_schema_path(file_path)
            if config.get('verbose'):
                click.echo(f"Interactive mode: using associated file path: {final_output}", err=True)

        # Write to output
        if final_output:
            final_output.write_text(formatted_output, encoding='utf-8')
            click.echo(f"Schema written to: {final_output}")

            # Show summary
            properties = schema.get('properties', {})
            click.echo(f"Generated schema with {len(properties)} property types")

            if 'headings' in properties:
                heading_levels = len(properties['headings'].get('properties', {}))
                click.echo(f"  - {heading_levels} heading levels found")

            structural_elements = ['paragraphs', 'lists', 'code_blocks', 'blockquotes', 'tables']
            found_elements = [elem for elem in structural_elements if elem in properties]
            if found_elements:
                click.echo(f"  - Structural elements: {', '.join(found_elements)}")
        else:
            click.echo(formatted_output)

    except FileNotFoundError as e:
        click.echo(f"File not found: {e}", err=True)
        sys.exit(1)
    except InvalidDepthError as e:
        click.echo(f"Invalid depth parameter: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"Schema generation error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('validate')
@click.argument('file_path', type=click.Path(exists=True, path_type=Path))
@click.option('--schema', '-s', type=click.Path(exists=True, path_type=Path),
              help='Path to JSON schema file (.json or .md)')
@click.option('--schema-json', type=str,
              help='JSON schema provided as a string')
@click.option('--quiet', '-q', is_flag=True,
              help='Only output validation result (true/false)')
@click.option('--detailed-errors', '--errors', is_flag=True,
              help='Show detailed validation errors (Issue #8)')
@click.option('--error-format', type=click.Choice(['text', 'json', 'markdown']), default='text',
              help='Format for detailed error output')
@click.option('--semantic/--no-semantic', default=True,
              help='Enable/disable semantic validation (sections, patterns, quality)')
@click.option('--check-links', is_flag=True,
              help='Enable link validation (may be slow, requires --semantic)')
@click.option('--strict', is_flag=True,
              help='Treat warnings as errors')
@pass_config
def validate(config, file_path, schema, schema_json, quiet, detailed_errors, error_format,
             semantic, check_links, strict):
    """
    Validate a markdown file against a JSON schema.

    ENHANCED: Now includes semantic validation of x-markitect extensions:
    - Section classifications (required, recommended, optional, discouraged, improper)
    - Content patterns (required_patterns, forbidden_patterns)
    - Quality metrics (min_words, max_words, min_sentences)

    Checks if a markdown document strictly adheres to the structure defined
    by a specified schema. Returns boolean result (True/False).

    Examples:
        # Structural + semantic validation (default)
        markitect validate doc.md --schema manpage-schema-v1.0.md

        # Only structural validation
        markitect validate doc.md --schema schema.json --no-semantic

        # Strict mode (warnings become errors)
        markitect validate doc.md --schema schema.json --strict

        # Legacy detailed errors
        markitect validate doc.md --schema schema.json --detailed-errors
    """
    try:
        validator = SchemaValidator()
        from .associated_files import AssociatedFilesManager
        associated_files = AssociatedFilesManager()

        # Validate schema source or auto-discover
        schema_sources = [schema, schema_json]
        provided_sources = [s for s in schema_sources if s is not None]

        if len(provided_sources) == 0:
            # Auto-discover associated schema file
            auto_schema = associated_files.find_associated_schema(file_path)
            if auto_schema:
                schema = auto_schema
                if config.get('verbose'):
                    click.echo(f"Auto-discovered associated schema: {schema}", err=True)
            else:
                click.echo("Error: No schema specified and no associated schema file found", err=True)
                click.echo("Provide --schema FILE or --schema-json JSON, or ensure an associated .json file exists", err=True)
                sys.exit(1)
        elif len(provided_sources) > 1:
            click.echo("Error: Specify exactly one schema source (--schema or --schema-json)", err=True)
            sys.exit(1)

        # Load schema dict (supports .json and .md)
        schema_dict = None
        if schema:
            from .semantic_validator import load_schema_from_path
            schema_dict = load_schema_from_path(schema)
            schema_source = f"schema file: {schema}"
        elif schema_json:
            schema_dict = json.loads(schema_json)
            schema_source = "provided JSON schema"

        # Perform validation (with or without detailed errors)
        if detailed_errors:
            # Use detailed error reporting for Issue #8
            error_collector = validator.validate_file_with_errors(file_path, schema_dict)
            is_valid = not error_collector.has_errors()

            # Output detailed errors
            if quiet:
                click.echo(str(is_valid).lower())
            else:
                status = "VALID" if is_valid else "INVALID"
                click.echo(f"Validation result: {status}")
                click.echo(f"File: {file_path}")
                click.echo(f"Schema: {schema_source}")

                if is_valid:
                    click.echo("✅ Document structure matches schema requirements")
                else:
                    click.echo("❌ Document structure does not match schema requirements")
                    click.echo()
                    click.echo(error_collector.format_errors(error_format))

        else:
            # Use simple boolean validation (original Issue #7 functionality)
            is_valid = validator.validate_file_against_schema(file_path, schema_dict)

            # Output results
            if quiet:
                click.echo(str(is_valid).lower())
            else:
                status = "VALID" if is_valid else "INVALID"
                click.echo(f"Validation result: {status}")
                click.echo(f"File: {file_path}")
                click.echo(f"Schema: {schema_source}")

                if is_valid:
                    click.echo("✅ Document structure matches schema requirements")
                else:
                    click.echo("❌ Document structure does not match schema requirements")
                    click.echo("💡 Use --detailed-errors to see specific validation issues")

        # Semantic validation (if enabled and schema has x-markitect extensions)
        semantic_report = None
        if semantic and schema_dict:
            try:
                from .semantic_validator import SemanticValidator

                # Check if schema has x-markitect extensions
                has_extensions = ('x-markitect-sections' in schema_dict or
                                'x-markitect-content-control' in schema_dict)

                if has_extensions:
                    sem_validator = SemanticValidator(schema_dict)
                    semantic_report = sem_validator.validate(file_path, check_links=check_links)

                    # Combine with structural validation result
                    if semantic_report and not quiet:
                        click.echo("")
                        click.echo("=" * 60)
                        click.echo("Semantic Validation Results:")
                        click.echo("=" * 60)
                        click.echo(semantic_report.format_text())

                    # Update validity based on semantic validation
                    if semantic_report:
                        if semantic_report.has_errors():
                            is_valid = False
                        elif strict and semantic_report.has_warnings():
                            is_valid = False

            except Exception as e:
                # Semantic validation failure doesn't fail the whole command
                # unless strict mode is enabled
                if not quiet:
                    click.echo(f"\n⚠️  Semantic validation error: {e}", err=True)
                if strict:
                    is_valid = False

        # Exit with appropriate code
        sys.exit(0 if is_valid else 1)

    except FileNotFoundError as e:
        click.echo(f"File not found: {e}", err=True)
        sys.exit(1)
    except (InvalidSchemaError, SchemaValidationError) as e:
        click.echo(f"Schema validation error: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"Validation error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# Schema management commands for Issue #3
@cli.command('schema-ingest')
@click.argument('schema_file', type=click.Path(exists=True, path_type=Path))
@click.option('--name', type=str, help='Custom name for the schema (default: filename)')
@pass_config
def schema_ingest(config, schema_file, name):
    """
    Read and store a schema file in the database.

    Supports both JSON (.json) and Markdown (.md) schema files.
    Validates schemas against the MarkiTect metaschema to ensure compatibility
    with MarkiTect features like heading text capture and content instructions.

    SCHEMA_FILE: Path to the schema file to store (.json or .md)

    Examples:
        markitect schema-ingest my_schema.json
        markitect schema-ingest manpage-schema-v1.0.md
        markitect schema-ingest external_schema.json --name custom-name
    """
    try:
        # Determine schema name
        schema_name = name if name else schema_file.name

        # Load schema based on file type
        if schema_file.suffix == '.md':
            # Load markdown schema
            from .schema_loader import MarkdownSchemaLoader
            loader = MarkdownSchemaLoader()

            try:
                schema_data_full = loader.load_schema(schema_file)
                schema_data = schema_data_full['schema']

                # Store the JSON content for database
                schema_content = json.dumps(schema_data, indent=2)

                if config.get('verbose'):
                    click.echo(f"✅ Loaded markdown schema: {schema_file.name}")
            except Exception as e:
                click.echo(f"Error: Failed to load markdown schema - {e}", err=True)
                sys.exit(1)
        else:
            # Load JSON schema
            with open(schema_file, 'r', encoding='utf-8') as f:
                schema_content = f.read()

            # Validate JSON format
            try:
                schema_data = json.loads(schema_content)
            except json.JSONDecodeError as e:
                click.echo(f"Error: Invalid JSON in schema file - {e}", err=True)
                sys.exit(1)

        # Validate against MarkiTect metaschema
        from .metaschema import MetaschemaValidator
        try:
            metaschema_validator = MetaschemaValidator()
            validation_result = metaschema_validator.validate_schema_with_errors(schema_data)

            if not validation_result.is_valid:
                click.echo("⚠️  Schema validation warnings against MarkiTect metaschema:", err=True)
                for error in validation_result.errors:
                    click.echo(f"   - {error.message}", err=True)
                click.echo("   Schema will be stored but may not be fully compatible with MarkiTect features.", err=True)
            else:
                if config.get('verbose'):
                    click.echo("✅ Schema validates successfully against MarkiTect metaschema")

        except Exception as e:
            if config.get('verbose'):
                click.echo(f"⚠️  Could not validate against metaschema: {e}", err=True)

        # Initialize database and store schema
        from .database import DatabaseManager
        db_path = config.get('database', 'markitect.db')
        db_manager = DatabaseManager(db_path)
        db_manager.initialize_database()

        record_id = db_manager.store_schema_file(schema_name, schema_content)

        if record_id:
            title = schema_data.get('title', schema_name)
            description = schema_data.get('description', '')

            click.echo(f"✅ Schema stored successfully")
            click.echo(f"   Name: {schema_name}")
            click.echo(f"   Title: {title}")
            if description:
                click.echo(f"   Description: {description}")
            click.echo(f"   Record ID: {record_id}")

            if config.get('verbose'):
                click.echo(f"   Source file: {schema_file}")
                click.echo(f"   Database: {db_path}")
        else:
            click.echo("❌ Failed to store schema in database", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"Schema ingest error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('schema-auto-ingest')
@pass_config
def schema_auto_ingest(config):
    """
    Automatically ingest all schemas from markitect/schemas/ directory.

    Scans the schemas directory for .md schema files and ingests any that
    are not already in the database. Skips schemas that have already been
    ingested.

    This command is useful for:
    - Post-install setup to register bundled schemas
    - Development workflow to sync schema changes
    - Updating schema registry after package updates

    Examples:
        markitect schema-auto-ingest
    """
    try:
        from .schema_loader import auto_ingest_schemas
        from .database import DatabaseManager

        # Initialize database
        db_path = config.get('database_path') or str(Path.home() / '.markitect' / 'markitect.db')
        db_manager = DatabaseManager(db_path)
        db_manager.initialize_database()

        verbose = config.get('verbose', False)

        # Run auto-ingestion
        results = auto_ingest_schemas(db_manager=db_manager, verbose=verbose)

        # Summary
        if not verbose:
            if results['ingested']:
                click.echo(f"✅ Ingested {len(results['ingested'])} schema(s)")
                for schema_name in results['ingested']:
                    click.echo(f"   - {schema_name}")

            if results['skipped']:
                click.echo(f"⏭️  Skipped {len(results['skipped'])} already-ingested schema(s)")

            if results['failed']:
                click.echo(f"❌ Failed to ingest {len(results['failed'])} schema(s):")
                for schema_name, error in results['failed']:
                    click.echo(f"   - {schema_name}: {error}")

        if not results['ingested'] and not results['failed']:
            if not results['skipped']:
                click.echo("ℹ️  No schemas found to ingest")
            else:
                click.echo("✅ All schemas already ingested")

    except Exception as e:
        click.echo(f"Auto-ingest error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('schema-list')
@click.option('--format', 'output_format', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
@click.option('--names-only', is_flag=True, help='Show only schema names (no metadata)')
@pass_config
def schema_list(config, output_format, names_only):
    """
    List all stored schema files.

    Shows metadata for all JSON schemas stored in the database,
    including their names, titles, descriptions, and timestamps.

    Examples:
        markitect schema-list
        markitect schema-list --format json
        markitect schema-list --format simple
        markitect schema-list --names-only
    """
    try:
        from .database import DatabaseManager

        db_path = config.get('database', 'markitect.db')
        db_manager = DatabaseManager(db_path)
        schemas = db_manager.list_schema_files()

        if not schemas:
            click.echo("No schemas found in database.")
            return

        # Handle names-only option
        if names_only:
            for schema_info in schemas:
                click.echo(schema_info['filename'])
            return

        # Add numbering to all schemas (1-indexed)
        for idx, schema_info in enumerate(schemas, 1):
            schema_info['number'] = idx

        # Handle different output formats
        if output_format == 'simple':
            # Simple emoji format like the original list command
            click.echo(f"Found {len(schemas)} schema(s):")
            click.echo()

            for schema_info in schemas:
                # Format timestamp for display (remove microseconds)
                created = schema_info['created_at']
                if created:
                    # Format: YYYY-MM-DD HH:MM:SS (remove microseconds if present)
                    if '.' in created:
                        created_display = created.split('.')[0]
                    else:
                        created_display = created
                    click.echo(f"[{schema_info['number']}] 🔧 {schema_info['filename']:<40} (added: {created_display})")
                else:
                    click.echo(f"[{schema_info['number']}] 🔧 {schema_info['filename']}")

                if config.get('verbose'):
                    click.echo(f"   Title: {schema_info['title']}")
                    click.echo(f"   Created: {schema_info['created_at']}")
                    click.echo(f"   Updated: {schema_info['updated_at']}")
                    if schema_info['description']:
                        click.echo(f"   Description: {schema_info['description']}")
                    click.echo()
        elif output_format == 'table':
            # Custom table format for better readability
            table_data = []
            for schema in schemas:
                # Format timestamps (remove microseconds)
                created_date = schema['created_at'].split('.')[0] if schema['created_at'] and '.' in schema['created_at'] else schema['created_at']
                updated_date = schema['updated_at'].split('.')[0] if schema['updated_at'] and '.' in schema['updated_at'] else schema['updated_at']

                table_data.append({
                    '#': schema['number'],
                    'Name': schema['filename'],
                    'Title': schema['title'] or '',
                    'Created': created_date or '',
                    'Updated': updated_date or ''
                })

            if table_data:
                headers = ['#', 'Name', 'Title', 'Created', 'Updated']
                rows = [[row[h] for h in headers] for row in table_data]
                click.echo(tabulate(rows, headers=headers, tablefmt='simple'))
        else:
            # Use structured format (json, yaml)
            formatted_output = format_output(schemas, output_format)
            click.echo(formatted_output)

        if config.get('verbose'):
            click.echo(f"\nTotal schemas: {len(schemas)}", err=True)

    except Exception as e:
        click.echo(f"Schema list error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('schema-get')
@click.argument('schema_name', type=str)
@click.option('--output', '-o', type=click.Path(path_type=Path),
              help='Output file path (default: stdout)')
@pass_config
def schema_get(config, schema_name, output):
    """
    Retrieve and output a stored schema file.

    Fetches a JSON schema from the database by name and outputs
    its content either to stdout or to a specified file.

    SCHEMA_NAME: Name of the stored schema to retrieve

    Examples:
        markitect schema-get my_schema.json
        markitect schema-get my_schema.json --output exported_schema.json
    """
    try:
        from .database import DatabaseManager

        db_path = config.get('database', 'markitect.db')
        db_manager = DatabaseManager(db_path)
        schema_data = db_manager.get_schema_file(schema_name)

        if not schema_data:
            click.echo(f"Error: Schema '{schema_name}' not found in database", err=True)
            sys.exit(1)

        schema_content = schema_data['schema_content']

        # Output to file or stdout
        if output:
            with open(output, 'w', encoding='utf-8') as f:
                f.write(schema_content)
            click.echo(f"✅ Schema exported to: {output}")

            if config.get('verbose'):
                click.echo(f"   Title: {schema_data['title']}")
                click.echo(f"   Description: {schema_data['description']}")
        else:
            click.echo(schema_content)

    except Exception as e:
        click.echo(f"Schema get error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('schema-delete')
@click.argument('schema_name', type=str)
@click.option('--confirm', is_flag=True, help='Skip confirmation prompt')
@pass_config
def schema_delete(config, schema_name, confirm):
    """
    Delete a stored schema file from the database.

    Removes a JSON schema from the database permanently.
    This action cannot be undone.

    SCHEMA_NAME: Name of the stored schema to delete

    Examples:
        markitect schema-delete old_schema.json
        markitect schema-delete old_schema.json --confirm
    """
    try:
        from .database import DatabaseManager

        db_path = config.get('database', 'markitect.db')
        db_manager = DatabaseManager(db_path)

        # Check if schema exists
        schema_data = db_manager.get_schema_file(schema_name)
        if not schema_data:
            click.echo(f"Error: Schema '{schema_name}' not found in database", err=True)
            sys.exit(1)

        # Confirmation prompt
        if not confirm:
            title = schema_data['title']
            click.echo(f"Schema to delete:")
            click.echo(f"   Name: {schema_name}")
            click.echo(f"   Title: {title}")
            click.echo(f"   Created: {schema_data['created_at']}")

            if not click.confirm("Are you sure you want to delete this schema?"):
                click.echo("Deletion cancelled.")
                return

        # Perform deletion
        success = db_manager.delete_schema_file(schema_name)

        if success:
            click.echo(f"✅ Schema '{schema_name}' deleted successfully")
        else:
            click.echo(f"❌ Failed to delete schema '{schema_name}'", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"Schema delete error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# Schema validation helper functions and dataclasses

@dataclass
class ValidationResult:
    """Result of validating a single schema."""
    number: Optional[int]  # Number in the list (if from registry)
    schema_name: str  # Display name
    source_type: str  # 'registry' or 'filesystem'
    is_valid: bool
    errors: List[str]
    title: Optional[str] = None
    version: Optional[str] = None
    schema_id: Optional[str] = None


def is_filesystem_path(selector: str) -> bool:
    """Check if selector looks like a filesystem path.

    Args:
        selector: User input string

    Returns:
        True if selector appears to be a filesystem path
    """
    return (
        selector.startswith('./') or
        selector.startswith('../') or
        selector.startswith('/') or
        '/' in selector
    )


def parse_schema_selector(selector: str, schemas: List[dict]) -> List[str]:
    """Parse user input into list of schema filenames.

    Supports:
    - Single number: "1"
    - Number range: "1-3"
    - Number list: "1,3,5"
    - Keyword "all": returns all schemas
    - Filename: "manpage-schema-v1.0.md"

    Args:
        selector: User input string
        schemas: List of schema dicts with 'number' and 'filename' keys

    Returns:
        List of schema filenames

    Raises:
        ValueError: If selector format is invalid or numbers out of range
    """
    if not selector or selector.lower() == 'all':
        return [s['filename'] for s in schemas]

    # Check if it looks like a filename (contains extension or is not a number/range)
    if not selector.replace(',', '').replace('-', '').replace(' ', '').isdigit():
        # Assume it's a filename
        return [selector]

    # Parse number selection
    selected_numbers = set()

    # Handle comma-separated list: "1,3,5"
    parts = [part.strip() for part in selector.split(',')]

    for part in parts:
        if '-' in part:
            # Handle range: "1-3"
            try:
                start_str, end_str = part.split('-', 1)
                start = int(start_str.strip())
                end = int(end_str.strip())

                if start < 1 or end > len(schemas):
                    raise ValueError(
                        f"Range {start}-{end} is out of bounds. "
                        f"Valid range: 1-{len(schemas)}"
                    )
                if start > end:
                    raise ValueError(f"Invalid range: {start}-{end} (start > end)")

                selected_numbers.update(range(start, end + 1))
            except ValueError as e:
                if "invalid literal" in str(e):
                    raise ValueError(f"Invalid range format: '{part}'")
                raise
        else:
            # Handle single number: "1"
            try:
                num = int(part)
                if num < 1 or num > len(schemas):
                    raise ValueError(
                        f"Number {num} is out of bounds. "
                        f"Valid range: 1-{len(schemas)}"
                    )
                selected_numbers.add(num)
            except ValueError as e:
                if "invalid literal" in str(e):
                    raise ValueError(f"Invalid number: '{part}'")
                raise

    # Convert numbers to filenames
    number_to_filename = {s['number']: s['filename'] for s in schemas}
    return [number_to_filename[num] for num in sorted(selected_numbers)]


def resolve_schema_source(identifier: str, db_manager: DatabaseManager) -> Tuple[str, dict, str]:
    """Resolve schema identifier to its source.

    Resolution order:
    1. Check registry by exact filename match
    2. If looks like path or not found in registry, try filesystem

    Args:
        identifier: Schema filename or path
        db_manager: Database manager instance

    Returns:
        Tuple of (source_type, schema_data, display_name)
        - source_type: 'registry' or 'filesystem'
        - schema_data: Dict with schema content or Path object
        - display_name: Human-readable name for display

    Raises:
        FileNotFoundError: If schema not found in registry or filesystem
    """
    # First, try registry (exact filename match)
    schema_data = db_manager.get_schema_file(identifier)
    if schema_data:
        return ('registry', schema_data, identifier)

    # If not found in registry, try filesystem
    # (either because it looks like a path or as a fallback)
    schema_path = Path(identifier)
    if schema_path.exists():
        return ('filesystem', {'path': schema_path}, str(schema_path))

    # Not found anywhere
    raise FileNotFoundError(
        f"Schema '{identifier}' not found in registry or filesystem. "
        f"Use 'markitect schema-list' to see available schemas."
    )


def format_validation_summary(results: List[ValidationResult]) -> str:
    """Format batch validation results as a table.

    Args:
        results: List of ValidationResult objects

    Returns:
        Formatted table string
    """
    if not results:
        return "No validation results."

    # Build table data
    table_data = []
    for result in results:
        # Number column (if available)
        num_str = str(result.number) if result.number else '-'

        # Status column
        status = '✅ Valid' if result.is_valid else '❌ Failed'

        # Details column
        if result.is_valid:
            details = f"v{result.version}" if result.version else 'OK'
        else:
            error_count = len(result.errors)
            details = f"{error_count} error{'s' if error_count != 1 else ''}"

        table_data.append([num_str, result.schema_name, status, details])

    # Format as table
    headers = ['#', 'Schema', 'Status', 'Details']
    table = tabulate(table_data, headers=headers, tablefmt='simple')

    return table


@cli.command('schema-validate')
@click.argument('schema_selector', type=str, required=False)
@click.option('--all', 'validate_all', is_flag=True, help='Validate all registered schemas')
@click.option('--detailed-errors', is_flag=True, help='Show detailed validation errors')
@pass_config
def schema_validate_cmd(config, schema_selector, validate_all, detailed_errors):
    """
    Validate schema file(s) against the schema-for-schemas metaschema.

    Ensures schema files follow MarkiTect conventions and standards:
    - Required fields ($schema, $id, title, description, version)
    - Version format (SemVer: major.minor.patch)
    - $id URL format (HTTPS with version)
    - MarkiTect extensions (x-markitect-*)
    - Section classification structures

    SCHEMA_SELECTOR: Schema selection (optional):
    - Number: "1"
    - Range: "1-3"
    - List: "1,3,5"
    - Filename: "manpage-schema-v1.0.md"
    - Path: "./my-schema.md"
    - Keyword: "all"

    If no selector provided and --all not specified, shows usage help.

    Examples:
        markitect schema-validate 1
        markitect schema-validate 1-3
        markitect schema-validate 1,3,5
        markitect schema-validate --all
        markitect schema-validate manpage-schema-v1.0.md
        markitect schema-validate ./my-schema.md --detailed-errors
    """
    try:
        from .schema_loader import MarkdownSchemaLoader
        try:
            import jsonschema
            from jsonschema import Draft7Validator, ValidationError
        except ImportError:
            click.echo("❌ Error: jsonschema package not installed", err=True)
            click.echo("Install it with: pip install jsonschema", err=True)
            sys.exit(1)

        # Determine what to validate
        if validate_all:
            selector = 'all'
        elif schema_selector:
            selector = schema_selector
        else:
            click.echo("❌ Error: No schema specified", err=True)
            click.echo("\nUsage:")
            click.echo("  markitect schema-validate 1           # Validate schema #1")
            click.echo("  markitect schema-validate 1-3         # Validate schemas #1-3")
            click.echo("  markitect schema-validate 1,3,5       # Validate schemas #1,3,5")
            click.echo("  markitect schema-validate --all       # Validate all schemas")
            click.echo("  markitect schema-validate schema.md   # Validate by filename")
            click.echo("  markitect schema-validate ./schema.md # Validate by path")
            click.echo("\nUse 'markitect schema-list' to see available schemas.")
            sys.exit(1)

        db_path = config.get('database', 'markitect.db')
        db_manager = DatabaseManager(db_path)
        loader = MarkdownSchemaLoader()

        # Load metaschema once
        metaschema_path = Path(__file__).parent / 'schemas' / 'schema-schema-v1.0.md'
        if not metaschema_path.exists():
            click.echo(f"❌ Metaschema not found: {metaschema_path}", err=True)
            sys.exit(1)

        try:
            metaschema_data = loader.load_schema(metaschema_path)
            metaschema = metaschema_data['schema']
        except Exception as e:
            click.echo(f"❌ Failed to load metaschema: {e}", err=True)
            sys.exit(1)

        # Resolve which schemas to validate
        schemas_to_validate = []

        # Check if selector is a filesystem path
        if selector != 'all' and is_filesystem_path(selector):
            # Direct filesystem path - validate single file
            schema_path = Path(selector)
            if not schema_path.exists():
                click.echo(f"❌ File not found: {selector}", err=True)
                sys.exit(1)
            schemas_to_validate.append({
                'identifier': selector,
                'number': None,
                'source_type': 'filesystem'
            })
        else:
            # Number/range/filename - get registry list and parse
            all_schemas = db_manager.list_schema_files()
            if not all_schemas:
                click.echo("❌ No schemas found in registry", err=True)
                click.echo("Use 'markitect schema-ingest' to add schemas first.", err=True)
                sys.exit(1)

            # Add numbering
            for idx, schema_info in enumerate(all_schemas, 1):
                schema_info['number'] = idx

            # Parse selector
            try:
                selected_filenames = parse_schema_selector(selector, all_schemas)
            except ValueError as e:
                click.echo(f"❌ Invalid selector: {e}", err=True)
                sys.exit(1)

            # Build list of schemas to validate
            filename_to_number = {s['filename']: s['number'] for s in all_schemas}
            for filename in selected_filenames:
                schemas_to_validate.append({
                    'identifier': filename,
                    'number': filename_to_number.get(filename),
                    'source_type': 'registry'
                })

        # Validate schemas
        results = []
        validator = Draft7Validator(metaschema)

        # Show progress for multiple schemas
        if len(schemas_to_validate) > 1:
            click.echo(f"Validating {len(schemas_to_validate)} schema(s)...\n")

        for schema_info in schemas_to_validate:
            identifier = schema_info['identifier']
            number = schema_info['number']
            source_type = schema_info['source_type']

            try:
                # Resolve and load schema
                if source_type == 'filesystem':
                    schema_path = Path(identifier)
                    if schema_path.suffix == '.md':
                        schema_data = loader.load_schema(schema_path)
                        schema = schema_data['schema']
                    else:
                        schema = json.loads(schema_path.read_text())
                    display_name = str(schema_path)
                else:
                    # From registry
                    source_type, schema_data, display_name = resolve_schema_source(
                        identifier, db_manager
                    )
                    if source_type == 'registry':
                        schema = json.loads(schema_data['schema_content'])
                    else:
                        # Fallback to filesystem
                        schema_path = schema_data['path']
                        if schema_path.suffix == '.md':
                            loaded = loader.load_schema(schema_path)
                            schema = loaded['schema']
                        else:
                            schema = json.loads(schema_path.read_text())

                # Validate
                errors = list(validator.iter_errors(schema))

                # Create result
                result = ValidationResult(
                    number=number,
                    schema_name=display_name,
                    source_type=source_type,
                    is_valid=(len(errors) == 0),
                    errors=[error.message for error in errors],
                    title=schema.get('title'),
                    version=schema.get('version'),
                    schema_id=schema.get('$id')
                )
                results.append(result)

            except FileNotFoundError as e:
                # Schema not found
                result = ValidationResult(
                    number=number,
                    schema_name=identifier,
                    source_type=source_type,
                    is_valid=False,
                    errors=[str(e)]
                )
                results.append(result)
            except Exception as e:
                # Other error
                result = ValidationResult(
                    number=number,
                    schema_name=identifier,
                    source_type=source_type,
                    is_valid=False,
                    errors=[f"Failed to load: {e}"]
                )
                results.append(result)

        # Display results
        if len(results) == 1:
            # Single schema - detailed output (backward compatible)
            result = results[0]
            if result.is_valid:
                click.echo(f"✅ Schema is valid: {result.schema_name}")
                if result.title:
                    click.echo(f"   Title: {result.title}")
                if result.version:
                    click.echo(f"   Version: {result.version}")
                if result.schema_id:
                    click.echo(f"   $id: {result.schema_id}")
            else:
                click.echo(f"❌ Schema validation failed: {result.schema_name}", err=True)
                click.echo(f"\nFound {len(result.errors)} validation error(s):\n", err=True)
                for i, error_msg in enumerate(result.errors, 1):
                    click.echo(f"{i}. {error_msg}", err=True)
                sys.exit(1)
        else:
            # Multiple schemas - summary table
            click.echo("Results:\n")
            click.echo(format_validation_summary(results))

            # Summary counts
            valid_count = sum(1 for r in results if r.is_valid)
            failed_count = len(results) - valid_count

            click.echo(f"\nSummary: {valid_count} valid, {failed_count} failed")

            # Show failed details
            if failed_count > 0:
                click.echo("\nFailed schemas:")
                for result in results:
                    if not result.is_valid:
                        num_str = f"{result.number}. " if result.number else ""
                        click.echo(f"  {num_str}{result.schema_name}", err=True)
                        for error_msg in result.errors[:3]:  # Show first 3 errors
                            click.echo(f"     - {error_msg}", err=True)
                        if len(result.errors) > 3:
                            click.echo(f"     ... and {len(result.errors) - 3} more", err=True)
                sys.exit(1)

    except Exception as e:
        click.echo(f"❌ Schema validation error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('schema-analyze')
@click.argument('schema_file', type=click.Path(exists=True))
@click.option('--verbose', '-v', is_flag=True, help='Show detailed analysis')
@pass_config
def schema_analyze_cmd(config, schema_file, verbose):
    """
    Analyze a schema for rigidity issues and suggest improvements.

    Examines JSON schemas to detect:
    - Exact counts that should be ranges
    - Missing classification system
    - Deprecated extensions
    - Overly specific constraints

    Returns exit code 0 for flexible schemas, 1 for rigid schemas, 2 for errors.

    Examples:
        markitect schema-analyze schema.json
        markitect schema-analyze schema.json --verbose
    """
    from .schema_analyzer import analyze_schema_cli
    sys.exit(analyze_schema_cli(schema_file, verbose=verbose))


@cli.command('schema-refine')
@click.argument('schema_file', type=click.Path(exists=True))
@click.option('--output', '-o', type=click.Path(),
              help='Output file (default: overwrite input file)')
@click.option('--loosen-counts', is_flag=True, default=True,
              help='Convert exact counts to flexible ranges (default: enabled)')
@click.option('--no-loosen-counts', is_flag=True,
              help='Disable count loosening')
@click.option('--round-numbers', is_flag=True, default=True,
              help='Round overly specific numbers (default: enabled)')
@click.option('--no-round-numbers', is_flag=True,
              help='Disable number rounding')
@click.option('--migrate-deprecated', is_flag=True, default=False,
              help='Migrate deprecated extensions (requires manual review)')
@click.option('--dry-run', is_flag=True,
              help='Show changes without applying them')
@click.option('--interactive', '-i', is_flag=True,
              help='Prompt for each refinement interactively')
@pass_config
def schema_refine_cmd(config, schema_file, output, loosen_counts, no_loosen_counts,
                      round_numbers, no_round_numbers, migrate_deprecated, dry_run, interactive):
    """
    Refine a schema by automatically applying fixes for rigidity issues.

    This command analyzes the schema and applies automatic fixes:
    - Converts exact counts to flexible ranges
    - Rounds overly specific numbers
    - Widens narrow integer constraints
    - Documents deprecated extension usage

    By default, the input file is overwritten. Use --output to save to a different file.

    Examples:
        # Refine schema in place
        markitect schema-refine schema.json

        # Preview changes without applying
        markitect schema-refine schema.json --dry-run

        # Review each fix interactively
        markitect schema-refine schema.json --interactive

        # Save refined schema to new file
        markitect schema-refine schema.json --output refined-schema.json

        # Disable specific refinements
        markitect schema-refine schema.json --no-loosen-counts
    """
    from .schema_refiner import refine_schema_cli

    # Handle flag conflicts
    loosen = loosen_counts and not no_loosen_counts
    round_nums = round_numbers and not no_round_numbers

    sys.exit(refine_schema_cli(
        schema_file,
        output=output,
        loosen_counts=loosen,
        migrate_deprecated=migrate_deprecated,
        round_numbers=round_nums,
        dry_run=dry_run,
        interactive=interactive
    ))


@cli.command('generate-stub')
@click.argument('schema_file', type=click.Path(exists=True, path_type=Path))
@click.option('--output', '-o', type=click.Path(path_type=Path),
              help='Output file path (default: stdout)')
@click.option('--style', type=click.Choice(['default', 'custom', 'detailed']),
              default='default', help='Placeholder content style')
@click.option('--title', type=str, help='Custom document title')
@pass_config
def generate_stub(config, schema_file, output, style, title):
    """
    Generate a markdown stub/template from a JSON schema.

    Creates a markdown document with proper heading hierarchy and placeholder
    content based on the structural definitions in the JSON schema. When schemas
    include content instructions (x-markitect-content-instructions), the generated
    stub will use specific guidance text instead of generic placeholders.

    SCHEMA_FILE: Path to the JSON schema file

    Examples:
        markitect generate-stub blog_schema.json
        markitect generate-stub schema.json --output template.md
        markitect generate-stub schema.json --style detailed --title "My Document"

        # Content instructions will be used automatically when present in schema
        markitect generate-stub schema_with_instructions.json

    Content Instructions:
        When a schema contains x-markitect-content-instructions-enabled: true,
        the generated stub will include specific content guidance from the schema
        instead of generic "TODO" placeholders. This is especially useful with
        schemas created using the --include-content-instructions option.

    Schema Reference:
        Generated stubs include a comment referencing the source schema file
        for validation and traceability purposes.
    """
    try:
        if config.get('verbose'):
            click.echo(f"Generating stub from schema: {schema_file}", err=True)

        from .stub_generator import StubGenerator
        from .associated_files import AssociatedFilesManager

        generator = StubGenerator()
        associated_files = AssociatedFilesManager()

        # Load schema (supports .json and .md)
        from .semantic_validator import load_schema_from_path
        schema = load_schema_from_path(schema_file)

        stub_content = generator.generate_stub_from_schema(
            schema, placeholder_style=style, title=title, schema_file_path=schema_file
        )

        # Mode-based output logic
        if not output and should_use_associated_files():
            # Interactive mode: use associated file path
            output = associated_files.get_associated_markdown_path(schema_file)
            if config.get('verbose'):
                click.echo(f"Interactive mode: using associated file path: {output}", err=True)

        # Output to file or stdout
        if output:
            generator.generate_stub_to_file(schema, output, style, title, schema_file)
            click.echo(f"✅ Stub generated: {output}")

            if config.get('verbose'):
                click.echo(f"Generated markdown template saved to: {output}", err=True)
        else:
            click.echo(stub_content)

            if config.get('verbose'):
                click.echo(f"Generated {len(stub_content)} characters of content", err=True)

    except FileNotFoundError as e:
        click.echo(f"Error: {e}", err=True)
        sys.exit(1)
    except json.JSONDecodeError as e:
        click.echo(f"Error: Invalid JSON in schema file - {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"Stub generation error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('generate-drafts')
@click.argument('schema_file', type=click.Path(exists=True, path_type=Path))
@click.argument('data_source', type=click.Path(exists=True, path_type=Path))
@click.option('--output-dir', '-o', type=click.Path(path_type=Path), required=True,
              help='Output directory for generated drafts')
@pass_config
def generate_drafts(config, schema_file, data_source, output_dir):
    """
    Generate multiple document drafts from a schema and data source.

    Creates multiple markdown documents by combining a JSON schema template
    with data from JSON or CSV sources. Each record in the data source
    generates a separate draft file with field mapping applied.

    SCHEMA_FILE: Path to the JSON schema file
    DATA_SOURCE: Path to JSON or CSV data source file

    Examples:
        markitect generate-drafts schema.json data.json -o ./drafts/
        markitect generate-drafts blog_schema.json posts.csv -o ./blog_posts/

    Field Mapping:
        Use x-markitect-field-mapping extension in schema to map data fields
        to content areas. Data validation ensures compatibility.

    Output:
        Generated drafts maintain schema references for validation and
        use automatic file naming based on data content.
    """
    try:
        if config.get('verbose'):
            click.echo(f"Generating drafts from schema: {schema_file}", err=True)
            click.echo(f"Using data source: {data_source}", err=True)
            click.echo(f"Output directory: {output_dir}", err=True)

        from .draft_generator import DraftGenerator

        generator = DraftGenerator()

        # Load schema
        import json
        with open(schema_file, 'r') as f:
            schema = json.load(f)

        # Generate drafts
        generated_files = generator.generate_drafts_from_data_source(
            schema=schema,
            data_source=data_source,
            output_dir=Path(output_dir),
            schema_file_path=str(schema_file)
        )

        # Report results
        click.echo(f"✅ Generated {len(generated_files)} drafts in {output_dir}")
        if config.get('verbose'):
            for file_path in generated_files:
                click.echo(f"  - {file_path}", err=True)

    except FileNotFoundError as e:
        click.echo(f"Error: {e}", err=True)
        sys.exit(1)
    except json.JSONDecodeError as e:
        click.echo(f"Error: Invalid JSON in schema file - {e}", err=True)
        sys.exit(1)
    except ValueError as e:
        click.echo(f"Error: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"Draft generation error: {e}", err=True)
        if config and config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.group('associated-files')
@pass_config
def associated_files_group(config):
    """
    Manage associated markdown and schema file pairs.

    Commands for working with files that follow the convention of having
    identical basenames with different extensions (e.g., document.md ↔ document.json).
    """
    pass


@associated_files_group.command('list')
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']),
              help='Output format')
@click.argument('directory', type=click.Path(exists=True, file_okay=False, path_type=Path), default='.')
@pass_config
def list_associated_files(config, format, directory):
    """
    List all associated file pairs in a directory.

    Shows markdown/schema file pairs that follow the naming convention.

    Examples:
        markitect associated-files list
        markitect associated-files list docs/
        markitect associated-files list --format json
    """
    try:
        from .associated_files import AssociatedFilesManager
        manager = AssociatedFilesManager()

        if config.get('verbose'):
            click.echo(f"Scanning directory: {directory}", err=True)

        pairs = manager.list_file_pairs(directory)

        if not pairs:
            click.echo("No associated file pairs found.")
            return

        # Format output
        if format == 'table':
            click.echo(f"Associated File Pairs in {directory}:")
            click.echo("=" * 60)
            for pair in pairs:
                click.echo(f"📄 {pair['basename']}")
                click.echo(f"   Markdown: {pair['markdown_file'].name}")
                click.echo(f"   Schema:   {pair['schema_file'].name}")
                click.echo()
        elif format == 'json':
            import json
            output_data = []
            for pair in pairs:
                output_data.append({
                    'basename': pair['basename'],
                    'markdown_file': str(pair['markdown_file']),
                    'schema_file': str(pair['schema_file']),
                    'both_exist': pair['both_exist']
                })
            click.echo(json.dumps(output_data, indent=2))
        elif format == 'yaml':
            import yaml
            output_data = []
            for pair in pairs:
                output_data.append({
                    'basename': pair['basename'],
                    'markdown_file': str(pair['markdown_file']),
                    'schema_file': str(pair['schema_file']),
                    'both_exist': pair['both_exist']
                })
            click.echo(yaml.dump(output_data, default_flow_style=False))
        else:
            # Simple format
            for pair in pairs:
                click.echo(f"{pair['basename']} ({pair['markdown_file'].name} ↔ {pair['schema_file'].name})")

        if config.get('verbose'):
            click.echo(f"Found {len(pairs)} associated file pairs", err=True)

    except Exception as e:
        click.echo(f"Error listing associated files: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@associated_files_group.command('info')
@click.argument('file_path', type=click.Path(exists=True, path_type=Path))
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']),
              help='Output format')
@pass_config
def associated_files_info(config, file_path, format):
    """
    Show detailed information about associated files.

    Displays information about a file and its associated counterpart.

    Examples:
        markitect associated-files info document.md
        markitect associated-files info schema.json --format json
    """
    try:
        from .associated_files import AssociatedFilesManager
        manager = AssociatedFilesManager()

        info = manager.get_file_pair_info(file_path)

        if format == 'table':
            click.echo(f"Associated Files Information:")
            click.echo("=" * 40)
            click.echo(f"Basename: {info['basename']}")
            click.echo(f"Markdown: {info['markdown_file']}")
            click.echo(f"  Exists: {'✅' if info['markdown_file'].exists() else '❌'}")
            if 'markdown_size' in info:
                click.echo(f"  Size: {info['markdown_size']} bytes")

            click.echo(f"Schema: {info['schema_file']}")
            click.echo(f"  Exists: {'✅' if info['schema_file'].exists() else '❌'}")
            if 'schema_size' in info:
                click.echo(f"  Size: {info['schema_size']} bytes")

            click.echo(f"Both exist: {'✅' if info['both_exist'] else '❌'}")

        elif format == 'json':
            import json
            # Convert Path objects to strings for JSON serialization
            json_info = {k: str(v) if isinstance(v, Path) else v for k, v in info.items()}
            click.echo(json.dumps(json_info, indent=2))

        elif format == 'yaml':
            import yaml
            # Convert Path objects to strings for YAML serialization
            yaml_info = {k: str(v) if isinstance(v, Path) else v for k, v in info.items()}
            click.echo(yaml.dump(yaml_info, default_flow_style=False))
        else:
            # Simple format
            status = "paired" if info['both_exist'] else "orphaned"
            click.echo(f"{info['basename']}: {status}")

    except Exception as e:
        click.echo(f"Error getting file info: {e}", err=True)
        sys.exit(1)


@associated_files_group.command('status')
@click.argument('directory', type=click.Path(exists=True, file_okay=False, path_type=Path), default='.')
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']),
              help='Output format')
@pass_config
def associated_files_status(config, directory, format):
    """
    Show status of associated files in a directory.

    Displays paired files and orphaned files (files without their counterpart).

    Examples:
        markitect associated-files status
        markitect associated-files status docs/
    """
    try:
        from .associated_files import AssociatedFilesManager
        manager = AssociatedFilesManager()

        status = manager.get_directory_status(directory)

        if format == 'table':
            click.echo(f"Associated Files Status for {directory}:")
            click.echo("=" * 50)
            click.echo(f"📌 Paired files: {status['paired_files']}")
            click.echo(f"📄 Orphaned markdown: {status['orphaned_markdown']}")
            click.echo(f"🔧 Orphaned schemas: {status['orphaned_schemas']}")

            if status['pairs']:
                click.echo("\n📌 Paired Files:")
                for pair in status['pairs']:
                    click.echo(f"  • {pair['basename']}")

            if status['orphaned']['orphaned_markdown']:
                click.echo("\n📄 Orphaned Markdown Files:")
                for md in status['orphaned']['orphaned_markdown']:
                    click.echo(f"  • {md.name}")

            if status['orphaned']['orphaned_schemas']:
                click.echo("\n🔧 Orphaned Schema Files:")
                for schema in status['orphaned']['orphaned_schemas']:
                    click.echo(f"  • {schema.name}")

        elif format == 'json':
            import json
            # Convert Path objects to strings for JSON serialization
            json_status = {
                'directory': str(status['directory']),
                'paired_files': status['paired_files'],
                'orphaned_markdown': status['orphaned_markdown'],
                'orphaned_schemas': status['orphaned_schemas'],
                'pairs': [{'basename': p['basename'],
                          'markdown_file': str(p['markdown_file']),
                          'schema_file': str(p['schema_file'])}
                         for p in status['pairs']],
                'orphaned': {
                    'orphaned_markdown': [str(f) for f in status['orphaned']['orphaned_markdown']],
                    'orphaned_schemas': [str(f) for f in status['orphaned']['orphaned_schemas']]
                }
            }
            click.echo(json.dumps(json_status, indent=2))

        elif format == 'yaml':
            import yaml
            yaml_status = {
                'directory': str(status['directory']),
                'paired_files': status['paired_files'],
                'orphaned_markdown': status['orphaned_markdown'],
                'orphaned_schemas': status['orphaned_schemas'],
                'pairs': [{'basename': p['basename'],
                          'markdown_file': str(p['markdown_file']),
                          'schema_file': str(p['schema_file'])}
                         for p in status['pairs']],
                'orphaned': {
                    'orphaned_markdown': [str(f) for f in status['orphaned']['orphaned_markdown']],
                    'orphaned_schemas': [str(f) for f in status['orphaned']['orphaned_schemas']]
                }
            }
            click.echo(yaml.dump(yaml_status, default_flow_style=False))
        else:
            # Simple format
            click.echo(f"Paired: {status['paired_files']}, Orphaned: {status['orphaned_markdown'] + status['orphaned_schemas']}")

    except Exception as e:
        click.echo(f"Error getting status: {e}", err=True)
        sys.exit(1)


@associated_files_group.command('create-schema')
@click.argument('markdown_file', type=click.Path(exists=True, path_type=Path))
@click.option('--max-depth', '-d', type=int, help='Maximum heading depth to include in schema')
@pass_config
def create_associated_schema(config, markdown_file, max_depth):
    """
    Create an associated schema file for a markdown file.

    Generates a JSON schema and places it next to the source markdown file
    with the same basename but .json extension.

    Examples:
        markitect associated-files create-schema document.md
        markitect associated-files create-schema doc.md --max-depth 3
    """
    try:
        from .associated_files import AssociatedFilesManager
        from .schema_generator import SchemaGenerator

        manager = AssociatedFilesManager()
        generator = SchemaGenerator()

        # Check if associated schema already exists
        existing_schema = manager.find_associated_schema(markdown_file)
        if existing_schema:
            if not click.confirm(f"Associated schema {existing_schema} already exists. Overwrite?"):
                click.echo("Operation cancelled.")
                return

        # Generate schema
        schema = generator.generate_schema_from_file(markdown_file, max_depth=max_depth)

        # Save to associated path
        schema_path = manager.get_associated_schema_path(markdown_file)

        import json
        with open(schema_path, 'w', encoding='utf-8') as f:
            json.dump(schema, f, indent=2, ensure_ascii=False)

        click.echo(f"✅ Created associated schema: {schema_path}")

        if config.get('verbose'):
            properties = schema.get('properties', {})
            click.echo(f"Generated schema with {len(properties)} property types", err=True)

    except Exception as e:
        click.echo(f"Error creating schema: {e}", err=True)
        sys.exit(1)


@associated_files_group.command('create-stub')
@click.argument('schema_file', type=click.Path(exists=True, path_type=Path))
@click.option('--style', type=click.Choice(['default', 'custom', 'detailed']),
              default='default', help='Placeholder content style')
@click.option('--title', type=str, help='Custom document title')
@pass_config
def create_associated_stub(config, schema_file, style, title):
    """
    Create an associated markdown stub for a schema file.

    Generates a markdown template and places it next to the source schema file
    with the same basename but .md extension.

    Examples:
        markitect associated-files create-stub schema.json
        markitect associated-files create-stub schema.json --style detailed
    """
    try:
        from .associated_files import AssociatedFilesManager
        from .stub_generator import StubGenerator

        manager = AssociatedFilesManager()
        generator = StubGenerator()

        # Check if associated markdown already exists
        existing_md = manager.find_associated_markdown(schema_file)
        if existing_md:
            if not click.confirm(f"Associated markdown {existing_md} already exists. Overwrite?"):
                click.echo("Operation cancelled.")
                return

        # Load schema and generate stub
        import json
        with open(schema_file, 'r') as f:
            schema = json.load(f)

        # Save to associated path
        md_path = manager.get_associated_markdown_path(schema_file)
        generator.generate_stub_to_file(schema, md_path, style, title)

        click.echo(f"✅ Created associated stub: {md_path}")

        if config.get('verbose'):
            content = md_path.read_text()
            click.echo(f"Generated {len(content)} characters of content", err=True)

    except Exception as e:
        click.echo(f"Error creating stub: {e}", err=True)
        sys.exit(1)


@cli.command('db-delete')
@click.option('--force', is_flag=True, help='Delete without confirmation prompt')
@click.option('--database', type=click.Path(), help='Database file path (overrides global setting)')
@pass_config
def db_delete(config, force, database):
    """
    Delete the database file.

    WARNING: This operation cannot be undone. All stored data will be lost.

    Examples:
        markitect db-delete
        markitect db-delete --force
        markitect db-delete --database /path/to/db.sqlite --force
    """
    try:
        # Use command-specific database option or fall back to global config
        if database:
            db_path = Path(database)
        else:
            db_path = Path(config.get('database_path', os.path.expanduser('~/.markitect/markitect.db')))

        if not db_path.exists():
            click.echo(f"Database file not found: {db_path}")
            return

        if not force:
            if not click.confirm(f"⚠️  Are you sure you want to delete the database at {db_path}?\nThis action cannot be undone."):
                click.echo("Operation cancelled.")
                return

        # Delete the database file
        db_path.unlink()
        click.echo(f"✅ Database deleted: {db_path}")

        if config.get('verbose'):
            click.echo("All stored data has been permanently removed.", err=True)

    except Exception as e:
        click.echo(f"Error deleting database: {e}", err=True)
        sys.exit(1)


@cli.command('db-stats')
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
@click.option('--database', type=click.Path(), help='Database file path (overrides global setting)')
@pass_config
def db_stats(config, format, database):
    """
    Show database statistics and information.

    Display database size and basic information. For detailed table analysis,
    use existing database commands after ensuring the database is accessible.

    Renamed from db-status for consistency with subsystem naming convention.

    Examples:
        markitect db-stats
        markitect db-stats --format json
        markitect db-stats --database /path/to/db.sqlite
    """
    try:
        # Use command-specific database option or fall back to global config
        if database:
            db_path = Path(database)
        else:
            db_path = Path(config.get('database_path', os.path.expanduser('~/.markitect/markitect.db')))

        if not db_path.exists():
            if format == 'json':
                click.echo('{"error": "Database not found", "path": "' + str(db_path) + '"}')
            elif format == 'yaml':
                click.echo(f'error: Database not found\npath: {db_path}')
            else:
                click.echo(f"Database file not found: {db_path}")
            return

        # Basic file information (no database connection needed)
        file_size = db_path.stat().st_size

        stats = {
            'database_path': str(db_path),
            'exists': True,
            'size_bytes': file_size,
            'size_human': format_file_size(file_size),
            'status': 'accessible' if db_path.is_file() else 'inaccessible'
        }

        # Format and display statistics
        formatted_output = format_output(stats, format)
        click.echo(formatted_output)

        if config.get('verbose'):
            click.echo(f"Database status retrieved successfully", err=True)

    except Exception as e:
        click.echo(f"Error getting database status: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command('db-data')
@click.argument('file_path', type=str)
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
@pass_config
def db_data(config, file_path, format):
    """
    Display complete file data including metadata, frontmatter, and content.

    Show comprehensive information about a specific file including its
    front matter, database metadata, and processing information.
    This is the new name for what was previously called 'metadata'.

    FILE_PATH: Name of the file to display data for

    Examples:
        markitect db-data README.md
        markitect db-data docs/guide.md --format json
        markitect db-data config.md --format yaml
    """
    try:
        if config['verbose']:
            click.echo(f"Retrieving complete data for: {file_path}", err=True)

        db_manager = config['db_manager']

        # Get file information from database
        file_info = db_manager.get_markdown_file(file_path)

        if not file_info:
            click.echo(f"File not found in database: {file_path}", err=True)
            click.echo("Use 'markitect ingest' to process the file first.", err=True)
            sys.exit(1)

        # Parse front matter for better display
        if file_info.get('front_matter'):
            try:
                if isinstance(file_info['front_matter'], str):
                    file_info['front_matter'] = eval(file_info['front_matter'])
            except (ValueError, TypeError, SyntaxError):
                if config['verbose']:
                    click.echo("Warning: Could not parse front matter", err=True)

        # Format and display complete data
        formatted_output = format_output(file_info, format)
        click.echo(formatted_output)

        if config['verbose']:
            content_length = len(file_info.get('content', ''))
            click.echo(f"Content length: {content_length} characters", err=True)

    except Exception as e:
        click.echo(f"Error retrieving file data: {e}", err=True)
        if config['verbose']:
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


def format_file_size(size_bytes):
    """Format file size in human-readable format."""
    if size_bytes < 1024:
        return f"{size_bytes} B"
    elif size_bytes < 1024 * 1024:
        return f"{size_bytes / 1024:.1f} KB"
    elif size_bytes < 1024 * 1024 * 1024:
        return f"{size_bytes / (1024 * 1024):.1f} MB"
    else:
        return f"{size_bytes / (1024 * 1024 * 1024):.1f} GB"


# Legacy Agent Management Commands
# =================================
# Comprehensive CLI interface for managing legacy interface lifecycle

@cli.group('legacy')
def legacy_management():
    """
    Manage legacy interface compatibility and lifecycle.

    Provides comprehensive tools for analyzing, managing, and cleaning up
    legacy interfaces including deprecation progression, migration assistance,
    and automated maintenance.
    """
    if not LEGACY_SYSTEM_AVAILABLE:
        click.echo("Error: Legacy management system not available", err=True)
        click.echo("Install with: pip install markitect[legacy]", err=True)
        sys.exit(1)


@legacy_management.command('status')
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default='table', help='Output format')
@click.option('--include-removed', is_flag=True, help='Include removed interfaces')
@pass_config
def legacy_status(config, format, include_removed):
    """
    Show status of all legacy interfaces.

    Displays comprehensive information about all registered legacy interfaces
    including their current status, deprecation dates, and removal schedules.

    Examples:
        markitect legacy status
        markitect legacy status --format json
        markitect legacy status --include-removed
    """
    try:
        registry = LegacyRegistry()

        # Get all legacy interfaces
        interfaces = []
        for command in registry._interfaces:
            for version, interface in registry._interfaces[command].items():
                if not include_removed and interface.status == LegacyStatus.REMOVED:
                    continue

                interfaces.append({
                    'command': interface.command,
                    'version': interface.version,
                    'status': interface.status.value,
                    'deprecated_date': interface.deprecated_date,
                    'removal_date': interface.removal_date,
                    'git_commit': interface.git_commit[:8] if interface.git_commit else 'N/A',
                    'description': interface.description or 'No description'
                })

        if format == 'json':
            click.echo(json.dumps(interfaces, indent=2))
        elif format == 'yaml':
            import yaml
            click.echo(yaml.dump(interfaces, default_flow_style=False))
        elif format == 'simple':
            for interface in interfaces:
                status_icon = {
                    'current': '✅',
                    'deprecated': '⚠️',
                    'legacy': '🔄',
                    'sunset': '🌅',
                    'removed': '❌'
                }.get(interface['status'], '❓')
                click.echo(f"{status_icon} {interface['command']} {interface['version']} ({interface['status']})")
        else:
            # Table format
            if interfaces:
                headers = ['Command', 'Version', 'Status', 'Deprecated', 'Removal', 'Commit', 'Description']
                rows = [[
                    i['command'], i['version'], i['status'],
                    i['deprecated_date'][:10] if i['deprecated_date'] else 'N/A',
                    i['removal_date'][:10] if i['removal_date'] else 'N/A',
                    i['git_commit'],
                    i['description'][:30] + '...' if len(i['description']) > 30 else i['description']
                ] for i in interfaces]
                click.echo(tabulate(rows, headers=headers, tablefmt='grid'))
            else:
                click.echo("No legacy interfaces found.")

        if config.get('verbose'):
            total = len(interfaces)
            by_status = {}
            for interface in interfaces:
                status = interface['status']
                by_status[status] = by_status.get(status, 0) + 1

            click.echo(f"\nSummary: {total} interfaces", err=True)
            for status, count in by_status.items():
                click.echo(f"  {status}: {count}", err=True)

    except Exception as e:
        click.echo(f"Error getting legacy status: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@legacy_management.command('analyze')
@click.argument('command', required=False)
@click.argument('version', required=False)
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'detailed']),
              default='detailed', help='Output format')
@pass_config
def legacy_analyze(config, command, version, format):
    """
    Analyze legacy interfaces for needed actions.

    Performs comprehensive analysis of legacy interfaces to identify
    deprecation candidates, migration opportunities, and cleanup needs.

    Examples:
        markitect legacy analyze
        markitect legacy analyze query
        markitect legacy analyze query v1.0
    """
    try:
        registry = LegacyRegistry()
        agent = LegacyAgent(registry=registry)

        if command and version:
            # Analyze specific interface
            interface = registry.get_legacy_interface(command, version)
            if not interface:
                click.echo(f"Legacy interface {command} {version} not found", err=True)
                sys.exit(1)

            analysis = {
                'command': interface.command,
                'version': interface.version,
                'current_status': interface.status.value,
                'deprecated_date': interface.deprecated_date,
                'removal_date': interface.removal_date,
                'git_commit': interface.git_commit,
                'breaking_changes': interface.breaking_changes,
                'migration_guide_available': bool(interface.migration_guide),
                'recommendations': []
            }

            # Add recommendations based on status
            if interface.status == LegacyStatus.DEPRECATED:
                analysis['recommendations'].append("Consider progressing to LEGACY status")
            elif interface.status == LegacyStatus.LEGACY:
                analysis['recommendations'].append("Monitor usage and prepare for SUNSET")
            elif interface.status == LegacyStatus.SUNSET:
                analysis['recommendations'].append("Schedule final removal")

            if not interface.migration_guide:
                analysis['recommendations'].append("Generate migration guide")

            if format == 'json':
                click.echo(json.dumps(analysis, indent=2))
            elif format == 'yaml':
                import yaml
                click.echo(yaml.dump(analysis, default_flow_style=False))
            else:
                click.echo(f"Analysis for {command} {version}")
                click.echo("=" * 40)
                click.echo(f"Status: {analysis['current_status']}")
                click.echo(f"Deprecated: {analysis['deprecated_date'] or 'N/A'}")
                click.echo(f"Removal: {analysis['removal_date'] or 'N/A'}")
                click.echo(f"Migration guide: {'Available' if analysis['migration_guide_available'] else 'Missing'}")

                if analysis['breaking_changes']:
                    click.echo(f"\nBreaking changes ({len(analysis['breaking_changes'])}):")
                    for change in analysis['breaking_changes']:
                        click.echo(f"  • {change}")

                if analysis['recommendations']:
                    click.echo(f"\nRecommendations:")
                    for rec in analysis['recommendations']:
                        click.echo(f"  • {rec}")

        else:
            # Analyze all interfaces
            candidates = registry.get_deprecation_candidates(days_ahead=30)
            usage_stats = registry.get_usage_statistics(days=30)

            analysis = {
                'total_interfaces': sum(len(versions) for versions in registry._interfaces.values()),
                'deprecation_candidates': len(candidates),
                'recent_usage': usage_stats['total_usage'],
                'cleanup_opportunities': 0,
                'migration_guides_needed': 0
            }

            # Count missing migration guides and cleanup opportunities
            for command_versions in registry._interfaces.values():
                for interface in command_versions.values():
                    if not interface.migration_guide and interface.status in [LegacyStatus.LEGACY, LegacyStatus.SUNSET]:
                        analysis['migration_guides_needed'] += 1
                    if interface.status == LegacyStatus.SUNSET:
                        analysis['cleanup_opportunities'] += 1

            if format == 'json':
                click.echo(json.dumps(analysis, indent=2))
            elif format == 'yaml':
                import yaml
                click.echo(yaml.dump(analysis, default_flow_style=False))
            else:
                click.echo("Legacy Interface Analysis")
                click.echo("=" * 30)
                click.echo(f"Total interfaces: {analysis['total_interfaces']}")
                click.echo(f"Deprecation candidates: {analysis['deprecation_candidates']}")
                click.echo(f"Recent usage events: {analysis['recent_usage']}")
                click.echo(f"Migration guides needed: {analysis['migration_guides_needed']}")
                click.echo(f"Cleanup opportunities: {analysis['cleanup_opportunities']}")

                if candidates:
                    click.echo(f"\nUpcoming removals:")
                    for candidate in candidates[:5]:  # Show first 5
                        click.echo(f"  • {candidate.command} {candidate.version} (removal: {candidate.removal_date})")

    except Exception as e:
        click.echo(f"Error analyzing legacy interfaces: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@legacy_management.command('migrate')
@click.argument('command')
@click.argument('version')
@click.option('--to-version', default='current', help='Target version for migration')
@pass_config
def legacy_migrate(config, command, version, to_version):
    """
    Get migration guidance for a legacy version.

    Provides detailed migration instructions and breaking change information
    for upgrading from a legacy interface version to current or another version.

    Examples:
        markitect legacy migrate query v1.0
        markitect legacy migrate query v1.0 --to-version v2.0
    """
    try:
        registry = LegacyRegistry()

        interface = registry.get_legacy_interface(command, version)
        if not interface:
            click.echo(f"Legacy version {command} {version} not found", err=True)
            sys.exit(1)

        migration = registry.get_migration_path(command, version, to_version)

        click.echo(f"Migration Guide: {command} {version} → {to_version}")
        click.echo("=" * 60)

        if interface.migration_guide:
            click.echo(interface.migration_guide)
        else:
            click.echo("No specific migration guide available.")
            click.echo("Consider generating one with: markitect legacy generate-guide")

        if migration['breaking_changes']:
            click.echo("\nBreaking Changes:")
            for i, change in enumerate(migration['breaking_changes'], 1):
                click.echo(f"{i}. {change}")

        if migration['steps']:
            click.echo("\nMigration Steps:")
            for i, step in enumerate(migration['steps'], 1):
                click.echo(f"{i}. {step}")

        # Show additional context
        click.echo(f"\nInterface Details:")
        click.echo(f"  Current status: {interface.status.value}")
        if interface.deprecated_date:
            click.echo(f"  Deprecated: {interface.deprecated_date}")
        if interface.removal_date:
            click.echo(f"  Removal scheduled: {interface.removal_date}")

    except Exception as e:
        click.echo(f"Error getting migration guide: {e}", err=True)
        sys.exit(1)


@legacy_management.command('cleanup')
@click.argument('command')
@click.argument('version')
@click.option('--force', is_flag=True, help='Force cleanup without confirmation')
@click.option('--backup', is_flag=True, default=True, help='Create backup before cleanup')
@pass_config
def legacy_cleanup(config, command, version, force, backup):
    """
    Clean up a specific legacy version.

    Permanently removes a legacy interface from the registry and optionally
    creates a backup for restoration if needed.

    Examples:
        markitect legacy cleanup query v1.0
        markitect legacy cleanup query v1.0 --force
        markitect legacy cleanup query v1.0 --no-backup
    """
    try:
        agent = LegacyAgent()

        if not force:
            interface = agent.registry.get_legacy_interface(command, version)
            if interface:
                click.echo(f"About to clean up {command} {version}")
                click.echo(f"Status: {interface.status.value}")
                if interface.removal_date:
                    click.echo(f"Scheduled removal: {interface.removal_date}")

                if interface.status not in [LegacyStatus.SUNSET, LegacyStatus.REMOVED]:
                    click.echo("Warning: Interface is not in SUNSET status")

                if not click.confirm("Are you sure you want to proceed?"):
                    click.echo("Cleanup cancelled.")
                    return

        # Configure backup behavior
        original_backup_config = agent.config.backup_before_cleanup
        agent.config.backup_before_cleanup = backup

        success = agent.force_cleanup(command, version)

        # Restore original config
        agent.config.backup_before_cleanup = original_backup_config

        if success:
            click.echo(f"✅ Successfully cleaned up {command} {version}")
            if backup:
                click.echo("📦 Backup created in agent data directory")
        else:
            click.echo(f"❌ Failed to clean up {command} {version}", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"Error during cleanup: {e}", err=True)
        sys.exit(1)


@legacy_management.command('agent-run')
@click.option('--dry-run', is_flag=True, help='Show what would be done without executing')
@pass_config
def legacy_agent_run(config, dry_run):
    """
    Run legacy agent maintenance cycle.

    Executes automated maintenance including deprecation progression,
    cleanup scheduling, migration guide generation, and user notifications.

    Examples:
        markitect legacy agent-run
        markitect legacy agent-run --dry-run
    """
    try:
        agent = LegacyAgent()

        if dry_run:
            click.echo("DRY RUN: Legacy agent maintenance preview")
            click.echo("=" * 50)

            # Show what would be done
            agent_config = AgentConfig(
                auto_progression=False,  # Disable actual changes
                cleanup_unused_days=agent.config.cleanup_unused_days,
                migration_guide_auto_generation=False,
                notification_threshold_days=agent.config.notification_threshold_days,
                max_concurrent_migrations=agent.config.max_concurrent_migrations,
                backup_before_cleanup=agent.config.backup_before_cleanup
            )

            # Create a preview agent
            preview_agent = LegacyAgent(config=agent_config)

            # Analyze what would be done
            preview_agent._analyze_legacy_interfaces()
            pending_tasks = [task for task in preview_agent._tasks if not task.completed]

            if pending_tasks:
                click.echo(f"Would schedule {len(pending_tasks)} tasks:")
                for task in pending_tasks:
                    click.echo(f"  • {task.action.value}: {task.command}:{task.version}")
            else:
                click.echo("No maintenance tasks needed")

        else:
            click.echo("Running legacy agent maintenance...")

            summary = agent.run_maintenance()

            click.echo("Maintenance Summary")
            click.echo("=" * 20)
            click.echo(f"Tasks executed: {summary['tasks_executed']}")
            click.echo(f"Progressions: {summary['progressions']}")
            click.echo(f"Cleanups: {summary['cleanups']}")
            click.echo(f"Notifications: {summary['notifications']}")

            if summary['errors']:
                click.echo(f"\nErrors ({len(summary['errors'])}):")
                for error in summary['errors']:
                    click.echo(f"  • {error}")

            click.echo(f"\nStarted: {summary['started_at']}")
            click.echo(f"Completed: {summary['completed_at']}")

    except Exception as e:
        click.echo(f"Error running agent maintenance: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@legacy_management.command('agent-status')
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml']),
              default='table', help='Output format')
@pass_config
def legacy_agent_status(config, format):
    """
    Show legacy agent status and statistics.

    Displays comprehensive information about the legacy agent including
    task queue status, configuration, and registry statistics.

    Examples:
        markitect legacy agent-status
        markitect legacy agent-status --format json
    """
    try:
        agent = LegacyAgent()
        status = agent.get_agent_status()

        if format == 'json':
            click.echo(json.dumps(status, indent=2))
        elif format == 'yaml':
            import yaml
            click.echo(yaml.dump(status, default_flow_style=False))
        else:
            click.echo("Legacy Agent Status")
            click.echo("=" * 30)
            click.echo(f"Data Directory: {status['data_directory']}")
            click.echo(f"Auto Progression: {'Enabled' if status['config']['auto_progression'] else 'Disabled'}")
            click.echo(f"Cleanup After: {status['config']['cleanup_unused_days']} days")

            click.echo(f"\nTask Queue:")
            click.echo(f"  Total: {status['tasks']['total']}")
            click.echo(f"  Pending: {status['tasks']['pending']}")
            click.echo(f"  Completed: {status['tasks']['completed']}")

            if status['next_maintenance']:
                click.echo(f"\nNext Maintenance: {status['next_maintenance']}")

            click.echo(f"\nRegistry Statistics:")
            for stat_name, stat_value in status['registry_stats'].items():
                if stat_name == 'commands':
                    click.echo(f"  Commands: {', '.join(stat_value) if stat_value else 'none'}")
                else:
                    click.echo(f"  {stat_name}: {stat_value}")

    except Exception as e:
        click.echo(f"Error getting agent status: {e}", err=True)
        sys.exit(1)


@legacy_management.command('usage-stats')
@click.option('--command', help='Filter by specific command')
@click.option('--days', type=int, default=30, help='Number of days to analyze')
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml']),
              default='table', help='Output format')
@pass_config
def legacy_usage_stats(config, command, days, format):
    """
    Show usage statistics for legacy interfaces.

    Displays usage patterns to help make informed decisions about
    deprecation timelines and cleanup priorities.

    Examples:
        markitect legacy usage-stats
        markitect legacy usage-stats --command query
        markitect legacy usage-stats --days 90 --format json
    """
    try:
        registry = LegacyRegistry()
        stats = registry.get_usage_statistics(command=command, days=days)

        if format == 'json':
            click.echo(json.dumps(stats, indent=2))
        elif format == 'yaml':
            import yaml
            click.echo(yaml.dump(stats, default_flow_style=False))
        else:
            click.echo(f"Legacy Interface Usage ({days} days)")
            click.echo("=" * 40)
            click.echo(f"Total usage events: {stats['total_usage']}")

            if stats['by_command']:
                click.echo(f"\nBy Command:")
                for cmd, versions in stats['by_command'].items():
                    total_cmd_usage = sum(v['usage_count'] for v in versions.values())
                    click.echo(f"  {cmd}: {total_cmd_usage} uses")
                    for version, data in versions.items():
                        click.echo(f"    {version}: {data['usage_count']} (last: {data['last_used'][:10]})")

            if stats['by_version']:
                click.echo(f"\nMost Used Versions:")
                sorted_versions = sorted(stats['by_version'].items(),
                                       key=lambda x: x[1], reverse=True)
                for version_key, count in sorted_versions[:10]:
                    click.echo(f"  {version_key}: {count} uses")

        if config.get('verbose'):
            click.echo(f"\nAnalysis period: {days} days", err=True)
            if command:
                click.echo(f"Filtered to command: {command}", err=True)

    except Exception as e:
        click.echo(f"Error getting usage statistics: {e}", err=True)
        sys.exit(1)


@legacy_management.command('generate-guide')
@click.argument('command')
@click.argument('version')
@click.option('--output', '-o', type=click.Path(), help='Output file (default: stdout)')
@pass_config
def legacy_generate_guide(config, command, version, output):
    """
    Generate migration guide for a legacy interface.

    Creates detailed migration documentation for upgrading from
    a legacy interface version to the current implementation.

    Examples:
        markitect legacy generate-guide query v1.0
        markitect legacy generate-guide query v1.0 --output migration_guide.md
    """
    try:
        registry = LegacyRegistry()
        interface = registry.get_legacy_interface(command, version)

        if not interface:
            click.echo(f"Legacy interface {command} {version} not found", err=True)
            sys.exit(1)

        # Generate guide content
        guide_content = f"""# Migration Guide: {command} {version} → Current

## Overview
This guide helps you migrate from the legacy `{command}` {version} interface to the current implementation.

**Status**: {interface.status.value}
**Deprecated**: {interface.deprecated_date or 'Not specified'}
**Removal Date**: {interface.removal_date or 'Not scheduled'}

## Breaking Changes
"""

        if interface.breaking_changes:
            for i, change in enumerate(interface.breaking_changes, 1):
                guide_content += f"{i}. {change}\n"
        else:
            guide_content += "No specific breaking changes documented.\n"

        guide_content += f"""
## Migration Steps

1. **Remove the legacy flag**: Stop using `--legacy-{version.replace('.', '-')}`
2. **Update command syntax**: Review the current command documentation
3. **Test thoroughly**: Verify that your use cases work with the new interface
4. **Update automation**: Modify any scripts or tools that use the legacy interface

## Getting Help

- Run: `markitect help {command}`
- Check the documentation for current syntax
- Review the changelog for detailed changes

## Example Migration

```bash
# Old (legacy {version})
markitect {command} --legacy-{version.replace('.', '-')} [arguments]

# New (current)
markitect {command} [arguments]
```

For specific parameter changes, refer to the breaking changes section above.
"""

        if interface.migration_guide:
            guide_content += f"\n## Additional Notes\n\n{interface.migration_guide}\n"

        # Output
        if output:
            with open(output, 'w', encoding='utf-8') as f:
                f.write(guide_content)
            click.echo(f"✅ Migration guide written to: {output}")
        else:
            click.echo(guide_content)

        # Update interface with generated guide if it didn't have one
        if not interface.migration_guide:
            interface.migration_guide = guide_content
            # Note: In a full implementation, this would save back to registry

    except Exception as e:
        click.echo(f"Error generating migration guide: {e}", err=True)
        sys.exit(1)


def main():
    """
    Main entry point for the CLI.

    This function is referenced in pyproject.toml console_scripts.
    """
    try:
        cli(standalone_mode=False)
    except KeyboardInterrupt:
        click.echo("\nOperation interrupted by user.", err=True)
        sys.exit(130)  # Standard exit code for SIGINT
    except Exception as e:
        click.echo(f"Unexpected error: {e}", err=True)
        sys.exit(1)


@cli.command('config-stats')
@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']),
              default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
@pass_config
def config_stats(config, format):
    """
    Display configuration statistics and status information.

    Shows comprehensive configuration information including current settings,
    file sources, validation status, and workspace information. Part of the
    config subsystem following the *-stats command convention.

    Examples:
        markitect config-stats
        markitect config-stats --format json
        markitect config-stats --format yaml
    """
    try:
        # Try to import the config system
        try:
            import sys
            from pathlib import Path

            # Add the CLI commands directory to path
            cli_path = Path(__file__).parent.parent / "cli" / "commands"
            if cli_path.exists():
                sys.path.insert(0, str(cli_path.parent))
                from commands.config import ConfigCommands

                # Use the existing config commands system
                config_commands = ConfigCommands()
                config_commands.show_config(show_sensitive=False)
                return

        except ImportError:
            pass

        # Fallback: Simple config stats if full system isn't available
        config_info = {
            'config_file': config.get('config_file', 'None specified'),
            'database_path': config.get('database_path', 'Default location'),
            'verbose_mode': config.get('verbose', False),
            'working_directory': os.getcwd()
        }

        # Add environment variables relevant to config
        env_vars = {}
        config_env_vars = ['MARKITECT_CONFIG', 'MARKITECT_DATABASE', 'MARKITECT_MODE']
        for var in config_env_vars:
            value = os.getenv(var)
            env_vars[var] = value if value else 'Not set'

        config_info['environment_variables'] = env_vars

        # Format output according to requested format
        if format == 'json':
            click.echo(json.dumps(config_info, indent=2))
        elif format == 'yaml':
            click.echo(yaml.dump(config_info, default_flow_style=False))
        elif format == 'simple':
            for key, value in config_info.items():
                if key == 'environment_variables':
                    click.echo(f"{key}:")
                    for env_key, env_value in value.items():
                        click.echo(f"  {env_key}: {env_value}")
                else:
                    click.echo(f"{key}: {value}")
        else:  # table format
            click.echo("📊 Configuration Statistics")
            click.echo("=" * 50)

            # Basic config
            click.echo("\n🔧 Basic Configuration:")
            for key, value in config_info.items():
                if key != 'environment_variables':
                    click.echo(f"  {key.replace('_', ' ').title()}: {value}")

            # Environment variables
            click.echo("\n🌍 Environment Variables:")
            for env_key, env_value in config_info['environment_variables'].items():
                status_icon = "✅" if env_value != 'Not set' else "❌"
                click.echo(f"  {status_icon} {env_key}: {env_value}")

            # Basic validation
            click.echo("\n✅ Basic Validation:")
            if config.get('database_path'):
                db_path = Path(config['database_path'])
                db_exists = db_path.exists() if db_path.is_absolute() else False
                status = "✅" if db_exists else "⚠️"
                click.echo(f"  {status} Database accessible: {db_exists}")

            click.echo(f"  ✅ Working directory accessible: {os.access(os.getcwd(), os.R_OK)}")

    except Exception as e:
        click.echo(f"Error getting configuration statistics: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# Content Commands (Issue #38)
from markitect_content.commands import content_get, content_stats

# Register content commands
cli.add_command(content_get)
cli.add_command(content_stats)

# Frontmatter Commands (Issue #38 - Cycle 2)
from .matter_frontmatter.commands import frontmatter_get, frontmatter_set, frontmatter_keys, frontmatter_stats

# Register frontmatter commands
cli.add_command(frontmatter_get)
cli.add_command(frontmatter_set)
cli.add_command(frontmatter_keys)
cli.add_command(frontmatter_stats)

# Contentmatter Commands (Issue #38 - Cycle 3)
from .matter_contentmatter.commands import contentmatter_get, contentmatter_set, contentmatter_keys, contentmatter_stats

# Register contentmatter commands
cli.add_command(contentmatter_get)
cli.add_command(contentmatter_set)
cli.add_command(contentmatter_keys)
cli.add_command(contentmatter_stats)

# Tailmatter Commands (Issue #38 - Cycles 4-5)
from .matter_tailmatter.commands import tailmatter_get, tailmatter_set, tailmatter_keys, tailmatter_stats, tailmatter_check

# Register tailmatter commands
cli.add_command(tailmatter_get)
cli.add_command(tailmatter_set)
cli.add_command(tailmatter_keys)
cli.add_command(tailmatter_stats)
cli.add_command(tailmatter_check)


# Template Rendering Command (Issue #65)
@cli.command(name='template-render')
@click.argument('template_file', type=click.Path(exists=True))
@click.argument('data_file', type=click.Path(exists=True))
@click.option('--output', '-o', type=click.Path(), help='Output file path (default: stdout)')
@click.option('--strict', is_flag=True, default=True, help='Strict mode: fail on missing variables (default: True)')
@click.option('--lenient', is_flag=True, help='Lenient mode: preserve placeholders for missing variables')
@click.option('--validate', is_flag=True, help='Validate template syntax before rendering')
@click.option('--check-data', is_flag=True, help='Check data completeness before rendering')
@click.option('--format', 'data_format', type=click.Choice(['json', 'yaml', 'auto']), default='auto', help='Data file format')
@pass_config
def template_render(config, template_file, data_file, output, strict, lenient, validate, check_data, data_format):
    """
    Render a template with data to generate documents.

    This command takes a template file containing variables in {{variable}} format
    and a data file (JSON or YAML) containing the values to substitute.

    Examples:
        markitect template-render invoice.md data.json
        markitect template-render report.md data.yaml --output report.pdf
        markitect template-render template.md data.json --lenient --validate
    """
    try:
        from .template.engine import TemplateEngine

        # Initialize template engine
        engine = TemplateEngine()

        # Read template file
        with open(template_file, 'r', encoding='utf-8') as f:
            template_content = f.read()

        # Determine data format
        if data_format == 'auto':
            if data_file.endswith('.json'):
                data_format = 'json'
            elif data_file.endswith('.yaml') or data_file.endswith('.yml'):
                data_format = 'yaml'
            else:
                data_format = 'json'  # Default to JSON

        # Read data file
        with open(data_file, 'r', encoding='utf-8') as f:
            if data_format == 'json':
                data = json.load(f)
            else:  # yaml
                data = yaml.safe_load(f)

        # Validate template if requested
        if validate:
            errors = engine.validate_template(template_content)
            if errors:
                click.echo("Template validation errors:", err=True)
                for error in errors:
                    click.echo(f"  - {error}", err=True)
                sys.exit(1)

        # Check data completeness if requested
        if check_data:
            completeness = engine.check_data_completeness(template_content, data)
            if completeness['missing']:
                click.echo("Missing variables in data:", err=True)
                for var in completeness['missing']:
                    click.echo(f"  - {var}", err=True)
                click.echo(f"Data completeness: {completeness['completeness']:.1%}", err=True)
                if strict:
                    sys.exit(1)

        # Determine render mode
        render_strict = strict and not lenient

        # Render template
        try:
            result = engine.render(template_content, data, strict=render_strict)

            # Output result
            if output:
                with open(output, 'w', encoding='utf-8') as f:
                    f.write(result)
                click.echo(f"Template rendered successfully to {output}")
            else:
                click.echo(result)

        except Exception as e:
            click.echo(f"Rendering failed: {e}", err=True)
            sys.exit(1)

    except ImportError:
        click.echo("Template engine not available. Make sure it's properly installed.", err=True)
        sys.exit(1)
    except FileNotFoundError as e:
        click.echo(f"File not found: {e}", err=True)
        sys.exit(1)
    except json.JSONDecodeError as e:
        click.echo(f"JSON parsing error: {e}", err=True)
        sys.exit(1)
    except yaml.YAMLError as e:
        click.echo(f"YAML parsing error: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"Unexpected error: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# Performance Validation Commands (Issue #16)
@cli.command(name='perf-benchmark')
@click.option('--operations', '-n', type=int, default=1000, help='Number of operations to benchmark')
@click.option('--test-type', type=click.Choice(['ingest', 'query', 'template', 'all']), default='all', help='Type of performance test')
@click.option('--format', 'output_format', type=click.Choice(['table', 'json', 'simple']), default='table', help='Output format')
@click.option('--output', '-o', type=click.Path(), help='Output file for results')
@pass_config
def perf_benchmark(config, operations, test_type, output_format, output):
    """Run performance benchmarks and measure system performance.

    Execute performance benchmarks to measure MarkiTect's performance across
    different operations including document ingestion, querying, and template rendering.

    Examples:
        markitect perf-benchmark --operations 500 --test-type ingest
        markitect perf-benchmark --test-type template --format json -o results.json
        markitect perf-benchmark --operations 2000 --test-type all
    """
    try:
        import time
        import tempfile
        import json as json_lib
        from pathlib import Path

        results = {}
        start_total = time.time()

        if test_type in ['ingest', 'all']:
            # Benchmark document ingestion
            click.echo("🚀 Running ingestion benchmark...")

            with tempfile.TemporaryDirectory() as temp_dir:
                temp_path = Path(temp_dir)

                # Create test documents
                test_docs = []
                for i in range(min(operations, 100)):  # Limit to 100 docs for ingestion
                    doc_path = temp_path / f"bench_doc_{i}.md"
                    content = f"# Benchmark Document {i}\n\nThis is test content for performance measurement.\n\n## Details\n\nDocument number: {i}\nContent: {'Lorem ipsum ' * 20}"
                    doc_path.write_text(content)
                    test_docs.append(str(doc_path))

                # Benchmark ingestion
                start_time = time.time()
                for doc_path in test_docs:
                    from .database import DatabaseManager
                    db = DatabaseManager(config['database_path'])
                    try:
                        # Use internal methods to avoid CLI overhead
                        db.process_file(doc_path)
                    except Exception:
                        pass  # Continue benchmarking even if some fail

                ingest_time = time.time() - start_time
                ingest_rate = len(test_docs) / ingest_time if ingest_time > 0 else 0

                results['ingestion'] = {
                    'operations': len(test_docs),
                    'time_seconds': round(ingest_time, 3),
                    'operations_per_second': round(ingest_rate, 1),
                    'status': 'completed'
                }

        if test_type in ['query', 'all']:
            # Benchmark database queries
            click.echo("🔍 Running query benchmark...")

            start_time = time.time()
            query_count = 0

            try:
                from .database import DatabaseManager
                db = DatabaseManager(config['database_path'])

                # Run various queries
                for i in range(min(operations, 500)):  # Limit query operations
                    try:
                        # Test different query types
                        if i % 3 == 0:
                            db.list_markdown_files()
                        elif i % 3 == 1:
                            db.list_schema_files()
                        else:
                            db.execute_query("SELECT COUNT(*) FROM markdown_files")
                        query_count += 1
                    except Exception:
                        pass  # Continue benchmarking

                query_time = time.time() - start_time
                query_rate = query_count / query_time if query_time > 0 else 0

                results['querying'] = {
                    'operations': query_count,
                    'time_seconds': round(query_time, 3),
                    'operations_per_second': round(query_rate, 1),
                    'status': 'completed'
                }
            except Exception as e:
                results['querying'] = {
                    'status': 'failed',
                    'error': str(e)
                }

        if test_type in ['template', 'all']:
            # Benchmark template rendering
            click.echo("📄 Running template rendering benchmark...")

            template_content = "# {{title}}\n\nHello {{user.name}}, welcome to {{company}}!\n\n## Stats\n- Count: {{count}}\n- Value: {{data.value}}"
            template_data = {
                "title": "Benchmark Template",
                "user": {"name": "Test User"},
                "company": "MarkiTect",
                "count": 42,
                "data": {"value": 3.14159}
            }

            start_time = time.time()
            template_count = 0

            try:
                from .template.engine import TemplateEngine
                engine = TemplateEngine()

                for i in range(min(operations, 1000)):  # Template operations
                    try:
                        result = engine.render(template_content, template_data)
                        template_count += 1
                    except Exception:
                        pass  # Continue benchmarking

                template_time = time.time() - start_time
                template_rate = template_count / template_time if template_time > 0 else 0

                results['template_rendering'] = {
                    'operations': template_count,
                    'time_seconds': round(template_time, 3),
                    'operations_per_second': round(template_rate, 1),
                    'status': 'completed'
                }
            except Exception as e:
                results['template_rendering'] = {
                    'status': 'failed',
                    'error': str(e)
                }

        total_time = time.time() - start_total
        results['summary'] = {
            'total_time_seconds': round(total_time, 3),
            'test_type': test_type,
            'requested_operations': operations,
            'timestamp': time.strftime('%Y-%m-%d %H:%M:%S')
        }

        # Format and output results
        if output_format == 'json':
            output_text = json_lib.dumps(results, indent=2)
        elif output_format == 'simple':
            output_lines = [f"Performance Benchmark Results - {test_type}"]
            for category, data in results.items():
                if category != 'summary':
                    if data.get('status') == 'completed':
                        output_lines.append(f"{category}: {data['operations']} ops in {data['time_seconds']}s ({data['operations_per_second']} ops/sec)")
                    else:
                        output_lines.append(f"{category}: {data.get('status', 'unknown')}")
            output_lines.append(f"Total time: {results['summary']['total_time_seconds']}s")
            output_text = '\n'.join(output_lines)
        else:  # table format
            from tabulate import tabulate
            table_data = []
            for category, data in results.items():
                if category != 'summary':
                    if data.get('status') == 'completed':
                        table_data.append([
                            category.replace('_', ' ').title(),
                            data['operations'],
                            f"{data['time_seconds']}s",
                            f"{data['operations_per_second']:.1f}",
                            data['status']
                        ])
                    else:
                        table_data.append([
                            category.replace('_', ' ').title(),
                            '-',
                            '-',
                            '-',
                            data.get('status', 'unknown')
                        ])

            output_text = tabulate(
                table_data,
                headers=['Operation', 'Count', 'Time', 'Ops/Sec', 'Status'],
                tablefmt='grid'
            )
            output_text += f"\n\nTotal benchmark time: {results['summary']['total_time_seconds']}s"

        if output:
            with open(output, 'w') as f:
                f.write(output_text)
            click.echo(f"✅ Benchmark results saved to {output}")
        else:
            click.echo(output_text)

    except ImportError as e:
        click.echo(f"Missing dependency for benchmarking: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"Benchmark failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='perf-validate')
@click.option('--threshold-ops', type=int, default=100, help='Minimum operations per second threshold')
@click.option('--threshold-memory', type=int, default=100, help='Maximum memory usage in MB')
@click.option('--test-duration', type=int, default=10, help='Test duration in seconds')
@click.option('--format', 'output_format', type=click.Choice(['table', 'json', 'simple']), default='table', help='Output format')
@pass_config
def perf_validate(config, threshold_ops, threshold_memory, test_duration, output_format):
    """Validate system performance against defined thresholds.

    Run performance validation tests to ensure MarkiTect meets performance
    requirements for production use.

    Examples:
        markitect perf-validate --threshold-ops 200 --threshold-memory 50
        markitect perf-validate --test-duration 30 --format json
    """
    try:
        import time
        import tempfile
        import json as json_lib
        from pathlib import Path

        validation_results = {}
        start_time = time.time()

        # Memory monitoring setup
        try:
            import psutil
            import os
            process = psutil.Process(os.getpid())
            initial_memory_mb = process.memory_info().rss / (1024 * 1024)
            memory_available = True
        except ImportError:
            memory_available = False
            initial_memory_mb = 0

        click.echo(f"🔍 Starting performance validation (duration: {test_duration}s)...")

        # Test 1: Template rendering performance
        click.echo("📄 Testing template rendering performance...")
        template_content = "# {{title}}\n\nProcessing {{item.name}} - {{item.value}}"
        operations_completed = 0

        try:
            from .template.engine import TemplateEngine
            engine = TemplateEngine()

            test_start = time.time()
            while (time.time() - test_start) < (test_duration / 3):  # Use 1/3 of time for templates
                template_data = {
                    "title": f"Test Document {operations_completed}",
                    "item": {"name": f"Item {operations_completed}", "value": operations_completed * 1.5}
                }
                result = engine.render(template_content, template_data)
                operations_completed += 1

            template_duration = time.time() - test_start
            template_rate = operations_completed / template_duration if template_duration > 0 else 0

            validation_results['template_rendering'] = {
                'operations_completed': operations_completed,
                'duration_seconds': round(template_duration, 3),
                'operations_per_second': round(template_rate, 1),
                'threshold_met': template_rate >= threshold_ops,
                'threshold_value': threshold_ops
            }
        except Exception as e:
            validation_results['template_rendering'] = {
                'status': 'failed',
                'error': str(e),
                'threshold_met': False
            }

        # Test 2: Database operations performance
        click.echo("🗄️  Testing database operations performance...")
        db_operations = 0

        try:
            from .database import DatabaseManager
            db = DatabaseManager(config['database_path'])

            test_start = time.time()
            while (time.time() - test_start) < (test_duration / 3):  # Use 1/3 of time for DB
                try:
                    # Rotate through different query types
                    if db_operations % 3 == 0:
                        db.list_markdown_files()
                    elif db_operations % 3 == 1:
                        db.list_schema_files()
                    else:
                        db.execute_query("SELECT COUNT(*) FROM markdown_files")
                    db_operations += 1
                except Exception:
                    pass  # Continue testing

            db_duration = time.time() - test_start
            db_rate = db_operations / db_duration if db_duration > 0 else 0

            validation_results['database_operations'] = {
                'operations_completed': db_operations,
                'duration_seconds': round(db_duration, 3),
                'operations_per_second': round(db_rate, 1),
                'threshold_met': db_rate >= threshold_ops,
                'threshold_value': threshold_ops
            }
        except Exception as e:
            validation_results['database_operations'] = {
                'status': 'failed',
                'error': str(e),
                'threshold_met': False
            }

        # Test 3: Memory usage validation
        if memory_available:
            click.echo("🧠 Testing memory usage...")
            current_memory_mb = process.memory_info().rss / (1024 * 1024)
            memory_increase_mb = current_memory_mb - initial_memory_mb

            validation_results['memory_usage'] = {
                'initial_memory_mb': round(initial_memory_mb, 2),
                'current_memory_mb': round(current_memory_mb, 2),
                'memory_increase_mb': round(memory_increase_mb, 2),
                'threshold_met': memory_increase_mb <= threshold_memory,
                'threshold_value': threshold_memory
            }
        else:
            validation_results['memory_usage'] = {
                'status': 'skipped',
                'reason': 'psutil not available',
                'threshold_met': True  # Assume pass if we can't measure
            }

        # Overall validation summary
        total_duration = time.time() - start_time
        all_tests_passed = all(
            result.get('threshold_met', False)
            for result in validation_results.values()
            if 'threshold_met' in result
        )

        validation_results['summary'] = {
            'total_duration_seconds': round(total_duration, 3),
            'validation_passed': all_tests_passed,
            'timestamp': time.strftime('%Y-%m-%d %H:%M:%S'),
            'thresholds': {
                'operations_per_second': threshold_ops,
                'memory_mb': threshold_memory,
                'test_duration': test_duration
            }
        }

        # Format output
        if output_format == 'json':
            output_text = json_lib.dumps(validation_results, indent=2)
        elif output_format == 'simple':
            output_lines = ["Performance Validation Results"]
            for test_name, data in validation_results.items():
                if test_name != 'summary':
                    if 'threshold_met' in data:
                        status = "✅ PASS" if data['threshold_met'] else "❌ FAIL"
                        if 'operations_per_second' in data:
                            output_lines.append(f"{test_name}: {data['operations_per_second']:.1f} ops/sec {status}")
                        elif 'memory_increase_mb' in data:
                            output_lines.append(f"{test_name}: {data['memory_increase_mb']:.2f} MB increase {status}")
                    else:
                        output_lines.append(f"{test_name}: {data.get('status', 'unknown')}")

            overall_status = "✅ VALIDATION PASSED" if all_tests_passed else "❌ VALIDATION FAILED"
            output_lines.append(f"\nOverall: {overall_status}")
            output_text = '\n'.join(output_lines)
        else:  # table format
            from tabulate import tabulate
            table_data = []
            for test_name, data in validation_results.items():
                if test_name != 'summary':
                    if 'threshold_met' in data:
                        status = "✅ PASS" if data['threshold_met'] else "❌ FAIL"
                        if 'operations_per_second' in data:
                            value = f"{data['operations_per_second']:.1f} ops/sec"
                            threshold = f">= {data['threshold_value']} ops/sec"
                        elif 'memory_increase_mb' in data:
                            value = f"{data['memory_increase_mb']:.2f} MB"
                            threshold = f"<= {data['threshold_value']} MB"
                        else:
                            value = "N/A"
                            threshold = "N/A"

                        table_data.append([
                            test_name.replace('_', ' ').title(),
                            value,
                            threshold,
                            status
                        ])
                    else:
                        table_data.append([
                            test_name.replace('_', ' ').title(),
                            data.get('status', 'unknown'),
                            '-',
                            '⚠️  SKIP'
                        ])

            output_text = tabulate(
                table_data,
                headers=['Test', 'Result', 'Threshold', 'Status'],
                tablefmt='grid'
            )

            overall_status = "✅ VALIDATION PASSED" if all_tests_passed else "❌ VALIDATION FAILED"
            output_text += f"\n\nOverall Result: {overall_status}"
            output_text += f"\nTotal validation time: {validation_results['summary']['total_duration_seconds']}s"

        click.echo(output_text)

        # Exit with appropriate code
        if not all_tests_passed:
            sys.exit(1)

    except Exception as e:
        click.echo(f"Performance validation failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='perf-monitor')
@click.option('--duration', type=int, default=60, help='Monitoring duration in seconds')
@click.option('--interval', type=int, default=5, help='Monitoring interval in seconds')
@click.option('--output', '-o', type=click.Path(), help='Output file for monitoring data')
@click.option('--format', 'output_format', type=click.Choice(['json', 'csv', 'simple']), default='simple', help='Output format')
@pass_config
def perf_monitor(config, duration, interval, output, output_format):
    """Monitor system performance over time.

    Continuously monitor MarkiTect performance metrics including memory usage,
    cache effectiveness, and database performance.

    Examples:
        markitect perf-monitor --duration 300 --interval 10
        markitect perf-monitor --duration 60 --format json -o monitoring.json
    """
    try:
        import time
        import json as json_lib

        # Memory monitoring setup
        try:
            import psutil
            import os
            process = psutil.Process(os.getpid())
            memory_available = True
        except ImportError:
            memory_available = False

        click.echo(f"📊 Starting performance monitoring (duration: {duration}s, interval: {interval}s)...")

        monitoring_data = []
        start_time = time.time()

        try:
            while (time.time() - start_time) < duration:
                measurement_time = time.time()
                data_point = {
                    'timestamp': time.strftime('%Y-%m-%d %H:%M:%S'),
                    'elapsed_seconds': round(measurement_time - start_time, 1)
                }

                # Memory metrics
                if memory_available:
                    memory_info = process.memory_info()
                    data_point.update({
                        'memory_rss_mb': round(memory_info.rss / (1024 * 1024), 2),
                        'memory_vms_mb': round(memory_info.vms / (1024 * 1024), 2)
                    })

                # System metrics
                try:
                    from .database import DatabaseManager
                    db = DatabaseManager(config['database_path'])
                    stats = db.get_statistics()
                    data_point.update({
                        'database_files': stats.get('file_count', 0),
                        'database_size_kb': stats.get('db_size_bytes', 0) / 1024
                    })
                except Exception:
                    data_point.update({
                        'database_files': 'error',
                        'database_size_kb': 'error'
                    })

                # Cache metrics
                try:
                    # Get cache info (simplified)
                    cache_dir = Path('.ast_cache')
                    if cache_dir.exists():
                        cache_files = len(list(cache_dir.glob('*')))
                        cache_size = sum(f.stat().st_size for f in cache_dir.glob('*') if f.is_file())
                        data_point.update({
                            'cache_files': cache_files,
                            'cache_size_kb': round(cache_size / 1024, 2)
                        })
                    else:
                        data_point.update({
                            'cache_files': 0,
                            'cache_size_kb': 0
                        })
                except Exception:
                    data_point.update({
                        'cache_files': 'error',
                        'cache_size_kb': 'error'
                    })

                monitoring_data.append(data_point)

                # Display current status
                if memory_available:
                    click.echo(f"⏱️  {data_point['elapsed_seconds']:>6.1f}s | "
                             f"Memory: {data_point['memory_rss_mb']:>6.1f}MB | "
                             f"DB Files: {data_point['database_files']:>4} | "
                             f"Cache: {data_point['cache_files']:>3} files")
                else:
                    click.echo(f"⏱️  {data_point['elapsed_seconds']:>6.1f}s | "
                             f"DB Files: {data_point['database_files']:>4} | "
                             f"Cache: {data_point['cache_files']:>3} files")

                # Wait for next interval
                time.sleep(interval)

        except KeyboardInterrupt:
            click.echo("\n⏹️  Monitoring stopped by user")

        # Format output
        total_duration = time.time() - start_time

        if output_format == 'json':
            output_data = {
                'monitoring_session': {
                    'start_time': time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(start_time)),
                    'duration_seconds': round(total_duration, 1),
                    'interval_seconds': interval,
                    'data_points': len(monitoring_data)
                },
                'measurements': monitoring_data
            }
            output_text = json_lib.dumps(output_data, indent=2)
        elif output_format == 'csv':
            if monitoring_data:
                headers = list(monitoring_data[0].keys())
                lines = [','.join(headers)]
                for data_point in monitoring_data:
                    values = [str(data_point.get(header, '')) for header in headers]
                    lines.append(','.join(values))
                output_text = '\n'.join(lines)
            else:
                output_text = "No monitoring data collected"
        else:  # simple format
            output_lines = [
                f"Performance Monitoring Summary",
                f"Duration: {total_duration:.1f}s",
                f"Data points: {len(monitoring_data)}",
                f"Interval: {interval}s"
            ]

            if monitoring_data and memory_available:
                memory_values = [d['memory_rss_mb'] for d in monitoring_data if isinstance(d.get('memory_rss_mb'), (int, float))]
                if memory_values:
                    output_lines.extend([
                        f"Memory usage: {min(memory_values):.1f}MB - {max(memory_values):.1f}MB",
                        f"Average memory: {sum(memory_values)/len(memory_values):.1f}MB"
                    ])

            output_text = '\n'.join(output_lines)

        if output:
            with open(output, 'w') as f:
                f.write(output_text)
            click.echo(f"📁 Monitoring data saved to {output}")
        else:
            click.echo("\n" + output_text)

    except Exception as e:
        click.echo(f"Performance monitoring failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='perf-track')
@click.option('--notes', '-n', type=str, default="", help='Optional notes for this performance snapshot')
@click.option('--output', '-o', type=click.Path(), help='Save results to file')
@click.option('--format', 'output_format', type=click.Choice(['table', 'json', 'simple']), default='table', help='Output format')
@pass_config
def perf_track(config, notes, output, output_format):
    """Record a performance snapshot and track it over time.

    Run comprehensive performance benchmarks and store the results in a tracking
    database for historical analysis and trend monitoring.

    Examples:
        markitect perf-track --notes "After optimization changes"
        markitect perf-track --format json -o perf-snapshot.json
        markitect perf-track --notes "Baseline before refactor"
    """
    try:
        import time
        import tempfile
        import json as json_lib
        from pathlib import Path
        from .performance_tracker import PerformanceTracker

        # Initialize performance tracker
        tracker_db = Path(config['database_path']).parent / 'performance_tracking.db'
        tracker = PerformanceTracker(str(tracker_db))

        click.echo("📊 Running performance benchmark for tracking...")

        # Run comprehensive benchmarks
        start_time = time.time()

        # Template rendering benchmark
        template_ops = 0
        try:
            from .template.engine import TemplateEngine
            engine = TemplateEngine()
            template_content = "# {{title}}\n\nProcessing {{item.name}} - {{item.value}}"

            test_start = time.time()
            while (time.time() - test_start) < 2.0:  # 2 second test
                template_data = {
                    "title": f"Benchmark {template_ops}",
                    "item": {"name": f"Item {template_ops}", "value": template_ops * 1.5}
                }
                result = engine.render(template_content, template_data)
                template_ops += 1

            template_duration = time.time() - test_start
            template_rate = template_ops / template_duration if template_duration > 0 else 0
        except Exception as e:
            template_rate = 0
            click.echo(f"⚠️  Template benchmark failed: {e}", err=True)

        # Database operations benchmark
        database_ops = 0
        try:
            from .database import DatabaseManager
            db = DatabaseManager(config['database_path'])

            test_start = time.time()
            while (time.time() - test_start) < 2.0:  # 2 second test
                try:
                    if database_ops % 3 == 0:
                        db.list_markdown_files()
                    elif database_ops % 3 == 1:
                        db.list_schema_files()
                    else:
                        db.execute_query("SELECT COUNT(*) FROM markdown_files")
                    database_ops += 1
                except Exception:
                    pass

            database_duration = time.time() - test_start
            database_rate = database_ops / database_duration if database_duration > 0 else 0
        except Exception as e:
            database_rate = 0
            click.echo(f"⚠️  Database benchmark failed: {e}", err=True)

        # Ingestion benchmark (limited to 20 operations for speed)
        ingestion_ops = 0
        try:
            with tempfile.TemporaryDirectory() as temp_dir:
                temp_path = Path(temp_dir)

                test_docs = []
                for i in range(20):  # Limited set for tracking
                    doc_path = temp_path / f"track_doc_{i}.md"
                    content = f"# Track Document {i}\n\nContent for benchmark tracking.\n\n## Details\n\nDocument: {i}"
                    doc_path.write_text(content)
                    test_docs.append(str(doc_path))

                test_start = time.time()
                for doc_path in test_docs:
                    try:
                        db = DatabaseManager(config['database_path'])
                        db.store_markdown_file(doc_path, Path(doc_path).read_text())
                        ingestion_ops += 1
                    except Exception:
                        pass

                ingestion_duration = time.time() - test_start
                ingestion_rate = ingestion_ops / ingestion_duration if ingestion_duration > 0 else 0
        except Exception as e:
            ingestion_rate = 0
            click.echo(f"⚠️  Ingestion benchmark failed: {e}", err=True)

        # Memory usage measurement
        memory_mb = 50.0  # Default fallback
        try:
            import psutil
            import os
            process = psutil.Process(os.getpid())
            memory_mb = process.memory_info().rss / (1024 * 1024)
        except ImportError:
            pass

        # Store performance snapshot
        snapshot_id = tracker.store_performance_snapshot(
            template_ops=template_rate,
            database_ops=database_rate,
            ingestion_ops=ingestion_rate,
            memory_mb=memory_mb,
            notes=notes
        )

        total_duration = time.time() - start_time

        # Get performance summary including the new snapshot
        summary = tracker.get_performance_summary()

        # Format output
        if output_format == 'json':
            output_data = {
                "snapshot_id": snapshot_id,
                "performance_results": {
                    "template_ops_per_sec": round(template_rate, 1),
                    "database_ops_per_sec": round(database_rate, 1),
                    "ingestion_ops_per_sec": round(ingestion_rate, 1),
                    "memory_usage_mb": round(memory_mb, 2),
                    "performance_index": summary["latest_snapshot"]["performance_index"]
                },
                "tracking_summary": summary,
                "benchmark_duration_seconds": round(total_duration, 3),
                "timestamp": summary["latest_snapshot"]["timestamp"],
                "notes": notes
            }
            output_text = json_lib.dumps(output_data, indent=2)
        elif output_format == 'table':
            # Current performance table
            perf_data = [
                ["Template Rendering", f"{template_rate:.1f} ops/sec"],
                ["Database Operations", f"{database_rate:.1f} ops/sec"],
                ["Document Ingestion", f"{ingestion_rate:.1f} ops/sec"],
                ["Memory Usage", f"{memory_mb:.1f} MB"],
                ["Performance Index", f"{summary['latest_snapshot']['performance_index']:.1f}/100"]
            ]

            output_lines = [
                f"📊 Performance Snapshot #{snapshot_id} Recorded",
                "",
                tabulate(perf_data, headers=["Metric", "Value"], tablefmt="grid"),
                "",
                f"🎯 Performance Index: {summary['latest_snapshot']['performance_index']:.1f}/100"
            ]

            # Add trend information if available
            if summary.get("trend_analysis", {}).get("trend") != "insufficient_data":
                trend = summary["trend_analysis"]
                trend_emoji = "📈" if trend["trend"] == "improving" else "📉" if trend["trend"] == "degrading" else "📊"
                output_lines.extend([
                    "",
                    f"{trend_emoji} Trend Analysis (30 days):",
                    f"   Direction: {trend['trend'].title()}",
                    f"   Change: {trend['trend_change_percent']:+.1f}%",
                    f"   Snapshots: {trend['snapshot_count']}"
                ])

            if notes:
                output_lines.extend(["", f"📝 Notes: {notes}"])

            output_text = '\n'.join(output_lines)
        else:  # simple format
            output_lines = [
                f"Performance Index: {summary['latest_snapshot']['performance_index']:.1f}/100",
                f"Template: {template_rate:.1f} ops/sec",
                f"Database: {database_rate:.1f} ops/sec",
                f"Ingestion: {ingestion_rate:.1f} ops/sec",
                f"Memory: {memory_mb:.1f} MB",
                f"Snapshot ID: {snapshot_id}"
            ]
            if notes:
                output_lines.append(f"Notes: {notes}")
            output_text = '\n'.join(output_lines)

        if output:
            with open(output, 'w') as f:
                f.write(output_text)
            click.echo(f"📁 Performance snapshot saved to {output}")
        else:
            click.echo(output_text)

    except Exception as e:
        click.echo(f"Performance tracking failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='perf-history')
@click.option('--limit', '-l', type=int, default=10, help='Number of recent snapshots to show')
@click.option('--trend-days', type=int, default=30, help='Days to analyze for trend')
@click.option('--format', 'output_format', type=click.Choice(['table', 'json', 'simple']), default='table', help='Output format')
@click.option('--output', '-o', type=click.Path(), help='Save results to file')
@pass_config
def perf_history(config, limit, trend_days, output_format, output):
    """Show performance history and trend analysis.

    Display historical performance data with trend analysis to track system
    performance evolution over time.

    Examples:
        markitect perf-history --limit 20
        markitect perf-history --trend-days 7 --format json
        markitect perf-history --format table -o performance-report.txt
    """
    try:
        import json as json_lib
        from pathlib import Path
        from .performance_tracker import PerformanceTracker

        # Initialize performance tracker
        tracker_db = Path(config['database_path']).parent / 'performance_tracking.db'
        tracker = PerformanceTracker(str(tracker_db))

        # Get performance data
        history = tracker.get_performance_history(limit=limit)
        summary = tracker.get_performance_summary()
        trend_analysis = tracker.analyze_performance_trend(days=trend_days)

        if not history:
            click.echo("📊 No performance data available. Run 'markitect perf-track' to create a baseline.")
            return

        # Format output
        if output_format == 'json':
            output_data = {
                "performance_summary": summary,
                "trend_analysis": trend_analysis,
                "history": [
                    {
                        "timestamp": snapshot.timestamp,
                        "performance_index": snapshot.performance_index,
                        "git_commit": snapshot.git_commit,
                        "template_ops_per_sec": snapshot.template_ops_per_sec,
                        "database_ops_per_sec": snapshot.database_ops_per_sec,
                        "ingestion_ops_per_sec": snapshot.ingestion_ops_per_sec,
                        "memory_usage_mb": snapshot.memory_usage_mb,
                        "notes": snapshot.notes
                    }
                    for snapshot in history
                ],
                "analysis_parameters": {
                    "history_limit": limit,
                    "trend_analysis_days": trend_days
                }
            }
            output_text = json_lib.dumps(output_data, indent=2)
        elif output_format == 'table':
            # Summary section
            latest = summary["latest_snapshot"]
            output_lines = [
                "📊 MarkiTect Performance History & Analysis",
                "=" * 50,
                "",
                f"🎯 Current Performance Index: {latest['performance_index']:.1f}/100"
            ]

            # Trend analysis
            if trend_analysis.get("trend") != "insufficient_data":
                trend_emoji = "📈" if trend_analysis["trend"] == "improving" else "📉" if trend_analysis["trend"] == "degrading" else "📊"
                output_lines.extend([
                    f"{trend_emoji} Trend ({trend_days} days): {trend_analysis['trend'].title()}",
                    f"   Change: {trend_analysis['trend_change_percent']:+.1f}% ({trend_analysis['trend_change_points']:+.2f} points)",
                    f"   Range: {trend_analysis['period_min']:.1f} - {trend_analysis['period_max']:.1f}",
                    f"   Average: {trend_analysis['period_avg']:.1f}",
                    ""
                ])

            # History table
            history_data = []
            for i, snapshot in enumerate(history):
                timestamp_short = snapshot.timestamp.split('T')[0] + ' ' + snapshot.timestamp.split('T')[1][:8]
                commit_short = snapshot.git_commit[:8] if snapshot.git_commit else "unknown"

                history_data.append([
                    len(history) - i,  # Reverse numbering (newest first)
                    timestamp_short,
                    f"{snapshot.performance_index:.1f}",
                    commit_short,
                    f"{snapshot.template_ops_per_sec:.0f}",
                    f"{snapshot.database_ops_per_sec:.0f}",
                    f"{snapshot.memory_usage_mb:.1f}",
                    snapshot.notes[:20] + "..." if len(snapshot.notes) > 20 else snapshot.notes
                ])

            output_lines.extend([
                "📈 Recent Performance History:",
                "",
                tabulate(history_data,
                        headers=["#", "Timestamp", "Index", "Commit", "Template", "Database", "Memory", "Notes"],
                        tablefmt="grid")
            ])

            output_text = '\n'.join(output_lines)
        else:  # simple format
            latest = summary["latest_snapshot"]
            output_lines = [
                f"Current Performance Index: {latest['performance_index']:.1f}/100"
            ]

            if trend_analysis.get("trend") != "insufficient_data":
                output_lines.append(f"Trend ({trend_days}d): {trend_analysis['trend']} ({trend_analysis['trend_change_percent']:+.1f}%)")

            output_lines.append(f"History entries: {len(history)}")

            # Show last few snapshots
            for i, snapshot in enumerate(history[:5]):
                date_part = snapshot.timestamp.split('T')[0]
                output_lines.append(f"  {date_part}: {snapshot.performance_index:.1f}")

            output_text = '\n'.join(output_lines)

        if output:
            with open(output, 'w') as f:
                f.write(output_text)
            click.echo(f"📁 Performance history saved to {output}")
        else:
            click.echo(output_text)

    except Exception as e:
        click.echo(f"Performance history retrieval failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# Batch Processing Commands - Issue #17


@cli.command(name='ingest-dir')
@click.argument('directory', type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path))
@click.option('--recursive', '-r', is_flag=True, help='Process directories recursively')
@click.option('--depth', type=int, help='Maximum depth for recursive processing')
@click.option('--pattern', default='*.md', help='File pattern to match (default: *.md)')
@click.option('--error-handling', type=click.Choice(['stop', 'continue', 'skip']),
              default='continue', help='Error handling strategy')
@click.option('--quiet', '-q', is_flag=True, help='Suppress progress output')
@pass_config
def ingest_dir(config, directory, recursive, depth, pattern, error_handling, quiet):
    """Process all Markdown files in directory.

    Ingests all markdown files found in the specified directory into the database.
    Supports recursive processing with depth control and flexible error handling.

    Examples:
        markitect ingest-dir ./docs
        markitect ingest-dir ./content --recursive --depth 3
        markitect ingest-dir ./articles --pattern "*.markdown" --error-handling stop
    """
    try:
        # Convert error handling string to enum
        error_strategy = ErrorHandling[error_handling.upper()]

        # Initialize batch processor
        processor = BatchProcessor(
            error_handling=error_strategy,
            show_progress=not quiet,
            max_depth=depth
        )

        # Find files to process
        if not quiet:
            click.echo(f"🔍 Searching for files in {directory}...")

        files = processor.find_markdown_files(
            directory=directory,
            pattern=pattern,
            recursive=recursive,
            depth=depth
        )

        if not files:
            click.echo(f"📭 No files found matching pattern '{pattern}' in {directory}")
            return

        # Create file processor for ingestion
        file_processor = create_file_processor(config, ProcessingMode.INGEST)

        # Process files
        result = processor.process_files(files, file_processor, "Ingesting")

        # Exit with error code if there were failures
        if result.failed > 0 and error_strategy == ErrorHandling.STOP:
            sys.exit(1)

    except Exception as e:
        click.echo(f"Directory ingestion failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='batch-process')
@click.argument('pattern', type=str)
@click.option('--operation', type=click.Choice(['ingest', 'status', 'validate']),
              default='ingest', help='Operation to perform on matched files')
@click.option('--error-handling', type=click.Choice(['stop', 'continue', 'skip']),
              default='continue', help='Error handling strategy')
@click.option('--quiet', '-q', is_flag=True, help='Suppress progress output')
@pass_config
def batch_process(config, pattern, operation, error_handling, quiet):
    """Process files matching glob pattern.

    Uses glob patterns to find and process files. Supports various operations
    including ingestion, status checking, and validation.

    Examples:
        markitect batch-process "**/*.md" --operation ingest
        markitect batch-process "docs/**/*.markdown" --operation status
        markitect batch-process "./content/*.md" --operation validate --error-handling stop
    """
    try:
        # Convert strings to enums
        error_strategy = ErrorHandling[error_handling.upper()]
        processing_mode = ProcessingMode[operation.upper()]

        # Initialize batch processor
        processor = BatchProcessor(
            error_handling=error_strategy,
            show_progress=not quiet
        )

        # Find files using glob pattern
        if not quiet:
            click.echo(f"🔍 Searching for files matching '{pattern}'...")

        files = processor.find_files_by_glob(pattern)

        if not files:
            click.echo(f"📭 No files found matching pattern '{pattern}'")
            return

        # Create file processor for the specified operation
        file_processor = create_file_processor(config, processing_mode)

        # Process files
        operation_name = f"{operation.title()}ing"
        result = processor.process_files(files, file_processor, operation_name)

        # Exit with error code if there were failures
        if result.failed > 0 and error_strategy == ErrorHandling.STOP:
            sys.exit(1)

    except Exception as e:
        click.echo(f"Batch processing failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='recursive')
@click.argument('directory', type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path))
@click.option('--depth', type=int, default=None, help='Maximum recursion depth')
@click.option('--operation', type=click.Choice(['ingest', 'status', 'validate']),
              default='status', help='Operation to perform')
@click.option('--pattern', default='*.md', help='File pattern to match (default: *.md)')
@click.option('--error-handling', type=click.Choice(['stop', 'continue', 'skip']),
              default='continue', help='Error handling strategy')
@click.option('--quiet', '-q', is_flag=True, help='Suppress progress output')
@pass_config
def recursive(config, directory, depth, operation, pattern, error_handling, quiet):
    """Recursive processing with depth control.

    Performs recursive operations on directory trees with configurable depth limits.
    This command provides fine-grained control over recursive processing behavior.

    Examples:
        markitect recursive ./docs --depth 2 --operation ingest
        markitect recursive ./content --depth 5 --operation status --pattern "*.markdown"
        markitect recursive ./src --operation validate --error-handling stop
    """
    try:
        # Convert strings to enums
        error_strategy = ErrorHandling[error_handling.upper()]
        processing_mode = ProcessingMode[operation.upper()]

        # Initialize batch processor with depth control
        processor = BatchProcessor(
            error_handling=error_strategy,
            show_progress=not quiet,
            max_depth=depth
        )

        # Find files recursively
        if not quiet:
            depth_str = f" (max depth: {depth})" if depth else ""
            click.echo(f"🔍 Recursively searching {directory}{depth_str}...")

        files = processor.find_markdown_files(
            directory=directory,
            pattern=pattern,
            recursive=True,
            depth=depth
        )

        if not files:
            click.echo(f"📭 No files found matching pattern '{pattern}' in {directory}")
            return

        # Create file processor for the specified operation
        file_processor = create_file_processor(config, processing_mode)

        # Process files
        operation_name = f"Recursively {operation}ing"
        result = processor.process_files(files, file_processor, operation_name)

        # Exit with error code if there were failures
        if result.failed > 0 and error_strategy == ErrorHandling.STOP:
            sys.exit(1)

    except Exception as e:
        click.echo(f"Recursive processing failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# Configuration Management Commands - Issue #18


@cli.command(name='config-show')
@click.option('--format', 'output_format', type=click.Choice(['yaml', 'json', 'simple']),
              default='yaml', help='Output format for configuration display')
@click.option('--show-sensitive', is_flag=True, help='Show sensitive values (tokens, passwords)')
@pass_config
def config_show(config, output_format, show_sensitive):
    """Display current configuration.

    Shows comprehensive configuration information including current settings,
    file sources, environment variables, and workspace information.

    Examples:
        markitect config-show
        markitect config-show --format json
        markitect config-show --format simple --show-sensitive
    """
    try:
        config_manager = ConfigurationManager()
        output = config_manager.display_config(
            show_sensitive=show_sensitive,
            output_format=output_format
        )
        click.echo(output)

    except Exception as e:
        click.echo(f"Failed to display configuration: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='config-set')
@click.argument('key', type=str)
@click.argument('value', type=str)
@click.option('--config-file', type=click.Path(), help='Target configuration file')
@click.option('--validate/--no-validate', default=True, help='Validate configuration after setting')
@pass_config
def config_set(config, key, value, config_file, validate):
    """Set configuration values.

    Sets a configuration value and persists it to a configuration file.
    Supports nested keys using dot notation (e.g., 'gitea.url').

    Examples:
        markitect config-set gitea_url http://localhost:3000
        markitect config-set repo_owner myorganization
        markitect config-set api_token abc123def456
        markitect config-set workspace.dir ./my_workspace
    """
    try:
        config_manager = ConfigurationManager()

        # Set the configuration value
        success = config_manager.set_config_value(key, value, config_file)

        if success:
            click.echo(f"✅ Configuration updated: {key} = {value}")

            # Show which file was updated
            target_file = config_manager._get_target_config_file(config_file)
            click.echo(f"📁 Updated file: {target_file}")

            # Validate configuration if requested
            if validate:
                validation_results = config_manager.validate_configuration()
                errors = [r for r in validation_results if r['status'] == 'error']
                if errors:
                    click.echo("⚠️  Configuration validation warnings:")
                    for error in errors:
                        click.echo(f"   • {error['key']}: {error['message']}")

        else:
            click.echo(f"❌ Failed to set configuration: {key}", err=True)
            sys.exit(1)

    except ValueError as e:
        click.echo(f"❌ Configuration error: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Failed to set configuration: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='config-init')
@click.option('--project-dir', type=click.Path(path_type=Path), help='Target project directory')
@click.option('--interactive/--no-interactive', default=True, help='Interactive configuration setup')
@click.option('--force', is_flag=True, help='Overwrite existing configuration')
@pass_config
def config_init(config, project_dir, interactive, force):
    """Initialize configuration for new project.

    Creates a new configuration file with sensible defaults and sets up
    the necessary directory structure for a MarkiTect project.

    Examples:
        markitect config-init
        markitect config-init --project-dir ./my-project
        markitect config-init --no-interactive --force
    """
    try:
        target_dir = project_dir or Path.cwd()
        config_file = target_dir / '.markitect.yml'

        # Check if configuration already exists
        if config_file.exists() and not force:
            click.echo(f"❌ Configuration file already exists: {config_file}")
            click.echo("   Use --force to overwrite or choose a different directory")
            sys.exit(1)

        config_manager = ConfigurationManager()

        # Interactive setup if requested
        initial_config = {
            'gitea_url': 'http://localhost:3000',
            'repo_owner': '',
            'repo_name': target_dir.name,
            'workspace_dir': '.markitect_workspace',
            'cache_dir': '.ast_cache',
            'tests_dir': 'tests',
            'test_file_pattern': 'test_issue_{issue_num}_{scenario}.py',
            'claude_code_command': 'claude'
        }

        if interactive:
            click.echo("🔧 Interactive MarkiTect configuration setup")
            click.echo(f"📁 Target directory: {target_dir}")
            click.echo()

            # Prompt for each configuration value
            initial_config['gitea_url'] = click.prompt(
                'Gitea server URL',
                default=initial_config['gitea_url']
            )
            initial_config['repo_owner'] = click.prompt(
                'Repository owner/organization',
                default=initial_config['repo_owner']
            )
            initial_config['repo_name'] = click.prompt(
                'Repository name',
                default=initial_config['repo_name']
            )

            if click.confirm('Configure API token now?', default=False):
                initial_config['api_token'] = click.prompt(
                    'API token',
                    default='',
                    hide_input=True
                )

            initial_config['workspace_dir'] = click.prompt(
                'Workspace directory',
                default=initial_config['workspace_dir']
            )
            initial_config['tests_dir'] = click.prompt(
                'Tests directory',
                default=initial_config['tests_dir']
            )

        # Initialize the project
        result = config_manager.initialize_project_config(target_dir, interactive=False)

        # Update with interactive values if provided
        if interactive:
            config_manager._save_config_file(initial_config, config_file)
            result['config'] = initial_config

        click.echo("✅ MarkiTect project initialized successfully!")
        click.echo(f"📄 Configuration file: {result['config_file']}")
        click.echo("📁 Created directories:")
        for directory in result['created_directories']:
            click.echo(f"   • {directory}")

        # Show validation results
        validation_results = config_manager.validate_configuration(result['config'])
        warnings = [r for r in validation_results if r['status'] == 'warning']
        errors = [r for r in validation_results if r['status'] == 'error']

        if warnings:
            click.echo("⚠️  Configuration warnings:")
            for warning in warnings:
                click.echo(f"   • {warning['message']}")

        if errors:
            click.echo("❌ Configuration errors:")
            for error in errors:
                click.echo(f"   • {error['message']}")
        else:
            click.echo("🎉 Configuration validation passed!")

    except Exception as e:
        click.echo(f"❌ Failed to initialize configuration: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='config-validate')
@click.option('--verbose', '-v', is_flag=True, help='Show detailed validation information')
@pass_config
def config_validate(config, verbose):
    """Validate current configuration.

    Checks the current configuration for common issues, missing required fields,
    and validates paths and URLs. Provides suggestions for fixing any problems.

    Examples:
        markitect config-validate
        markitect config-validate --verbose
    """
    try:
        config_manager = ConfigurationManager()
        validation_results = config_manager.validate_configuration()

        # Categorize results
        errors = [r for r in validation_results if r['status'] == 'error']
        warnings = [r for r in validation_results if r['status'] == 'warning']
        ok_results = [r for r in validation_results if r['status'] == 'ok']

        # Display summary
        click.echo(f"📊 Configuration Validation Summary:")
        click.echo(f"   ✅ OK: {len(ok_results)}")
        click.echo(f"   ⚠️  Warnings: {len(warnings)}")
        click.echo(f"   ❌ Errors: {len(errors)}")
        click.echo()

        # Show errors
        if errors:
            click.echo("❌ Configuration Errors:")
            for error in errors:
                click.echo(f"   • {error['key']}: {error['message']}")
            click.echo()

        # Show warnings
        if warnings:
            click.echo("⚠️  Configuration Warnings:")
            for warning in warnings:
                click.echo(f"   • {warning['key']}: {warning['message']}")
            click.echo()

        # Show OK results in verbose mode
        if verbose and ok_results:
            click.echo("✅ Valid Configuration:")
            for ok_result in ok_results:
                click.echo(f"   • {ok_result['key']}: {ok_result['message']}")
            click.echo()

        # Overall status
        if errors:
            click.echo("❌ Configuration validation failed")
            sys.exit(1)
        elif warnings:
            click.echo("⚠️  Configuration validation passed with warnings")
        else:
            click.echo("✅ Configuration validation passed")

    except Exception as e:
        click.echo(f"❌ Configuration validation failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='config-help')
@click.argument('key', required=False)
@pass_config
def config_help(config, key):
    """Get help information for configuration keys.

    Provides detailed information about available configuration options,
    their purposes, and example values.

    Examples:
        markitect config-help
        markitect config-help gitea_url
        markitect config-help api_token
    """
    try:
        config_manager = ConfigurationManager()
        help_text = config_manager.get_config_help(key)
        click.echo(help_text)

    except Exception as e:
        click.echo(f"❌ Failed to get configuration help: {e}", err=True)
        sys.exit(1)


# Import PluginType for the CLI commands
from .plugins.base import PluginType

# Plugin Management Commands

@cli.command(name='plugin-list')
@click.option('--type', 'plugin_type', type=click.Choice([pt.value for pt in PluginType]),
              help='Filter by plugin type')
@click.option('--format', 'output_format', type=click.Choice(['table', 'json', 'yaml']),
              default='table', help='Output format')
@pass_config
def plugin_list(config, plugin_type, output_format):
    """List all available plugins.

    Shows discovered and loaded plugins with their metadata and status.

    Examples:
        markitect plugin-list
        markitect plugin-list --type processor
        markitect plugin-list --format json
    """
    try:
        from .plugins import PluginManager, PluginType

        manager = PluginManager()
        manager.discover_plugins()

        # Filter by type if specified
        filter_type = None
        if plugin_type:
            filter_type = PluginType(plugin_type)

        plugins = manager.list_plugins(filter_type)

        if output_format == 'table':
            if not plugins:
                click.echo("No plugins found.")
                return

            # Create table output
            click.echo("📦 Available Plugins:")
            click.echo()

            for name, info in plugins.items():
                status = "✅ Loaded" if info.get('loaded', False) else "⚪ Available"
                click.echo(f"{status} {name}")
                click.echo(f"   Type: {info.get('type', 'unknown')}")
                click.echo(f"   Version: {info.get('version', 'unknown')}")
                click.echo(f"   Description: {info.get('description', 'No description')}")
                if info.get('author'):
                    click.echo(f"   Author: {info['author']}")
                click.echo()

        else:
            click.echo(format_output(plugins, output_format))

    except Exception as e:
        click.echo(f"❌ Failed to list plugins: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='plugin-load')
@click.argument('plugin_name', type=str)
@click.option('--config-data', type=str, help='JSON configuration data for plugin')
@pass_config
def plugin_load(config, plugin_name, config_data):
    """Load a specific plugin.

    Load and initialize a plugin with optional configuration.

    Examples:
        markitect plugin-load json_formatter
        markitect plugin-load my_processor --config-data '{"param": "value"}'
    """
    try:
        from .plugins import PluginManager
        import json

        manager = PluginManager()

        # Parse config data if provided
        plugin_config = {}
        if config_data:
            try:
                plugin_config = json.loads(config_data)
            except json.JSONDecodeError as e:
                click.echo(f"❌ Invalid JSON in config-data: {e}", err=True)
                sys.exit(1)

        if config.get('verbose'):
            click.echo(f"🔍 Attempting to load plugin '{plugin_name}'...")

        plugin = manager.load_plugin(plugin_name, plugin_config)

        if plugin:
            click.echo(f"✅ Plugin '{plugin_name}' loaded successfully")
            click.echo(f"   Type: {plugin.metadata.plugin_type.value}")
            click.echo(f"   Version: {plugin.metadata.version}")
        else:
            click.echo(f"❌ Failed to load plugin '{plugin_name}'", err=True)
            if config.get('verbose'):
                # Additional debug info
                discovered = manager.discover_plugins()
                if plugin_name in discovered:
                    click.echo(f"   Plugin found in discovery: {discovered[plugin_name]}")
                else:
                    click.echo(f"   Plugin not found in discovery. Available: {list(discovered.keys())[:5]}")
            sys.exit(1)

    except Exception as e:
        click.echo(f"❌ Failed to load plugin: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='plugin-unload')
@click.argument('plugin_name', type=str)
@pass_config
def plugin_unload(config, plugin_name):
    """Unload a plugin.

    Unload and cleanup a previously loaded plugin.

    Examples:
        markitect plugin-unload json_formatter
    """
    try:
        from .plugins import PluginManager

        manager = PluginManager()

        if manager.unload_plugin(plugin_name):
            click.echo(f"✅ Plugin '{plugin_name}' unloaded successfully")
        else:
            click.echo(f"❌ Plugin '{plugin_name}' not found or not loaded", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"❌ Failed to unload plugin: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='plugin-info')
@click.argument('plugin_name', type=str)
@click.option('--format', 'output_format', type=click.Choice(['simple', 'json', 'yaml']),
              default='simple', help='Output format')
@pass_config
def plugin_info(config, plugin_name, output_format):
    """Show detailed information about a plugin.

    Display comprehensive information about a specific plugin including
    metadata, configuration, and status.

    Examples:
        markitect plugin-info json_formatter
        markitect plugin-info my_processor --format json
    """
    try:
        from .plugins import PluginManager

        manager = PluginManager()
        manager.discover_plugins()

        plugins = manager.list_plugins()

        if plugin_name not in plugins:
            click.echo(f"❌ Plugin '{plugin_name}' not found", err=True)
            sys.exit(1)

        plugin_info = plugins[plugin_name]

        if output_format == 'simple':
            click.echo(f"📦 Plugin: {plugin_name}")
            click.echo(f"   Name: {plugin_info.get('name', 'N/A')}")
            click.echo(f"   Version: {plugin_info.get('version', 'N/A')}")
            click.echo(f"   Type: {plugin_info.get('type', 'N/A')}")
            click.echo(f"   Description: {plugin_info.get('description', 'N/A')}")
            click.echo(f"   Author: {plugin_info.get('author', 'N/A')}")
            click.echo(f"   Status: {'Loaded' if plugin_info.get('loaded', False) else 'Available'}")

            if plugin_info.get('dependencies'):
                click.echo(f"   Dependencies: {', '.join(plugin_info['dependencies'])}")

            if plugin_info.get('markitect_version'):
                click.echo(f"   MarkiTect Version: {plugin_info['markitect_version']}")
        else:
            click.echo(format_output(plugin_info, output_format))

    except Exception as e:
        click.echo(f"❌ Failed to get plugin info: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='plugin-discover')
@click.option('--refresh', is_flag=True, help='Force refresh of plugin discovery')
@pass_config
def plugin_discover(config, refresh):
    """Discover available plugins.

    Scan for plugins in configured directories and report findings.

    Examples:
        markitect plugin-discover
        markitect plugin-discover --refresh
    """
    try:
        from .plugins import PluginManager

        manager = PluginManager()
        discovered = manager.discover_plugins(refresh=refresh)

        click.echo(f"🔍 Plugin Discovery Complete")
        click.echo(f"   Found {len(discovered)} plugins")

        if discovered:
            click.echo("   Discovered plugins:")
            for name in sorted(discovered.keys()):
                click.echo(f"     • {name}")
        else:
            click.echo("   No plugins found")

    except Exception as e:
        click.echo(f"❌ Failed to discover plugins: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# GraphQL Commands

@cli.command(name='graphql-serve')
@click.option('--host', default='127.0.0.1', help='Host to bind to')
@click.option('--port', default=5000, type=int, help='Port to bind to')
@click.option('--debug', is_flag=True, help='Enable debug mode')
@click.option('--no-cors', is_flag=True, help='Disable CORS')
@pass_config
def graphql_serve(config, host, port, debug, no_cors):
    """Start GraphQL server for MarkiTect API.

    Starts a GraphQL server that exposes MarkiTect's database content
    including markdown files, schemas, and ASTs through a GraphQL interface.

    Examples:
        markitect graphql-serve
        markitect graphql-serve --host 0.0.0.0 --port 8000
        markitect graphql-serve --debug --no-cors
    """
    try:
        from .graphql import GraphQLServer

        server = GraphQLServer(
            db_path=config['database_path'],
            enable_cors=not no_cors
        )
        server.run(host=host, port=port, debug=debug)

    except ImportError:
        click.echo("❌ GraphQL server requires additional dependencies.", err=True)
        click.echo("Install with: pip install flask flask-cors", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Failed to start GraphQL server: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='graphql-query')
@click.argument('query', type=str)
@click.option('--variables', type=str, help='JSON variables for the query')
@click.option('--endpoint', default='http://localhost:5000/graphql', help='GraphQL endpoint URL')
@click.option('--local', is_flag=True, help='Execute query locally without HTTP')
@click.option('--format', 'output_format', type=click.Choice(['json', 'yaml', 'table']),
              default='json', help='Output format')
@pass_config
def graphql_query(config, query, variables, endpoint, local, output_format):
    """Execute GraphQL query against MarkiTect API.

    Execute GraphQL queries to retrieve data from MarkiTect's database.
    Can run against a local server or execute queries directly.

    Examples:
        markitect graphql-query "{ markdownFiles { id filename } }"
        markitect graphql-query "query GetFile($id: Int!) { markdownFile(id: $id) { filename content } }" --variables '{"id": 1}'
        markitect graphql-query "{ databaseStats { totalFiles totalSchemas } }" --local
    """
    try:
        from .graphql import GraphQLClient
        import json as json_module

        # Parse variables if provided
        parsed_variables = {}
        if variables:
            try:
                parsed_variables = json_module.loads(variables)
            except json_module.JSONDecodeError as e:
                click.echo(f"❌ Invalid JSON in variables: {e}", err=True)
                sys.exit(1)

        # Execute query
        if local:
            client = GraphQLClient()
            result = client.execute_local(query, parsed_variables)
        else:
            client = GraphQLClient(endpoint)
            result = client.execute(query, parsed_variables)

        # Format output
        if result.get('errors'):
            click.echo("❌ GraphQL Errors:", err=True)
            for error in result['errors']:
                click.echo(f"   {error.get('message', str(error))}", err=True)

        if result.get('data'):
            if output_format == 'json':
                click.echo(json_module.dumps(result['data'], indent=2))
            elif output_format == 'yaml':
                import yaml
                click.echo(yaml.dump(result['data'], default_flow_style=False))
            elif output_format == 'table':
                # Simple table format for basic data
                click.echo(format_output(result['data'], 'table'))

    except ImportError as e:
        if 'requests' in str(e):
            click.echo("❌ GraphQL client requires requests library.", err=True)
            click.echo("Install with: pip install requests", err=True)
        else:
            click.echo(f"❌ Missing dependency: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Failed to execute GraphQL query: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='graphql-schema')
@click.option('--endpoint', default='http://localhost:5000/graphql', help='GraphQL endpoint URL')
@click.option('--local', is_flag=True, help='Get schema locally without HTTP')
@click.option('--format', 'output_format', type=click.Choice(['sdl', 'json']),
              default='sdl', help='Schema format (SDL or introspection JSON)')
@pass_config
def graphql_schema(config, endpoint, local, output_format):
    """Get GraphQL schema definition.

    Retrieve and display the GraphQL schema for MarkiTect's API.
    Useful for understanding available queries and types.

    Examples:
        markitect graphql-schema
        markitect graphql-schema --local
        markitect graphql-schema --format json
    """
    try:
        if local:
            from .graphql import schema
            try:
                from graphql.utilities import print_schema
                schema_sdl = print_schema(schema.graphql_schema)
            except (AttributeError, ImportError):
                # Fallback to simple string representation
                schema_sdl = str(schema)

            if output_format == 'sdl':
                click.echo(schema_sdl)
            else:
                # For JSON, we'd need introspection query
                introspection_query = """
                query IntrospectionQuery {
                  __schema {
                    queryType { name }
                    mutationType { name }
                    subscriptionType { name }
                    types {
                      ...FullType
                    }
                  }
                }
                fragment FullType on __Type {
                  kind
                  name
                  description
                  fields(includeDeprecated: true) {
                    name
                    description
                    args {
                      ...InputValue
                    }
                    type {
                      ...TypeRef
                    }
                  }
                }
                fragment InputValue on __InputValue {
                  name
                  description
                  type { ...TypeRef }
                  defaultValue
                }
                fragment TypeRef on __Type {
                  kind
                  name
                  ofType {
                    kind
                    name
                    ofType {
                      kind
                      name
                    }
                  }
                }
                """
                from .graphql import GraphQLClient
                client = GraphQLClient()
                result = client.execute_local(introspection_query)
                import json
                click.echo(json.dumps(result, indent=2))
        else:
            # Get from HTTP endpoint
            import requests
            if output_format == 'sdl':
                # Try to get SDL from /schema endpoint
                try:
                    response = requests.get(endpoint.replace('/graphql', '/schema'))
                    if response.status_code == 200:
                        schema_data = response.json()
                        click.echo(schema_data.get('schema', 'Schema not available'))
                    else:
                        click.echo(f"❌ Failed to get schema: HTTP {response.status_code}", err=True)
                        sys.exit(1)
                except requests.RequestException as e:
                    click.echo(f"❌ Failed to connect to GraphQL server: {e}", err=True)
                    sys.exit(1)
            else:
                # Get introspection JSON
                from .graphql import GraphQLClient
                client = GraphQLClient(endpoint)
                # Use introspection query (same as above)
                result = client.execute(introspection_query)
                import json
                click.echo(json.dumps(result, indent=2))

    except ImportError as e:
        click.echo(f"❌ Missing dependency: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Failed to get GraphQL schema: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@cli.command(name='graphql-examples')
@pass_config
def graphql_examples(config):
    """Show example GraphQL queries for MarkiTect.

    Display common GraphQL query examples to help users get started
    with querying MarkiTect's data through the GraphQL interface.
    """
    examples = """
📊 MarkiTect GraphQL Query Examples
===================================

🔍 Basic Queries:

# Get all markdown files with basic info
{
  markdownFiles(limit: 10) {
    id
    filename
    hasFrontMatter
    wordCount
    createdAt
  }
}

# Get specific file by ID
{
  markdownFile(id: 1) {
    filename
    content
    frontMatter {
      key
      value
    }
    wordCount
    lineCount
  }
}

# Get file by filename
{
  markdownFile(filename: "docs/README.md") {
    id
    content
    frontMatterRaw
  }
}

📋 Schema Queries:

# List all schemas
{
  schemas {
    id
    filename
    title
    description
    schemaVersion
    propertyCount
  }
}

# Get specific schema
{
  schema(id: 1) {
    filename
    title
    schemaContent
    createdAt
  }
}

🌳 AST Queries:

# Get AST for a file
{
  ast(fileId: 1) {
    filename
    headingCount
    linkCount
    imageCount
    codeBlockCount
    tree {
      type
      value
      level
    }
  }
}

# JSONPath query on AST
{
  astQuery(fileId: 1, jsonpath: "$..heading") {
    # Returns array of heading nodes
  }
}

🔍 Search Queries:

# Search across files and schemas
{
  search(query: "markdown", limit: 5) {
    type
    score
    highlight
    file {
      filename
      wordCount
    }
    schema {
      title
      description
    }
  }
}

# Search only files
{
  search(query: "README", type: "file") {
    type
    score
    file {
      filename
      content
    }
  }
}

📊 Statistics:

# Database overview
{
  databaseStats {
    totalFiles
    totalSchemas
    totalSizeBytes
    lastUpdated
  }
}

🔍 Filtering:

# Files with front matter created after date
{
  markdownFiles(
    hasFrontMatter: true,
    createdAfter: "2023-01-01T00:00:00"
  ) {
    filename
    frontMatterRaw
    createdAt
  }
}

💡 Usage Examples:

# Execute a query locally
markitect graphql-query "{ databaseStats { totalFiles } }" --local

# Execute with variables
markitect graphql-query \\
  "query GetFile($id: Int!) { markdownFile(id: $id) { filename } }" \\
  --variables '{"id": 1}' --local

# Start GraphQL server
markitect graphql-serve --port 5000

# Query running server
markitect graphql-query "{ markdownFiles { filename } }" \\
  --endpoint http://localhost:5000/graphql

🛠️ Mutation Examples (Write Operations):

# Add a new markdown file
markitect graphql-mutate \\
  'mutation { addMarkdownFile(filename: "new-doc.md", content: "# New Document\\n\\nContent here") { success markdownFile { id filename } errors } }' \\
  --local

# Update existing file
markitect graphql-mutate \\
  'mutation { updateMarkdownFile(id: 1, content: "# Updated\\n\\nNew content") { success errors } }' \\
  --local

# Add a JSON schema
markitect graphql-mutate \\
  'mutation { addSchema(filename: "user-schema.json", schemaContent: "{\\"type\\": \\"object\\", \\"properties\\": {\\"name\\": {\\"type\\": \\"string\\"}}}") { success schema { id title } errors } }' \\
  --local

# Delete a schema
markitect graphql-mutate \\
  'mutation { deleteSchema(filename: "old-schema.json") { success deletedFilename errors } }' \\
  --local

💡 Access GraphQL Playground at http://localhost:5000/graphql when server is running
"""

    click.echo(examples)


@cli.command(name='graphql-mutate')
@click.argument('mutation', required=True)
@click.option('--variables', default='{}', help='JSON string of mutation variables')
@click.option('--endpoint', default='http://localhost:5000/graphql', help='GraphQL endpoint URL')
@click.option('--local', is_flag=True, help='Execute mutation locally without HTTP')
@click.option('--format', 'output_format', type=click.Choice(['json', 'yaml', 'table']),
              default='json', help='Output format')
@pass_config
def graphql_mutate(config, mutation, variables, endpoint, local, output_format):
    """Execute GraphQL mutations for write operations.

    Execute GraphQL mutations to add, update, or delete data in MarkiTect.
    Supports both local and remote execution modes.

    Examples:
        # Add a new markdown file locally
        markitect graphql-mutate 'mutation { addMarkdownFile(filename: "test.md", content: "# Test\\nContent") { success markdown_file { id filename } } }' --local

        # Update an existing file
        markitect graphql-mutate 'mutation { updateMarkdownFile(id: 1, content: "# Updated\\nContent") { success errors } }' --local

        # Add a schema with variables
        markitect graphql-mutate 'mutation($filename: String!, $content: JSONString!) { addSchema(filename: $filename, schemaContent: $content) { success schema { id title } } }' --variables '{"filename": "test.json", "content": "{\\"type\\": \\"object\\"}"}' --local
    """
    import sys
    import json
    import yaml

    try:
        # Parse variables
        try:
            mutation_variables = json.loads(variables) if variables != '{}' else {}
        except json.JSONDecodeError:
            click.echo("❌ Invalid JSON in variables parameter", err=True)
            sys.exit(1)

        if local:
            # Execute locally using the GraphQL client
            try:
                from .graphql import GraphQLClient
                client = GraphQLClient()
                result = client.execute_local(mutation, variables=mutation_variables)
            except ImportError as e:
                click.echo(f"❌ Missing dependency: {e}", err=True)
                sys.exit(1)
        else:
            # Execute remotely
            try:
                from .graphql import GraphQLClient
                client = GraphQLClient(endpoint)
                result = client.execute(mutation, variables=mutation_variables)
            except ImportError as e:
                click.echo(f"❌ Missing dependency: {e}", err=True)
                sys.exit(1)

        # Format and display output
        if output_format == 'json':
            click.echo(json.dumps(result, indent=2))
        elif output_format == 'yaml':
            click.echo(yaml.dump(result, default_flow_style=False))
        elif output_format == 'table':
            # For mutations, simple table output
            if result.get('data'):
                click.echo("Mutation Result:")
                for key, value in result['data'].items():
                    if isinstance(value, dict):
                        click.echo(f"  {key}:")
                        for sub_key, sub_value in value.items():
                            click.echo(f"    {sub_key}: {sub_value}")
                    else:
                        click.echo(f"  {key}: {value}")

            if result.get('errors'):
                click.echo("Errors:")
                for error in result['errors']:
                    click.echo(f"  - {error.get('message', error)}")

    except ImportError as e:
        click.echo(f"❌ Missing dependency: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Failed to execute mutation: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# =============================================================================
# Full Text Search Commands (Issue #83)
# =============================================================================

@cli.group('search')
@pass_config
def search_group(config):
    """Full text search operations using FTS5."""
    pass


@search_group.command('init')
@click.option('--rebuild', is_flag=True, help='Rebuild existing indexes')
@pass_config
def search_init(config, rebuild):
    """Initialize full text search indexes."""
    db_path = get_database_path(config)

    try:
        from .plugins.builtin.search import FTSSearchPlugin

        search_plugin = FTSSearchPlugin()
        search_plugin.initialize(db_path)

        if rebuild:
            click.echo("🔄 Rebuilding search indexes...")
            stats = search_plugin.rebuild_index(db_path)
            click.echo(f"✅ Indexed {stats.get('files_indexed', 0)} files and {stats.get('schemas_indexed', 0)} schemas")

            if 'error' in stats:
                click.echo(f"⚠️ Warning: {stats['error']}", err=True)
        else:
            click.echo("✅ Search indexes initialized")

        # Show status
        search_stats = search_plugin.get_search_stats(db_path)
        if search_stats.get('fts_enabled'):
            click.echo(f"📊 FTS5 enabled with {len(search_stats.get('fts_tables', []))} tables")
        else:
            click.echo("⚠️ FTS5 not available, will fall back to simple search")

    except ImportError as e:
        click.echo(f"❌ Search plugin not available: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Failed to initialize search: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@search_group.command('query')
@click.argument('query')
@click.option('--type', 'content_type', default='all',
              type=click.Choice(['all', 'files', 'schemas']),
              help='Content type to search')
@click.option('--limit', default=20, help='Maximum number of results')
@click.option('--offset', default=0, help='Result offset for pagination')
@click.option('--format', 'output_format', default='table',
              type=click.Choice(['json', 'yaml', 'table']),
              help='Output format')
@click.option('--no-highlight', is_flag=True, help='Disable result highlighting')
@pass_config
def search_query(config, query, content_type, limit, offset, output_format, no_highlight):
    """Perform full text search query."""
    db_path = get_database_path(config)

    try:
        from .plugins.builtin.search import FTSSearchPlugin

        search_plugin = FTSSearchPlugin()
        results = search_plugin.search(db_path, query, content_type, limit, offset)

        if output_format == 'json':
            click.echo(json.dumps(results, indent=2, default=str))
        elif output_format == 'yaml':
            click.echo(yaml.dump(results, default_flow_style=False))
        else:
            # Table format
            if not results:
                click.echo(f"No results found for '{query}'")
                return

            # Prepare table data
            table_data = []
            headers = ['Score', 'Type', 'File/Schema', 'Preview']

            for result in results:
                score = f"{result.get('score', 0):.2f}"
                result_type = result.get('type', 'unknown')

                if result_type == 'file':
                    file_info = result.get('file', {})
                    name = file_info.get('filename', 'Unknown')
                    if not no_highlight:
                        preview = result.get('highlight', '')[:80]
                    else:
                        content = file_info.get('content', '')
                        preview = content[:80] + '...' if len(content) > 80 else content
                elif result_type == 'schema':
                    schema_info = result.get('schema', {})
                    name = schema_info.get('filename', 'Unknown')
                    if not no_highlight:
                        preview = result.get('highlight', '')[:80]
                    else:
                        desc = schema_info.get('description', '')
                        preview = desc[:80] + '...' if len(desc) > 80 else desc
                else:
                    name = 'Unknown'
                    preview = ''

                table_data.append([score, result_type, name, preview])

            click.echo(f"\n🔍 Found {len(results)} results for '{query}':\n")
            click.echo(tabulate(table_data, headers=headers, tablefmt='grid'))

            if len(results) == limit:
                click.echo(f"\n💡 Showing first {limit} results. Use --limit and --offset for more.")

    except ImportError as e:
        click.echo(f"❌ Search plugin not available: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Search failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@search_group.command('status')
@click.option('--format', 'output_format', default='table',
              type=click.Choice(['json', 'yaml', 'table']),
              help='Output format')
@pass_config
def search_status(config, output_format):
    """Show search index status and statistics."""
    db_path = get_database_path(config)

    try:
        from .plugins.builtin.search import FTSSearchPlugin

        search_plugin = FTSSearchPlugin()
        stats = search_plugin.get_search_stats(db_path)

        if output_format == 'json':
            click.echo(json.dumps(stats, indent=2))
        elif output_format == 'yaml':
            click.echo(yaml.dump(stats, default_flow_style=False))
        else:
            # Table format
            click.echo("📊 Search Index Status\n")

            if stats.get('fts_enabled'):
                click.echo("✅ FTS5 Full Text Search: Enabled")

                # Show table information
                if stats.get('fts_tables'):
                    click.echo(f"📋 FTS Tables: {', '.join(stats['fts_tables'])}")

                # Show document counts
                for key, value in stats.items():
                    if key.endswith('_documents'):
                        table_name = key.replace('_documents', '')
                        click.echo(f"📄 {table_name}: {value} documents")

            else:
                click.echo("❌ FTS5 Full Text Search: Disabled")
                if 'error' in stats:
                    click.echo(f"   Error: {stats['error']}")
                click.echo("   Falling back to simple LIKE-based search")

            # Additional index info
            from .plugins.builtin.search import SearchIndexer
            indexer = SearchIndexer()
            index_info = indexer.get_index_info(db_path)

            if index_info.get('integrity_check'):
                status = "✅" if index_info['integrity_check'] == 'passed' else "❌"
                click.echo(f"{status} Index Integrity: {index_info['integrity_check']}")

    except ImportError as e:
        click.echo(f"❌ Search plugin not available: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Failed to get search status: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


@search_group.command('rebuild')
@click.option('--optimize', is_flag=True, help='Optimize indexes after rebuild')
@pass_config
def search_rebuild(config, optimize):
    """Rebuild search indexes from scratch."""
    db_path = get_database_path(config)

    try:
        from .plugins.builtin.search import FTSSearchPlugin, SearchIndexer

        click.echo("🔄 Rebuilding search indexes...")

        search_plugin = FTSSearchPlugin()
        stats = search_plugin.rebuild_index(db_path)

        if 'error' in stats:
            click.echo(f"❌ Rebuild failed: {stats['error']}", err=True)
            sys.exit(1)

        click.echo(f"✅ Rebuilt indexes successfully")
        click.echo(f"📄 Files indexed: {stats.get('files_indexed', 0)}")
        click.echo(f"📋 Schemas indexed: {stats.get('schemas_indexed', 0)}")

        if optimize:
            click.echo("🔧 Optimizing indexes...")
            indexer = SearchIndexer()
            indexer.optimize_index(db_path)
            click.echo("✅ Indexes optimized")

    except ImportError as e:
        click.echo(f"❌ Search plugin not available: {e}", err=True)
        sys.exit(1)
    except Exception as e:
        click.echo(f"❌ Rebuild failed: {e}", err=True)
        if config.get('verbose'):
            import traceback
            click.echo(traceback.format_exc(), err=True)
        sys.exit(1)


# Register search commands
cli.add_command(search_group)


# =============================================================================
# Feature Wishlist Commands (Issue #85)
# =============================================================================

@cli.group('wish')
@pass_config
def wishlist_group(config):
    """Feature wishlist management for capturing and refining ideas."""
    pass


@wishlist_group.command('create')
@click.argument('title')
@click.option('--description', '-d', help='Wish description')
@click.option('--stage', default='discussion',
              type=click.Choice(['discussion', 'draft', 'ready']),
              help='Initial wishlist stage')
@click.option('--priority', type=click.Choice(['low', 'medium', 'high']),
              help='Priority level for the wish')
@pass_config
def wish_create(config, title, description, stage, priority):
    """Create a new feature wishlist item."""
    try:
        # Build description with template
        wish_description = f"""## 💡 Feature Wish

**Summary**: {description or 'No description provided'}

## Current Thinking

*What's the initial idea or inspiration?*

## Potential Benefits

*Why might this be valuable?*

## Questions to Explore

*What aspects need more thought?*

## Related Concepts

*Are there similar ideas or existing features this relates to?*

---

📋 **Wishlist Stage**: {stage}
🏷️ **Auto-labeled**: `wish`, `wish/{stage}`
"""

        # Prepare labels
        labels = ['wish', f'wish/{stage}']
        if priority:
            labels.append(f'priority/{priority}')

        # Create the issue
        import subprocess
        result = subprocess.run([
            'tea', 'issue', 'create',
            '--title', f"💡 Wish: {title}",
            '--description', wish_description,
            '--labels', ','.join(labels)
        ], capture_output=True, text=True)

        if result.returncode == 0:
            click.echo(f"✅ Created wishlist item: '{title}'")
            click.echo(f"🏷️ Labels: {', '.join(labels)}")
            click.echo(f"📋 Stage: {stage}")
        else:
            click.echo(f"❌ Failed to create wish: {result.stderr}", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"❌ Error creating wish: {e}", err=True)
        sys.exit(1)


@wishlist_group.command('list')
@click.option('--stage', type=click.Choice(['discussion', 'draft', 'ready', 'archived', 'all']),
              default='all', help='Filter by wishlist stage')
@click.option('--format', 'output_format', default='table',
              type=click.Choice(['table', 'simple', 'json']),
              help='Output format')
@pass_config
def wish_list(config, stage, output_format):
    """List feature wishlist items."""
    try:
        # Build label filter
        if stage == 'all':
            label_filter = 'wish'
        else:
            label_filter = f'wish/{stage}'

        # Get issues with wish labels using simple output and parse manually
        import subprocess
        result = subprocess.run([
            'tea', 'issue', 'list',
            '--labels', label_filter,
            '--output', 'simple'
        ], capture_output=True, text=True)

        if result.returncode != 0:
            click.echo(f"❌ Failed to fetch wishlist: {result.stderr}", err=True)
            sys.exit(1)

        # Parse the simple output: number title status assignee labels
        issues = []
        if result.stdout.strip():
            lines = result.stdout.strip().split('\n')
            for line in lines:
                if line.strip():
                    # Parse: number title status assignee labels
                    parts = line.split()
                    if len(parts) >= 2:
                        issue_number = parts[0].strip()
                        # Find where title ends (before status/assignee)
                        title_parts = []
                        labels = []
                        collecting_title = True

                        for part in parts[1:]:
                            if collecting_title and part not in ['open', 'closed'] and not part.startswith('wish'):
                                title_parts.append(part)
                            else:
                                collecting_title = False
                                if part.startswith('wish'):
                                    labels.append(part)

                        title = ' '.join(title_parts)
                        created_at = "2025-10-03"  # Default for simple format

                        issues.append({
                            'number': int(issue_number),
                            'title': title,
                            'labels': [{'name': label} for label in labels],
                            'created_at': created_at
                        })

        if not issues:
            click.echo(f"No wishlist items found for stage: {stage}")
            return

        if output_format == 'json':
            click.echo(json.dumps(issues, indent=2))
        elif output_format == 'simple':
            for issue in issues:
                click.echo(f"#{issue['number']}: {issue['title']}")
        else:
            # Table format
            table_data = []
            for issue in issues:
                # Extract stage from labels
                stage_labels = [label['name'] for label in issue.get('labels', [])
                               if label['name'].startswith('wish/')]
                current_stage = stage_labels[0].replace('wish/', '') if stage_labels else 'unknown'

                table_data.append([
                    f"#{issue['number']}",
                    current_stage,
                    issue['title'].replace('💡 Wish: ', ''),
                    issue['created_at'][:10]  # Just the date
                ])

            from tabulate import tabulate
            headers = ['Issue', 'Stage', 'Title', 'Created']
            click.echo(f"\n💡 Feature Wishlist ({len(issues)} items):\n")
            click.echo(tabulate(table_data, headers=headers, tablefmt='grid'))

    except Exception as e:
        click.echo(f"❌ Error listing wishes: {e}", err=True)
        sys.exit(1)


@wishlist_group.command('promote')
@click.argument('issue_number', type=int)
@click.option('--stage', type=click.Choice(['draft', 'ready', 'archived']),
              help='Promote to specific stage')
@pass_config
def wish_promote(config, issue_number, stage):
    """Promote a wishlist item to the next stage or specific stage."""
    try:
        if not stage:
            # Auto-determine next stage
            click.echo("🔄 Auto-promoting to next logical stage...")
            # This would require fetching current labels and determining next stage
            stage = 'draft'  # Default progression

        # Remove old stage labels and add new one
        import subprocess

        # Get current issue info using the list format and extract labels for our issue
        result = subprocess.run([
            'tea', 'issue', 'list', '--output', 'simple'
        ], capture_output=True, text=True)

        if result.returncode != 0:
            click.echo(f"❌ Failed to fetch issues", err=True)
            sys.exit(1)

        # Parse output to find our issue and extract its current labels
        current_labels = []
        if result.stdout.strip():
            lines = result.stdout.strip().split('\n')
            for line in lines:
                if line.strip() and line.split()[0].strip() == str(issue_number):
                    # Found our issue, extract labels from the end of the line
                    parts = line.split()
                    for part in parts:
                        if part.startswith('wish'):
                            current_labels.append(part)
                    break

        if not current_labels:
            click.echo(f"❌ Issue #{issue_number} not found or has no wish labels", err=True)
            sys.exit(1)

        # Build new labels (remove old wish/ stage labels)
        new_labels = [label for label in current_labels if not label.startswith('wish/')]
        new_labels.append(f'wish/{stage}')

        # Update labels
        result = subprocess.run([
            'tea', 'issue', 'edit', str(issue_number),
            '--labels', ','.join(new_labels)
        ], capture_output=True, text=True)

        if result.returncode == 0:
            click.echo(f"✅ Promoted wish #{issue_number} to stage: {stage}")
            click.echo(f"🏷️ Updated labels: {', '.join(new_labels)}")
        else:
            click.echo(f"❌ Failed to promote wish: {result.stderr}", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"❌ Error promoting wish: {e}", err=True)
        sys.exit(1)


@wishlist_group.command('convert')
@click.argument('issue_number', type=int)
@click.option('--title', help='New title for the regular issue')
@click.option('--copy-content', is_flag=True, default=True,
              help='Copy wishlist content to new issue')
@pass_config
def wish_convert(config, issue_number, title, copy_content):
    """Convert a ready wishlist item to a regular issue."""
    try:
        import subprocess
        import json
        from datetime import datetime

        # Get the wishlist issue
        result = subprocess.run([
            'tea', 'issue', 'view', str(issue_number), '--output', 'json'
        ], capture_output=True, text=True)

        if result.returncode != 0:
            click.echo(f"❌ Failed to fetch wish #{issue_number}", err=True)
            sys.exit(1)

        wish_issue = json.loads(result.stdout)

        # Check if it's ready for conversion
        labels = [label['name'] for label in wish_issue.get('labels', [])]
        if 'wish/ready' not in labels:
            click.echo(f"⚠️ Wish #{issue_number} is not marked as 'ready'. Current stage: {[l for l in labels if l.startswith('wish/')]}")
            if not click.confirm('Convert anyway?'):
                return

        # Prepare new issue content
        new_title = title or wish_issue['title'].replace('💡 Wish: ', '')

        if copy_content:
            new_description = f"""## Converted from Wishlist

Originally tracked as wishlist item #{issue_number}.

## Description

{wish_issue.get('body', '')}

---
*Converted from feature wishlist on {datetime.now().strftime('%Y-%m-%d')}*
"""
        else:
            new_description = f"Converted from wishlist item #{issue_number}"

        # Create new regular issue
        result = subprocess.run([
            'tea', 'issue', 'create',
            '--title', new_title,
            '--description', new_description
        ], capture_output=True, text=True)

        if result.returncode == 0:
            # Close the wishlist item with reference to new issue
            # Extract issue number from tea output (usually shows the URL)
            lines = result.stdout.strip().split('\n')
            new_issue_url = lines[-1] if lines else ""
            new_issue_number = new_issue_url.split('/')[-1] if '/' in new_issue_url else "unknown"

            # Close wishlist item
            subprocess.run([
                'tea', 'issue', 'close', str(issue_number),
                '--comment', f'Converted to regular issue #{new_issue_number}'
            ], capture_output=True, text=True)

            click.echo(f"✅ Converted wish #{issue_number} to regular issue #{new_issue_number}")
            click.echo(f"🏷️ Original wishlist item closed")
            click.echo(f"📋 New issue: {new_title}")
        else:
            click.echo(f"❌ Failed to create new issue: {result.stderr}", err=True)
            sys.exit(1)

    except Exception as e:
        click.echo(f"❌ Error converting wish: {e}", err=True)
        sys.exit(1)


# Register wishlist commands
cli.add_command(wishlist_group)


# Register issue management commands


# Register worktime tracking commands
from markitect.finance.worktime_commands import worktime as worktime_group
cli.add_command(worktime_group)



# Query Paradigm Commands - Issue #62
@click.group()
def paradigms():
    """Discover and explore different query paradigms in MarkiTect."""
    pass


@paradigms.command('list')
@pass_config
def list_paradigms(config):
    """List all available query paradigms."""
    from .query_paradigms.registry import registry

    paradigms = registry.list_all()
    print(f"📚 MarkiTect Query Paradigms ({len(paradigms)} available)")
    print("=" * 50)

    # Group by category
    categories = {}
    for paradigm in paradigms:
        if paradigm.category not in categories:
            categories[paradigm.category] = []
        categories[paradigm.category].append(paradigm)

    for category, paradigm_list in categories.items():
        print(f"\n🏷️  {category.upper()} PARADIGMS")
        print("-" * 30)

        for paradigm in paradigm_list:
            status = "✅ IMPLEMENTED" if paradigm.name in ['SQL', 'FTS', 'GraphQL', 'JSONPath', 'Natural Language'] else "📋 DOCUMENTED"
            print(f"  {status} {paradigm.name} ({paradigm.complexity})")
            print(f"    {paradigm.description}")
            print()


@paradigms.command()
@click.argument('query')
@pass_config
def search(config, query):
    """Search paradigms by name or description."""
    from .query_paradigms.registry import registry

    results = registry.search_paradigms(query)

    if not results:
        print(f"❌ No paradigms found matching '{query}'")
        return

    print(f"🔍 Search results for '{query}' ({len(results)} found)")
    print("=" * 40)

    for paradigm in results:
        status = "✅ IMPLEMENTED" if paradigm.name in ['SQL', 'FTS', 'GraphQL', 'JSONPath', 'Natural Language'] else "📋 DOCUMENTED"
        print(f"  {status} {paradigm.name} ({paradigm.category}, {paradigm.complexity})")
        print(f"    {paradigm.description}")
        print()


@paradigms.command()
@click.argument('name')
@pass_config
def show(config, name):
    """Show detailed information about a specific paradigm."""
    from .query_paradigms.registry import registry

    paradigm = registry.get(name)

    if not paradigm:
        print(f"❌ Paradigm '{name}' not found.")
        print("\nAvailable paradigms:")
        for p in registry.list_all():
            print(f"  - {p.name}")
        return

    status = "✅ IMPLEMENTED" if paradigm.name in ['SQL', 'FTS', 'GraphQL', 'JSONPath', 'Natural Language'] else "📋 DOCUMENTED"

    print(f"🔍 {paradigm.name} Query Paradigm")
    print("=" * (len(paradigm.name) + 20))
    print(f"Status: {status}")
    print(f"Category: {paradigm.category}")
    print(f"Complexity: {paradigm.complexity}")
    print(f"Description: {paradigm.description}")
    print()

    print("📝 Syntax Help:")
    print("-" * 15)
    print(paradigm.get_syntax_help())
    print()

    print("💡 Examples:")
    print("-" * 12)
    examples = paradigm.get_examples()
    for i, example in enumerate(examples, 1):
        print(f"{i}. {example['name']}")
        print(f"   {example['description']}")
        print(f"   Query: {example['query']}")
        print()


@paradigms.command()
@click.argument('paradigm_name')
@click.argument('query')
@click.option('--config-data', type=str, help='JSON configuration for the query')
@pass_config
def exec(config, paradigm_name, query, config_data):
    """Execute a query using specified paradigm."""
    from .query_paradigms.registry import registry
    import json

    paradigm = registry.get(paradigm_name)

    if not paradigm:
        print(f"❌ Paradigm '{paradigm_name}' not found.")
        return

    # Parse config if provided
    query_config = {}
    if config_data:
        try:
            query_config = json.loads(config_data)
        except json.JSONDecodeError:
            print("❌ Invalid JSON in config-data parameter")
            return

    # Add database path from global config
    db_path = get_database_path(config)
    query_config['db_path'] = db_path

    # Validate query first
    valid, error = paradigm.validate_query(query)
    if not valid:
        print(f"❌ Invalid query: {error}")
        return

    print(f"🚀 Executing {paradigm.name} query...")
    print(f"Query: {query}")
    if config_data:
        print(f"Config: {query_config}")
    print()

    try:
        result = paradigm.execute(query, query_config)

        print(f"⏱️  Execution time: {result.execution_time_ms:.2f}ms")
        print(f"📊 Result count: {result.result_count}")
        print(f"✅ Success: {result.success}")

        if result.error_message:
            print(f"❌ Error: {result.error_message}")

        if result.metadata:
            print("\n📋 Metadata:")
            for key, value in result.metadata.items():
                print(f"  {key}: {value}")

        if result.results:
            print(f"\n📄 Results:")
            for i, row in enumerate(result.results[:5], 1):  # Show first 5 results
                print(f"  {i}. {row}")

            if len(result.results) > 5:
                print(f"  ... and {len(result.results) - 5} more results")

    except Exception as e:
        print(f"❌ Execution error: {e}")


@paradigms.command()
@pass_config
def categories(config):
    """List all available paradigm categories."""
    from .query_paradigms.registry import registry

    categories = registry.get_categories()
    print("📂 Available Categories:")
    for category in sorted(categories):
        paradigms = registry.list_by_category(category)
        print(f"  {category}: {len(paradigms)} paradigms")


# Register cost tracking commands
if COST_TRACKING_AVAILABLE:
    cli.add_command(cost_commands)

# Register profile management commands
if PROFILE_MANAGEMENT_AVAILABLE:
    cli.add_command(profile_commands)

# Register paradigms commands
cli.add_command(paradigms)

# Register asset management commands - Issue #143
try:
    from .asset_commands import asset, package, workspace
    cli.add_command(asset)
    cli.add_command(package)
    cli.add_command(workspace)
    ASSET_COMMANDS_AVAILABLE = True
except ImportError:
    ASSET_COMMANDS_AVAILABLE = False

# Register markdown commands plugin
try:
    from .plugins.builtin.markdown_commands import MarkdownCommandsPlugin
    plugin_instance = MarkdownCommandsPlugin()
    plugin_instance.initialize()
    for command_name, command_func in plugin_instance.get_commands().items():
        cli.add_command(command_func, name=command_name)
except ImportError:
    pass  # Plugin not available

# Register prompt dependency resolution commands
try:
    from markitect.prompts.cli import prompt_commands
    cli.add_command(prompt_commands)
except ImportError:
    pass  # Prompts module not available

# Make cli function available as main entry point
main = cli

if __name__ == '__main__':
    main()