skill-seekers-reference/src/skill_seekers/cli/codebase_scraper.py

#!/usr/bin/env python3
"""
Codebase Scraper CLI Tool

Standalone tool for analyzing local codebases without GitHub API.
Extracts code signatures, comments, and optionally generates API documentation.

Usage:
    codebase-scraper --directory /path/to/repo --output output/codebase/
    codebase-scraper --directory . --depth deep --languages Python,JavaScript
    codebase-scraper --directory /path/to/repo --build-api-reference

Features:
    - File tree walking with .gitignore support
    - Multi-language code analysis (9 languages: Python, JavaScript/TypeScript, C/C++, C#, Go, Rust, Java, Ruby, PHP)
    - API reference generation
    - Comment extraction
    - Dependency graph analysis
    - Configurable depth levels

Credits:
    - Language parsing patterns inspired by official language specifications
    - NetworkX for dependency graph analysis: https://networkx.org/
    - pathspec for .gitignore support: https://pypi.org/project/pathspec/
"""

import argparse
import json
import logging
import os
import re
import sys
from pathlib import Path
from typing import Any

from skill_seekers.cli.api_reference_builder import APIReferenceBuilder
from skill_seekers.cli.code_analyzer import CodeAnalyzer
from skill_seekers.cli.config_extractor import ConfigExtractor
from skill_seekers.cli.dependency_analyzer import DependencyAnalyzer
from skill_seekers.cli.signal_flow_analyzer import SignalFlowAnalyzer
from skill_seekers.cli.utils import setup_logging

# Try to import pathspec for .gitignore support
try:
    import pathspec

    PATHSPEC_AVAILABLE = True
except ImportError:
    PATHSPEC_AVAILABLE = False

logger = logging.getLogger(__name__)


# Language extension mapping
LANGUAGE_EXTENSIONS = {
    ".py": "Python",
    ".js": "JavaScript",
    ".jsx": "JavaScript",
    ".ts": "TypeScript",
    ".tsx": "TypeScript",
    ".cpp": "C++",
    ".cc": "C++",
    ".cxx": "C++",
    ".h": "C++",
    ".hpp": "C++",
    ".hxx": "C++",
    ".c": "C",
    ".cs": "C#",
    ".gd": "GDScript",  # Godot scripting language
    ".tscn": "GodotScene",  # Godot scene files
    ".tres": "GodotResource",  # Godot resource files
    ".gdshader": "GodotShader",  # Godot shader files
    ".go": "Go",
    ".rs": "Rust",
    ".java": "Java",
    ".rb": "Ruby",
    ".php": "PHP",
}

# Documentation file extensions
MARKDOWN_EXTENSIONS = {".md", ".markdown", ".mdown", ".mkd"}
RST_EXTENSIONS = {".rst", ".rest"}  # ReStructuredText (Sphinx, Godot docs, etc.)
DOC_EXTENSIONS = MARKDOWN_EXTENSIONS | RST_EXTENSIONS  # All supported doc formats

# Common documentation folders to scan
DOC_FOLDERS = {"docs", "doc", "documentation", "wiki", ".github"}

# Root-level doc files → category mapping
ROOT_DOC_CATEGORIES = {
    "readme": "overview",
    "contributing": "contributing",
    "changelog": "changelog",
    "history": "changelog",
    "license": "license",
    "authors": "authors",
    "code_of_conduct": "community",
    "security": "security",
    "architecture": "architecture",
    "design": "architecture",
}

# Folder name → category mapping
FOLDER_CATEGORIES = {
    "architecture": "architecture",
    "arch": "architecture",
    "design": "architecture",
    "guides": "guides",
    "guide": "guides",
    "tutorials": "guides",
    "tutorial": "guides",
    "howto": "guides",
    "how-to": "guides",
    "workflows": "workflows",
    "workflow": "workflows",
    "templates": "templates",
    "template": "templates",
    "api": "api",
    "reference": "api",
    "examples": "examples",
    "example": "examples",
    "specs": "specifications",
    "spec": "specifications",
    "rfcs": "specifications",
    "rfc": "specifications",
    "features": "features",
    "feature": "features",
}

# Default directories to exclude
DEFAULT_EXCLUDED_DIRS = {
    # Python/Node
    "node_modules",
    "venv",
    "__pycache__",
    ".git",
    ".svn",
    ".hg",
    "build",
    "dist",
    "target",
    ".pytest_cache",
    ".tox",
    ".mypy_cache",
    "htmlcov",
    "coverage",
    ".coverage",
    ".eggs",
    "*.egg-info",
    # IDE
    ".idea",
    ".vscode",
    ".vs",
    "__pypackages__",
    # Unity (critical - contains massive build cache)
    "Library",
    "Temp",
    "Logs",
    "UserSettings",
    "MemoryCaptures",
    "Recordings",
    # Unreal Engine
    "Intermediate",
    "Saved",
    "DerivedDataCache",
    # Godot
    ".godot",
    ".import",
    # Misc
    "tmp",
    ".tmp",
}


def detect_language(file_path: Path) -> str:
    """
    Detect programming language from file extension.

    Args:
        file_path: Path to source file

    Returns:
        Language name or 'Unknown'
    """
    extension = file_path.suffix.lower()
    return LANGUAGE_EXTENSIONS.get(extension, "Unknown")


def load_gitignore(directory: Path) -> pathspec.PathSpec | None:
    """
    Load .gitignore file and create pathspec matcher.

    Args:
        directory: Root directory to search for .gitignore

    Returns:
        PathSpec object if .gitignore found, None otherwise
    """
    if not PATHSPEC_AVAILABLE:
        logger.warning("pathspec not installed - .gitignore support disabled")
        logger.warning("Install with: pip install pathspec")
        return None

    gitignore_path = directory / ".gitignore"
    if not gitignore_path.exists():
        logger.debug(f"No .gitignore found in {directory}")
        return None

    try:
        with open(gitignore_path, encoding="utf-8") as f:
            spec = pathspec.PathSpec.from_lines("gitwildmatch", f)
        logger.info(f"Loaded .gitignore from {gitignore_path}")
        return spec
    except Exception as e:
        logger.warning(f"Failed to load .gitignore: {e}")
        return None


def should_exclude_dir(dir_name: str, excluded_dirs: set) -> bool:
    """
    Check if directory should be excluded from analysis.

    Args:
        dir_name: Directory name
        excluded_dirs: Set of directory names to exclude

    Returns:
        True if directory should be excluded
    """
    return dir_name in excluded_dirs


def walk_directory(
    root: Path,
    patterns: list[str] | None = None,
    gitignore_spec: pathspec.PathSpec | None = None,
    excluded_dirs: set | None = None,
) -> list[Path]:
    """
    Walk directory tree and collect source files.

    Args:
        root: Root directory to walk
        patterns: Optional file patterns to include (e.g., ['*.py', '*.js'])
        gitignore_spec: Optional PathSpec object for .gitignore rules
        excluded_dirs: Set of directory names to exclude

    Returns:
        List of source file paths
    """
    if excluded_dirs is None:
        excluded_dirs = DEFAULT_EXCLUDED_DIRS

    files = []
    root = Path(root).resolve()

    for dirpath, dirnames, filenames in os.walk(root):
        current_dir = Path(dirpath)

        # Filter out excluded directories (in-place modification)
        dirnames[:] = [d for d in dirnames if not should_exclude_dir(d, excluded_dirs)]

        for filename in filenames:
            file_path = current_dir / filename

            # Check .gitignore rules
            if gitignore_spec:
                try:
                    rel_path = file_path.relative_to(root)
                    if gitignore_spec.match_file(str(rel_path)):
                        logger.debug(f"Skipping (gitignore): {rel_path}")
                        continue
                except ValueError:
                    # File is outside root, skip it
                    continue

            # Check file extension
            if file_path.suffix.lower() not in LANGUAGE_EXTENSIONS:
                continue

            # Check file patterns if provided
            if patterns and not any(file_path.match(pattern) for pattern in patterns):
                continue

            files.append(file_path)

    return sorted(files)


def walk_markdown_files(
    root: Path,
    gitignore_spec: pathspec.PathSpec | None = None,
    excluded_dirs: set | None = None,
) -> list[Path]:
    """
    Walk directory tree and collect markdown documentation files.

    Args:
        root: Root directory to walk
        gitignore_spec: Optional PathSpec object for .gitignore rules
        excluded_dirs: Set of directory names to exclude

    Returns:
        List of markdown file paths
    """
    if excluded_dirs is None:
        excluded_dirs = DEFAULT_EXCLUDED_DIRS

    files = []
    root = Path(root).resolve()

    for dirpath, dirnames, filenames in os.walk(root):
        current_dir = Path(dirpath)

        # Filter out excluded directories (in-place modification)
        dirnames[:] = [d for d in dirnames if not should_exclude_dir(d, excluded_dirs)]

        for filename in filenames:
            file_path = current_dir / filename

            # Check .gitignore rules
            if gitignore_spec:
                try:
                    rel_path = file_path.relative_to(root)
                    if gitignore_spec.match_file(str(rel_path)):
                        logger.debug(f"Skipping (gitignore): {rel_path}")
                        continue
                except ValueError:
                    continue

            # Check if documentation file (markdown or RST)
            if file_path.suffix.lower() not in DOC_EXTENSIONS:
                continue

            files.append(file_path)

    return sorted(files)


def categorize_markdown_file(file_path: Path, root: Path) -> str:
    """
    Categorize a markdown file based on its location and filename.

    Args:
        file_path: Path to the markdown file
        root: Root directory of the project

    Returns:
        Category name (e.g., 'overview', 'guides', 'architecture')
    """
    try:
        rel_path = file_path.relative_to(root)
    except ValueError:
        return "other"

    # Check root-level files by filename
    if len(rel_path.parts) == 1:
        filename_lower = file_path.stem.lower().replace("-", "_").replace(" ", "_")
        for key, category in ROOT_DOC_CATEGORIES.items():
            if key in filename_lower:
                return category
        return "overview"  # Default for root .md files

    # Check folder-based categorization
    for part in rel_path.parts[:-1]:  # Exclude filename
        part_lower = part.lower().replace("-", "_").replace(" ", "_")
        for key, category in FOLDER_CATEGORIES.items():
            if key in part_lower:
                return category

    # Default category
    return "other"


def extract_markdown_structure(content: str) -> dict[str, Any]:
    """
    Extract structure from markdown content (headers, code blocks, links).

    Args:
        content: Markdown file content

    Returns:
        Dictionary with extracted structure
    """
    structure = {
        "title": None,
        "headers": [],
        "code_blocks": [],
        "links": [],
        "word_count": len(content.split()),
        "line_count": len(content.split("\n")),
    }

    lines = content.split("\n")

    # Extract headers
    for i, line in enumerate(lines):
        header_match = re.match(r"^(#{1,6})\s+(.+)$", line)
        if header_match:
            level = len(header_match.group(1))
            text = header_match.group(2).strip()
            structure["headers"].append(
                {
                    "level": level,
                    "text": text,
                    "line": i + 1,
                }
            )
            # First h1 is the title
            if level == 1 and structure["title"] is None:
                structure["title"] = text

    # Extract code blocks (fenced)
    code_block_pattern = re.compile(r"```(\w*)\n(.*?)```", re.DOTALL)
    for match in code_block_pattern.finditer(content):
        language = match.group(1) or "text"
        code = match.group(2).strip()
        if len(code) > 0:
            structure["code_blocks"].append(
                {
                    "language": language,
                    "code": code,  # Full code - no truncation
                    "full_length": len(code),
                }
            )

    # Extract links
    link_pattern = re.compile(r"\[([^\]]+)\]\(([^)]+)\)")
    for match in link_pattern.finditer(content):
        structure["links"].append(
            {
                "text": match.group(1),
                "url": match.group(2),
            }
        )

    return structure


def extract_rst_structure(content: str) -> dict[str, Any]:
    """
    Extract structure from ReStructuredText (RST) content.

    Uses the enhanced unified RST parser for comprehensive extraction.

    RST uses underline-style headers:
        Title
        =====

        Section
        -------

        Subsection
        ~~~~~~~~~~

    Args:
        content: RST file content

    Returns:
        Dictionary with extracted structure including:
        - title: Document title
        - headers: List of headers with levels
        - code_blocks: Code blocks with language and content
        - tables: Tables with rows and headers
        - links: External links
        - cross_references: Internal cross-references
        - word_count: Total word count
        - line_count: Total line count
    """
    # Use the enhanced unified RST parser
    try:
        from skill_seekers.cli.parsers.extractors import RstParser

        parser = RstParser()
        result = parser.parse_string(content, "<string>")

        if result.success and result.document:
            doc = result.document

            # Convert to legacy structure format for backward compatibility
            structure = {
                "title": doc.title,
                "headers": [
                    {"level": h.level, "text": h.text, "line": h.source_line} for h in doc.headings
                ],
                "code_blocks": [
                    {
                        "language": cb.language or "text",
                        "code": cb.code,  # Full code - no truncation
                        "full_length": len(cb.code),
                        "quality_score": cb.quality_score,
                    }
                    for cb in doc.code_blocks
                ],
                "tables": [
                    {
                        "caption": t.caption,
                        "headers": t.headers,
                        "rows": t.rows,
                        "row_count": t.num_rows,
                        "col_count": t.num_cols,
                    }
                    for t in doc.tables
                ],
                "links": [
                    {"text": x.text or x.target, "url": x.target} for x in doc.external_links
                ],
                "cross_references": [
                    {"type": x.ref_type.value, "target": x.target} for x in doc.internal_links
                ],
                "word_count": len(content.split()),
                "line_count": len(content.split("\n")),
                # New enhanced fields
                "_enhanced": True,
                "_extraction_stats": {
                    "total_blocks": doc.stats.total_blocks,
                    "code_blocks": len(doc.code_blocks),
                    "tables": len(doc.tables),
                    "headings": len(doc.headings),
                    "cross_references": len(doc.internal_links),
                },
            }
            return structure
    except Exception as e:
        # Fall back to basic extraction if unified parser fails
        logger.warning(f"Enhanced RST parser failed: {e}, using basic parser")

    # Legacy basic extraction (fallback)
    structure = {
        "title": None,
        "headers": [],
        "code_blocks": [],
        "tables": [],
        "links": [],
        "cross_references": [],
        "word_count": len(content.split()),
        "line_count": len(content.split("\n")),
        "_enhanced": False,
    }

    lines = content.split("\n")
    underline_chars = ["=", "-", "~", "^", '"', "'", "`", ":", "."]

    # Extract headers (RST style: text on one line, underline on next)
    for i in range(len(lines) - 1):
        current_line = lines[i].strip()
        next_line = lines[i + 1].strip()

        if (
            current_line
            and next_line
            and len(set(next_line)) == 1
            and next_line[0] in underline_chars
            and len(next_line) >= len(current_line) - 2
        ):
            level = underline_chars.index(next_line[0]) + 1
            text = current_line.strip()
            structure["headers"].append({"level": level, "text": text, "line": i + 1})
            if structure["title"] is None:
                structure["title"] = text

    # Basic code block extraction
    code_block_pattern = re.compile(
        r"\.\.\s+code-block::\s+(\w+)\s*\n\s+(.*?)(?=\n\S|\Z)", re.DOTALL
    )
    for match in code_block_pattern.finditer(content):
        language = match.group(1) or "text"
        code = match.group(2).strip()
        if code:
            structure["code_blocks"].append(
                {
                    "language": language,
                    "code": code,  # Full code - no truncation
                    "full_length": len(code),
                }
            )

    # Basic link extraction
    link_pattern = re.compile(r"`([^<`]+)\s+<([^>]+)>`_")
    for match in link_pattern.finditer(content):
        structure["links"].append({"text": match.group(1).strip(), "url": match.group(2)})

    return structure


def generate_markdown_summary(
    content: str, structure: dict[str, Any], max_length: int = 500
) -> str:
    """
    Generate a summary of markdown content.

    Args:
        content: Full markdown content
        structure: Extracted structure from extract_markdown_structure()
        max_length: Maximum summary length

    Returns:
        Summary string
    """
    # Start with title if available
    summary_parts = []

    if structure.get("title"):
        summary_parts.append(f"**{structure['title']}**")

    # Add header outline (first 5 h2/h3 headers)
    h2_h3 = [h for h in structure.get("headers", []) if h["level"] in (2, 3)][:5]
    if h2_h3:
        sections = [h["text"] for h in h2_h3]
        summary_parts.append(f"Sections: {', '.join(sections)}")

    # Extract first paragraph (skip headers and empty lines)
    lines = content.split("\n")
    first_para = []
    in_para = False
    for line in lines:
        stripped = line.strip()
        if stripped.startswith("#") or stripped.startswith("```"):
            if in_para:
                break
            continue
        if stripped:
            in_para = True
            first_para.append(stripped)
        elif in_para:
            break

    if first_para:
        para_text = " ".join(first_para)
        if len(para_text) > 200:
            para_text = para_text[:200] + "..."
        summary_parts.append(para_text)

    # Add stats
    stats = f"({structure.get('word_count', 0)} words, {len(structure.get('code_blocks', []))} code blocks)"
    summary_parts.append(stats)

    summary = "\n".join(summary_parts)
    if len(summary) > max_length:
        summary = summary[:max_length] + "..."

    return summary


def process_markdown_docs(
    directory: Path,
    output_dir: Path,
    depth: str = "deep",
    gitignore_spec: pathspec.PathSpec | None = None,
    enhance_with_ai: bool = False,
    ai_mode: str = "none",
) -> dict[str, Any]:
    """
    Process all markdown documentation files in a directory.

    Args:
        directory: Root directory to scan
        output_dir: Output directory for processed docs
        depth: Processing depth ('surface', 'deep', 'full')
        gitignore_spec: Optional .gitignore spec
        enhance_with_ai: Whether to use AI enhancement
        ai_mode: AI mode ('none', 'auto', 'api', 'local')

    Returns:
        Dictionary with processed documentation data
    """
    logger.info("Scanning for markdown documentation...")

    # Find all markdown files
    md_files = walk_markdown_files(directory, gitignore_spec)
    logger.info(f"Found {len(md_files)} markdown files")

    if not md_files:
        return {"files": [], "categories": {}, "total_files": 0}

    # Process each file
    processed_docs = []
    categories = {}

    # Pre-import parsers once outside the loop
    try:
        from skill_seekers.cli.parsers.extractors import RstParser, MarkdownParser
    except ImportError:
        RstParser = None  # type: ignore[assignment,misc]
        MarkdownParser = None  # type: ignore[assignment,misc]
        logger.debug("Unified parsers not available, using legacy parsers")

    for md_path in md_files:
        try:
            content = md_path.read_text(encoding="utf-8", errors="ignore")
            rel_path = str(md_path.relative_to(directory))
            category = categorize_markdown_file(md_path, directory)

            doc_data = {
                "path": rel_path,
                "filename": md_path.name,
                "category": category,
                "size_bytes": len(content.encode("utf-8")),
            }

            # Surface depth: just path and category
            if depth == "surface":
                processed_docs.append(doc_data)
            else:
                # Deep/Full: extract structure and summary using unified parsers
                structure = None
                parsed_doc = None

                try:
                    if RstParser is None or MarkdownParser is None:
                        raise ImportError("Parsers not available")

                    # Use appropriate unified parser based on file extension
                    if md_path.suffix.lower() in RST_EXTENSIONS:
                        parser = RstParser()
                        result = parser.parse_string(content, str(md_path))
                        if result.success:
                            parsed_doc = result.document
                            # Convert to legacy structure format for backward compatibility
                            structure = {
                                "title": parsed_doc.title,
                                "headers": [
                                    {"level": h.level, "text": h.text, "line": h.source_line}
                                    for h in parsed_doc.headings
                                ],
                                "code_blocks": [
                                    {"language": cb.language, "code": cb.code}  # Full code
                                    for cb in parsed_doc.code_blocks
                                ],
                                "tables": len(parsed_doc.tables),
                                "cross_refs": len(parsed_doc.internal_links),
                                "directives": len(
                                    [b for b in parsed_doc.blocks if b.type.value == "admonition"]
                                ),
                                "word_count": parsed_doc.stats.total_blocks
                                if parsed_doc.stats
                                else 0,
                                "line_count": len(content.split("\n")),
                            }
                    else:
                        parser = MarkdownParser()
                        result = parser.parse_string(content, str(md_path))
                        if result.success:
                            parsed_doc = result.document
                            # Convert to legacy structure format
                            structure = {
                                "title": parsed_doc.title,
                                "headers": [
                                    {"level": h.level, "text": h.text, "line": h.source_line}
                                    for h in parsed_doc.headings
                                ],
                                "code_blocks": [
                                    {"language": cb.language, "code": cb.code}  # Full code
                                    for cb in parsed_doc.code_blocks
                                ],
                                "tables": len(parsed_doc.tables),
                                "images": len(parsed_doc.images),
                                "links": len(parsed_doc.external_links),
                                "word_count": parsed_doc.stats.total_blocks
                                if parsed_doc.stats
                                else 0,
                                "line_count": len(content.split("\n")),
                            }
                except ImportError:
                    # Fallback to old parsers if unified parsers not available
                    logger.debug("Unified parsers not available, using legacy parsers")
                    if md_path.suffix.lower() in RST_EXTENSIONS:
                        structure = extract_rst_structure(content)
                    else:
                        structure = extract_markdown_structure(content)

                # Generate summary
                if structure is None:
                    # Fallback if parsing failed
                    if md_path.suffix.lower() in RST_EXTENSIONS:
                        structure = extract_rst_structure(content)
                    else:
                        structure = extract_markdown_structure(content)

                summary = generate_markdown_summary(content, structure)

                doc_data.update(
                    {
                        "title": structure.get("title") or md_path.stem,
                        "structure": structure,
                        "summary": summary,
                        "content": content if depth == "full" else None,
                        "_enhanced": parsed_doc is not None,  # Mark if enhanced parser was used
                    }
                )

                # If we have rich parsed data, save it
                if parsed_doc:
                    doc_data["parsed_data"] = {
                        "tables": len(parsed_doc.tables),
                        "cross_references": len(parsed_doc.internal_links),
                        "code_blocks": len(parsed_doc.code_blocks),
                        "images": len(getattr(parsed_doc, "images", [])),
                        "quality_scores": {
                            "avg_code_quality": sum(
                                cb.quality_score or 0 for cb in parsed_doc.code_blocks
                            )
                            / len(parsed_doc.code_blocks)
                            if parsed_doc.code_blocks
                            else 0,
                        },
                    }

                processed_docs.append(doc_data)

            # Track categories
            if category not in categories:
                categories[category] = []
            categories[category].append(rel_path)

        except Exception as e:
            logger.warning(f"Failed to process {md_path}: {e}")
            continue

    # AI Enhancement (if enabled and enhance_level >= 2)
    if enhance_with_ai and ai_mode != "none" and processed_docs:
        logger.info("🤖 Enhancing documentation analysis with AI...")
        try:
            processed_docs = _enhance_docs_with_ai(processed_docs, ai_mode)
            logger.info("✅ AI documentation enhancement complete")
        except Exception as e:
            logger.warning(f"⚠️  AI enhancement failed: {e}")

    # Save processed docs to output
    docs_output_dir = output_dir / "documentation"
    docs_output_dir.mkdir(parents=True, exist_ok=True)

    # Copy files organized by category
    for doc in processed_docs:
        try:
            src_path = directory / doc["path"]
            category = doc["category"]
            category_dir = docs_output_dir / category
            category_dir.mkdir(parents=True, exist_ok=True)

            # Copy file to category folder
            dest_path = category_dir / doc["filename"]
            import shutil

            shutil.copy2(src_path, dest_path)
        except Exception as e:
            logger.debug(f"Failed to copy {doc['path']}: {e}")

    # Save documentation index
    index_data = {
        "total_files": len(processed_docs),
        "categories": categories,
        "files": processed_docs,
    }

    index_json = docs_output_dir / "documentation_index.json"
    with open(index_json, "w", encoding="utf-8") as f:
        json.dump(index_data, f, indent=2, default=str)

    # Save extraction summary (tables, cross-refs, etc.)
    enhanced_count = sum(1 for doc in processed_docs if doc.get("_enhanced", False))
    if enhanced_count > 0:
        total_tables = sum(doc.get("parsed_data", {}).get("tables", 0) for doc in processed_docs)
        total_xrefs = sum(
            doc.get("parsed_data", {}).get("cross_references", 0) for doc in processed_docs
        )
        total_code_blocks = sum(
            doc.get("parsed_data", {}).get("code_blocks", 0) for doc in processed_docs
        )

        extraction_summary = {
            "enhanced_files": enhanced_count,
            "total_files": len(processed_docs),
            "extraction_stats": {
                "tables": total_tables,
                "cross_references": total_xrefs,
                "code_blocks": total_code_blocks,
            },
            "parser_version": "unified_v1.0.0",
        }

        summary_json = docs_output_dir / "extraction_summary.json"
        with open(summary_json, "w", encoding="utf-8") as f:
            json.dump(extraction_summary, f, indent=2)

        logger.info(f"📊 Extraction Summary:")
        logger.info(f"   - Enhanced files: {enhanced_count}/{len(processed_docs)}")
        logger.info(f"   - Tables extracted: {total_tables}")
        logger.info(f"   - Cross-references: {total_xrefs}")
        logger.info(f"   - Code blocks: {total_code_blocks}")

    logger.info(
        f"✅ Processed {len(processed_docs)} documentation files in {len(categories)} categories"
    )
    logger.info(f"📁 Saved to: {docs_output_dir}")

    return index_data


def _enhance_docs_with_ai(docs: list[dict], ai_mode: str) -> list[dict]:
    """
    Enhance documentation analysis with AI.

    Args:
        docs: List of processed document dictionaries
        ai_mode: AI mode ('api' or 'local')

    Returns:
        Enhanced document list
    """
    # Try API mode first
    if ai_mode in ("api", "auto"):
        api_key = os.environ.get("ANTHROPIC_API_KEY")
        if api_key:
            return _enhance_docs_api(docs, api_key)

    # Fall back to LOCAL mode
    if ai_mode in ("local", "auto"):
        return _enhance_docs_local(docs)

    return docs


def _enhance_docs_api(docs: list[dict], api_key: str) -> list[dict]:
    """Enhance docs using Claude API."""
    try:
        import anthropic

        client = anthropic.Anthropic(api_key=api_key)

        # Batch documents for efficiency
        batch_size = 10
        for i in range(0, len(docs), batch_size):
            batch = docs[i : i + batch_size]

            # Create prompt for batch
            docs_text = "\n\n".join(
                [
                    f"## {d.get('title', d['filename'])}\nCategory: {d['category']}\nSummary: {d.get('summary', 'N/A')}"
                    for d in batch
                    if d.get("summary")
                ]
            )

            if not docs_text:
                continue

            prompt = f"""Analyze these documentation files and provide:
1. A brief description of what each document covers
2. Key topics/concepts mentioned
3. How they relate to each other

Documents:
{docs_text}

Return JSON with format:
{{"enhancements": [{{"filename": "...", "description": "...", "key_topics": [...], "related_to": [...]}}]}}"""

            response = client.messages.create(
                model="claude-sonnet-4-20250514",
                max_tokens=2000,
                messages=[{"role": "user", "content": prompt}],
            )

            # Parse response and merge enhancements
            try:
                json_match = re.search(r"\{.*\}", response.content[0].text, re.DOTALL)
                if json_match:
                    enhancements = json.loads(json_match.group())
                    for enh in enhancements.get("enhancements", []):
                        for doc in batch:
                            if doc["filename"] == enh.get("filename"):
                                doc["ai_description"] = enh.get("description")
                                doc["ai_topics"] = enh.get("key_topics", [])
                                doc["ai_related"] = enh.get("related_to", [])
            except Exception:
                pass

    except Exception as e:
        logger.warning(f"API enhancement failed: {e}")

    return docs


def _enhance_docs_local(docs: list[dict]) -> list[dict]:
    """Enhance docs using Claude Code CLI (LOCAL mode)."""
    import subprocess
    import tempfile

    # Prepare batch of docs for enhancement
    docs_with_summary = [d for d in docs if d.get("summary")]
    if not docs_with_summary:
        return docs

    docs_text = "\n\n".join(
        [
            f"## {d.get('title', d['filename'])}\nCategory: {d['category']}\nPath: {d['path']}\nSummary: {d.get('summary', 'N/A')}"
            for d in docs_with_summary[:20]  # Limit to 20 docs
        ]
    )

    prompt = f"""Analyze these documentation files from a codebase and provide insights.

For each document, provide:
1. A brief description of what it covers
2. Key topics/concepts
3. Related documents

Documents:
{docs_text}

Output JSON only:
{{"enhancements": [{{"filename": "...", "description": "...", "key_topics": ["..."], "related_to": ["..."]}}]}}"""

    try:
        with tempfile.NamedTemporaryFile(mode="w", suffix=".txt", delete=False) as f:
            f.write(prompt)
            prompt_file = f.name

        result = subprocess.run(
            ["claude", "--dangerously-skip-permissions", "-p", prompt],
            capture_output=True,
            text=True,
            timeout=120,
        )

        os.unlink(prompt_file)

        if result.returncode == 0 and result.stdout:
            json_match = re.search(r"\{.*\}", result.stdout, re.DOTALL)
            if json_match:
                enhancements = json.loads(json_match.group())
                for enh in enhancements.get("enhancements", []):
                    for doc in docs:
                        if doc["filename"] == enh.get("filename"):
                            doc["ai_description"] = enh.get("description")
                            doc["ai_topics"] = enh.get("key_topics", [])
                            doc["ai_related"] = enh.get("related_to", [])

    except Exception as e:
        logger.warning(f"LOCAL enhancement failed: {e}")

    return docs


def analyze_codebase(
    directory: Path,
    output_dir: Path,
    depth: str = "deep",
    languages: list[str] | None = None,
    file_patterns: list[str] | None = None,
    build_api_reference: bool = True,
    extract_comments: bool = True,
    build_dependency_graph: bool = True,
    detect_patterns: bool = True,
    extract_test_examples: bool = True,
    build_how_to_guides: bool = True,
    extract_config_patterns: bool = True,
    extract_docs: bool = True,
    enhance_level: int = 0,
    skill_name: str | None = None,
    skill_description: str | None = None,
    doc_version: str = "",
) -> dict[str, Any]:
    """
    Analyze local codebase and extract code knowledge.

    Args:
        directory: Directory to analyze
        output_dir: Output directory for results
        depth: Analysis depth (surface, deep, full)
        languages: Optional list of languages to analyze
        file_patterns: Optional file patterns to include
        build_api_reference: Generate API reference markdown
        extract_comments: Extract inline comments
        build_dependency_graph: Generate dependency graph and detect circular dependencies
        detect_patterns: Detect design patterns (Singleton, Factory, Observer, etc.)
        extract_test_examples: Extract usage examples from test files
        build_how_to_guides: Build how-to guides from workflow examples (C3.3)
        extract_config_patterns: Extract configuration patterns from config files (C3.4)
        extract_docs: Extract and process markdown documentation files (default: True)
        enhance_level: AI enhancement level (0=off, 1=SKILL.md only, 2=+config+arch+docs, 3=full)
        skill_name: Optional override for skill name (default: directory name)
        skill_description: Optional override for skill description

    Returns:
        Analysis results dictionary
    """
    # Determine AI enhancement settings based on level
    # Level 0: No AI enhancement
    # Level 1: SKILL.md only (handled in main.py)
    # Level 2: Architecture + Config AI enhancement
    # Level 3: Full AI enhancement (patterns, tests, config, architecture)
    enhance_patterns = enhance_level >= 3
    enhance_tests = enhance_level >= 3
    enhance_config = enhance_level >= 2
    enhance_architecture = enhance_level >= 2
    ai_mode = "auto" if enhance_level > 0 else "none"

    if enhance_level > 0:
        level_names = {1: "SKILL.md only", 2: "SKILL.md+Architecture+Config", 3: "full"}
        logger.info(
            f"🤖 AI Enhancement Level: {enhance_level} ({level_names.get(enhance_level, 'unknown')})"
        )
    # Resolve directory to absolute path to avoid relative_to() errors
    directory = Path(directory).resolve()

    logger.info(f"Analyzing codebase: {directory}")
    logger.info(f"Depth: {depth}")

    # Create output directory
    output_dir = Path(output_dir)
    output_dir.mkdir(parents=True, exist_ok=True)

    # Load .gitignore
    gitignore_spec = load_gitignore(directory)

    # Walk directory tree
    logger.info("Scanning directory tree...")
    files = walk_directory(directory, patterns=file_patterns, gitignore_spec=gitignore_spec)

    logger.info(f"Found {len(files)} source files")

    # Filter by language if specified
    if languages:
        language_set = set(languages)
        files = [f for f in files if detect_language(f) in language_set]
        logger.info(f"Filtered to {len(files)} files for languages: {', '.join(languages)}")

    # Initialize code analyzer
    analyzer = CodeAnalyzer(depth=depth)

    # Analyze each file
    results = {"files": []}
    analyzed_count = 0

    for file_path in files:
        try:
            content = file_path.read_text(encoding="utf-8", errors="ignore")
            language = detect_language(file_path)

            if language == "Unknown":
                continue

            # Analyze file
            analysis = analyzer.analyze_file(str(file_path), content, language)

            # Only include files with actual analysis results
            # Check for any meaningful content (classes, functions, imports, nodes, properties, etc.)
            # IMPORTANT: Include files with imports for framework detection (fixes #239)
            has_content = (
                analysis.get("classes")
                or analysis.get("functions")
                or analysis.get("imports")  # Include import-only files (fixes #239)
                or analysis.get("nodes")  # Godot scenes
                or analysis.get("properties")  # Godot resources
                or analysis.get("uniforms")  # Godot shaders
                or analysis.get("signals")  # GDScript signals
                or analysis.get("exports")  # GDScript exports
            )

            if analysis and has_content:
                results["files"].append(
                    {
                        "file": str(file_path.relative_to(directory)),
                        "language": language,
                        **analysis,
                    }
                )
                analyzed_count += 1

                if analyzed_count % 10 == 0:
                    logger.info(f"Analyzed {analyzed_count}/{len(files)} files...")

        except Exception as e:
            logger.warning(f"Error analyzing {file_path}: {e}")
            continue

    logger.info(f"✅ Successfully analyzed {analyzed_count} files")

    # Save results
    output_json = output_dir / "code_analysis.json"
    with open(output_json, "w", encoding="utf-8") as f:
        json.dump(results, f, indent=2)

    logger.info(f"📁 Saved analysis to: {output_json}")

    # Build API reference if requested
    if build_api_reference and results["files"]:
        logger.info("Building API reference documentation...")
        builder = APIReferenceBuilder(results)
        api_output_dir = output_dir / "api_reference"
        generated_files = builder.build_reference(api_output_dir)
        logger.info(f"✅ Generated {len(generated_files)} API reference files")
        logger.info(f"📁 API reference: {api_output_dir}")

    # Build dependency graph if requested (C2.6)
    if build_dependency_graph:
        logger.info("Building dependency graph...")
        dep_analyzer = DependencyAnalyzer()

        # Analyze dependencies for all files
        for file_path in files:
            try:
                content = file_path.read_text(encoding="utf-8", errors="ignore")
                language = detect_language(file_path)

                if language != "Unknown":
                    # Use relative path from directory for better graph readability
                    rel_path = str(file_path.relative_to(directory))
                    dep_analyzer.analyze_file(rel_path, content, language)
            except Exception as e:
                logger.warning(f"Error analyzing dependencies for {file_path}: {e}")
                continue

        # Build the graph
        graph = dep_analyzer.build_graph()

        # Detect circular dependencies
        cycles = dep_analyzer.detect_cycles()
        if cycles:
            logger.warning(f"⚠️  Found {len(cycles)} circular dependencies:")
            for i, cycle in enumerate(cycles[:5], 1):  # Show first 5
                cycle_str = " → ".join(cycle) + f" → {cycle[0]}"
                logger.warning(f"  {i}. {cycle_str}")
            if len(cycles) > 5:
                logger.warning(f"  ... and {len(cycles) - 5} more")
        else:
            logger.info("✅ No circular dependencies found")

        # Save dependency graph data
        dep_output_dir = output_dir / "dependencies"
        dep_output_dir.mkdir(parents=True, exist_ok=True)

        # Export as JSON
        dep_json = dep_output_dir / "dependency_graph.json"
        with open(dep_json, "w", encoding="utf-8") as f:
            json.dump(dep_analyzer.export_json(), f, indent=2)
        logger.info(f"📁 Saved dependency graph: {dep_json}")

        # Export as Mermaid diagram
        mermaid_file = dep_output_dir / "dependency_graph.mmd"
        mermaid_file.write_text(dep_analyzer.export_mermaid())
        logger.info(f"📁 Saved Mermaid diagram: {mermaid_file}")

        # Save statistics
        stats = dep_analyzer.get_statistics()
        stats_file = dep_output_dir / "statistics.json"
        with open(stats_file, "w", encoding="utf-8") as f:
            json.dump(stats, f, indent=2)
        logger.info(
            f"📊 Statistics: {stats['total_files']} files, "
            f"{stats['total_dependencies']} dependencies, "
            f"{stats['circular_dependencies']} cycles"
        )

        # Try to export as DOT (requires pydot)
        try:
            dot_file = dep_output_dir / "dependency_graph.dot"
            dep_analyzer.export_dot(str(dot_file))
        except Exception:
            pass  # pydot not installed, skip DOT export

    # Detect design patterns if requested (C3.1)
    if detect_patterns:
        logger.info("Detecting design patterns...")
        from skill_seekers.cli.pattern_recognizer import PatternRecognizer

        # Step 1: Detect patterns WITHOUT enhancement (collect all first)
        pattern_recognizer = PatternRecognizer(depth=depth, enhance_with_ai=False)
        pattern_results = []

        for file_path in files:
            try:
                content = file_path.read_text(encoding="utf-8", errors="ignore")
                language = detect_language(file_path)

                if language != "Unknown":
                    report = pattern_recognizer.analyze_file(str(file_path), content, language)

                    if report.patterns:
                        pattern_results.append(report.to_dict())
            except Exception as e:
                logger.warning(f"Pattern detection failed for {file_path}: {e}")
                continue

        # Step 2: Enhance ALL patterns at once (batched across all files)
        if enhance_patterns and pattern_results:
            logger.info("🤖 Enhancing patterns with AI (batched)...")
            from skill_seekers.cli.ai_enhancer import PatternEnhancer

            enhancer = PatternEnhancer()

            # Flatten all patterns from all files
            all_patterns = []
            pattern_map = []  # Track (report_idx, pattern_idx) for each pattern

            for report_idx, report in enumerate(pattern_results):
                for pattern_idx, pattern in enumerate(report.get("patterns", [])):
                    all_patterns.append(pattern)
                    pattern_map.append((report_idx, pattern_idx))

            if all_patterns:
                # Enhance all patterns in batches (this is where batching happens!)
                enhanced_patterns = enhancer.enhance_patterns(all_patterns)

                # Map enhanced patterns back to their reports
                for i, (report_idx, pattern_idx) in enumerate(pattern_map):
                    if i < len(enhanced_patterns):
                        pattern_results[report_idx]["patterns"][pattern_idx] = enhanced_patterns[i]

        # Save pattern results with multi-level filtering (Issue #240)
        if pattern_results:
            pattern_output = output_dir / "patterns"
            pattern_output.mkdir(parents=True, exist_ok=True)

            # Import filtering utilities
            from skill_seekers.cli.pattern_recognizer import create_multi_level_report

            # Create multi-level report
            multi_level = create_multi_level_report(pattern_results)
            stats = multi_level["statistics"]

            # Save all patterns (unfiltered)
            all_patterns_json = pattern_output / "all_patterns.json"
            with open(all_patterns_json, "w", encoding="utf-8") as f:
                json.dump(pattern_results, f, indent=2)

            # Save high-confidence patterns (>= 0.70) for detailed analysis
            high_confidence_json = pattern_output / "high_confidence_patterns.json"
            with open(high_confidence_json, "w", encoding="utf-8") as f:
                json.dump(multi_level["high_confidence"], f, indent=2)

            # Save critical patterns (>= 0.80) for ARCHITECTURE.md
            critical_json = pattern_output / "critical_patterns.json"
            with open(critical_json, "w", encoding="utf-8") as f:
                json.dump(multi_level["critical"], f, indent=2)

            # Save summary statistics
            summary_json = pattern_output / "summary.json"
            with open(summary_json, "w", encoding="utf-8") as f:
                json.dump(
                    {
                        "statistics": stats,
                        "thresholds": multi_level["thresholds"],
                        "files_analyzed": len(pattern_results),
                    },
                    f,
                    indent=2,
                )

            # Log results with breakdown by confidence
            logger.info(f"✅ Detected {stats['total']} patterns in {len(pattern_results)} files")
            logger.info(f"   🔴 Critical (≥0.80): {stats['critical_count']} patterns")
            logger.info(f"   🟠 High (≥0.70): {stats['high_confidence_count']} patterns")
            logger.info(f"   🟡 Medium (≥0.60): {stats['medium_count']} patterns")
            logger.info(f"   ⚪ Low (<0.60): {stats['low_count']} patterns")
            logger.info(f"📁 Saved to: {pattern_output}/")
        else:
            logger.info("No design patterns detected")

    # Extract test examples if requested (C3.2)
    if extract_test_examples:
        logger.info("Extracting usage examples from test files...")
        from skill_seekers.cli.test_example_extractor import TestExampleExtractor

        # Create extractor
        test_extractor = TestExampleExtractor(
            min_confidence=0.5,
            max_per_file=10,
            languages=languages,
            enhance_with_ai=enhance_tests,
        )

        # Extract examples from directory
        try:
            example_report = test_extractor.extract_from_directory(directory, recursive=True)

            if example_report.total_examples > 0:
                # Save results
                examples_output = output_dir / "test_examples"
                examples_output.mkdir(parents=True, exist_ok=True)

                # Save as JSON
                examples_json = examples_output / "test_examples.json"
                with open(examples_json, "w", encoding="utf-8") as f:
                    json.dump(example_report.to_dict(), f, indent=2)

                # Save as Markdown
                examples_md = examples_output / "test_examples.md"
                examples_md.write_text(example_report.to_markdown(), encoding="utf-8")

                logger.info(
                    f"✅ Extracted {example_report.total_examples} test examples "
                    f"({example_report.high_value_count} high-value)"
                )
                logger.info(f"📁 Saved to: {examples_output}")
            else:
                logger.info("No test examples extracted")

        except Exception as e:
            logger.warning(f"Test example extraction failed: {e}")
            example_report = None

    # Build how-to guides from workflow examples (C3.3)
    if build_how_to_guides and extract_test_examples:
        logger.info("Building how-to guides from workflow examples...")
        try:
            from skill_seekers.cli.how_to_guide_builder import HowToGuideBuilder

            # Create guide builder (uses same enhance level as test examples)
            guide_builder = HowToGuideBuilder(enhance_with_ai=enhance_tests)

            # Build guides from workflow examples
            tutorials_dir = output_dir / "tutorials"

            # Get workflow examples from the example_report if available
            if (
                "example_report" in locals()
                and example_report
                and example_report.total_examples > 0
            ):
                # Convert example_report to list of dicts for processing
                examples_list = example_report.to_dict().get("examples", [])

                guide_collection = guide_builder.build_guides_from_examples(
                    examples_list,
                    grouping_strategy="ai-tutorial-group",
                    output_dir=tutorials_dir,
                    enhance_with_ai=enhance_tests,
                    ai_mode=ai_mode,
                )

                if guide_collection and guide_collection.total_guides > 0:
                    # Save collection summary
                    collection_json = tutorials_dir / "guide_collection.json"
                    with open(collection_json, "w", encoding="utf-8") as f:
                        json.dump(guide_collection.to_dict(), f, indent=2)

                    logger.info(f"✅ Built {guide_collection.total_guides} how-to guides")
                    logger.info(f"📁 Saved to: {tutorials_dir}")
                else:
                    logger.info("No how-to guides generated (insufficient workflow examples)")
            else:
                logger.info("No workflow examples available for guide generation")

        except Exception as e:
            logger.warning(f"How-to guide building failed: {e}")

    # Extract configuration patterns (C3.4)
    if extract_config_patterns:
        logger.info("Extracting configuration patterns...")
        try:
            config_extractor = ConfigExtractor()

            # Extract config patterns from directory
            extraction_result = config_extractor.extract_from_directory(directory)

            if extraction_result.config_files:
                # Convert to dict for enhancement
                result_dict = config_extractor.to_dict(extraction_result)

                # AI Enhancement (if enabled - level 2+)
                if enhance_config and ai_mode != "none":
                    try:
                        from skill_seekers.cli.config_enhancer import ConfigEnhancer

                        logger.info(f"🤖 Enhancing config analysis with AI (mode: {ai_mode})...")
                        enhancer = ConfigEnhancer(mode=ai_mode)
                        result_dict = enhancer.enhance_config_result(result_dict)
                        logger.info("✅ AI enhancement complete")
                    except Exception as e:
                        logger.warning(f"⚠️  Config AI enhancement failed: {e}")

                # Save results
                config_output = output_dir / "config_patterns"
                config_output.mkdir(parents=True, exist_ok=True)

                # Save as JSON
                config_json = config_output / "config_patterns.json"
                with open(config_json, "w", encoding="utf-8") as f:
                    json.dump(result_dict, f, indent=2)

                # Save as Markdown (basic - AI enhancements in JSON only for now)
                config_md = config_output / "config_patterns.md"
                config_md.write_text(extraction_result.to_markdown(), encoding="utf-8")

                # Count total settings across all files
                total_settings = sum(len(cf.settings) for cf in extraction_result.config_files)
                total_patterns = sum(len(cf.patterns) for cf in extraction_result.config_files)

                logger.info(
                    f"✅ Extracted {len(extraction_result.config_files)} config files "
                    f"with {total_settings} settings and {total_patterns} detected patterns"
                )

                if "ai_enhancements" in result_dict:
                    insights = result_dict["ai_enhancements"].get("overall_insights", {})
                    if insights.get("security_issues_found"):
                        logger.info(
                            f"🔐 Security issues found: {insights['security_issues_found']}"
                        )

                logger.info(f"📁 Saved to: {config_output}")
            else:
                logger.info("No configuration files found")

        except Exception as e:
            logger.warning(f"Config pattern extraction failed: {e}")

    # Detect architectural patterns (C3.7)
    # Always run this - it provides high-level overview
    logger.info("Analyzing architectural patterns...")
    from skill_seekers.cli.architectural_pattern_detector import ArchitecturalPatternDetector

    arch_detector = ArchitecturalPatternDetector(enhance_with_ai=enhance_architecture)
    arch_report = arch_detector.analyze(directory, results["files"])

    # Save architecture analysis if we have patterns OR frameworks (fixes #239)
    if arch_report.patterns or arch_report.frameworks_detected:
        arch_output = output_dir / "architecture"
        arch_output.mkdir(parents=True, exist_ok=True)

        # Save as JSON
        arch_json = arch_output / "architectural_patterns.json"
        with open(arch_json, "w", encoding="utf-8") as f:
            json.dump(arch_report.to_dict(), f, indent=2)

        if arch_report.patterns:
            logger.info(f"🏗️  Detected {len(arch_report.patterns)} architectural patterns")
            for pattern in arch_report.patterns:
                logger.info(f"   - {pattern.pattern_name} (confidence: {pattern.confidence:.2f})")
        else:
            logger.info("No clear architectural patterns detected")

        if arch_report.frameworks_detected:
            logger.info(f"📦 Detected {len(arch_report.frameworks_detected)} frameworks")

        logger.info(f"📁 Saved to: {arch_json}")
    else:
        logger.info("No architectural patterns or frameworks detected")

    # Analyze signal flow patterns (C3.10) - Godot projects only
    signal_analysis = None
    has_godot_files = any(
        f.get("language") in ("GDScript", "GodotScene", "GodotResource", "GodotShader")
        for f in results.get("files", [])
    )

    if has_godot_files:
        logger.info("Analyzing signal flow patterns (Godot)...")
        try:
            signal_analyzer = SignalFlowAnalyzer(results)
            signal_output = signal_analyzer.save_analysis(output_dir, ai_mode)
            signal_analysis = signal_analyzer.analyze()

            stats = signal_analysis["statistics"]
            logger.info(f"📡 Signal Analysis Complete:")
            logger.info(f"   - {stats['total_signals']} signal declarations")
            logger.info(f"   - {stats['total_connections']} signal connections")
            logger.info(f"   - {stats['total_emissions']} signal emissions")
            logger.info(f"   - {len(signal_analysis['patterns'])} patterns detected")
            logger.info(f"📁 Saved to: {signal_output}")
        except Exception as e:
            logger.warning(f"Signal flow analysis failed: {e}")

    # Extract markdown documentation (C3.9)
    docs_data = None
    if extract_docs:
        logger.info("Extracting project documentation...")
        try:
            # Determine AI enhancement for docs (level 2+)
            enhance_docs_ai = enhance_level >= 2
            docs_data = process_markdown_docs(
                directory=directory,
                output_dir=output_dir,
                depth=depth,
                gitignore_spec=gitignore_spec,
                enhance_with_ai=enhance_docs_ai,
                ai_mode=ai_mode,
            )

            if docs_data and docs_data.get("total_files", 0) > 0:
                logger.info(
                    f"✅ Extracted {docs_data['total_files']} documentation files "
                    f"in {len(docs_data.get('categories', {}))} categories"
                )
            else:
                logger.info("No markdown documentation files found")
        except Exception as e:
            logger.warning(f"Documentation extraction failed: {e}")
            docs_data = None

    # Generate SKILL.md and references/ directory
    logger.info("Generating SKILL.md and references...")
    _generate_skill_md(
        output_dir=output_dir,
        directory=directory,
        results=results,
        depth=depth,
        build_api_reference=build_api_reference,
        build_dependency_graph=build_dependency_graph,
        detect_patterns=detect_patterns,
        extract_test_examples=extract_test_examples,
        extract_config_patterns=extract_config_patterns,
        extract_docs=extract_docs,
        docs_data=docs_data,
        skill_name=skill_name,
        skill_description=skill_description,
        doc_version=doc_version,
    )

    return results


def _generate_skill_md(
    output_dir: Path,
    directory: Path,
    results: dict[str, Any],
    depth: str,
    build_api_reference: bool,
    build_dependency_graph: bool,
    detect_patterns: bool,
    extract_test_examples: bool,
    extract_config_patterns: bool,
    extract_docs: bool = True,
    docs_data: dict[str, Any] | None = None,
    skill_name: str | None = None,
    skill_description: str | None = None,
    doc_version: str = "",
):
    """
    Generate rich SKILL.md from codebase analysis results.

    Creates a 300+ line skill file with:
    - Front matter (name, description)
    - Repository info (path, languages, file count)
    - When to Use section
    - Quick Reference (patterns, languages, stats)
    - Code Examples (from test files)
    - API Reference (from code analysis)
    - Architecture Overview
    - Configuration Patterns
    - Available References
    """
    repo_name = directory.name

    # Generate skill name (lowercase, hyphens only, max 64 chars)
    # Use CLI override if provided, otherwise derive from directory name
    if skill_name:
        skill_name = skill_name.lower().replace("_", "-").replace(" ", "-")[:64]
    else:
        skill_name = repo_name.lower().replace("_", "-").replace(" ", "-")[:64]

    # Generate description (use CLI override if provided)
    description = skill_description or f"Local codebase analysis for {repo_name}"

    # Count files by language
    language_stats = _get_language_stats(results.get("files", []))
    total_files = len(results.get("files", []))

    # Start building content
    skill_content = f"""---
name: {skill_name}
description: {description}
doc_version: {doc_version}
---

# {repo_name} Codebase

## Description

Local codebase analysis and documentation generated from code analysis.

**Path:** `{directory}`
**Files Analyzed:** {total_files}
**Languages:** {", ".join(language_stats.keys())}
**Analysis Depth:** {depth}

## When to Use This Skill

Use this skill when you need to:
- Understand the codebase architecture and design patterns
- Find implementation examples and usage patterns
- Review API documentation extracted from code
- Check configuration patterns and best practices
- Explore test examples and real-world usage
- Navigate the codebase structure efficiently

## ⚡ Quick Reference

### Codebase Statistics

"""

    # Language breakdown
    skill_content += "**Languages:**\n"
    for lang, count in sorted(language_stats.items(), key=lambda x: x[1], reverse=True):
        percentage = (count / total_files * 100) if total_files > 0 else 0
        skill_content += f"- **{lang}**: {count} files ({percentage:.1f}%)\n"
    skill_content += "\n"

    # Analysis features performed
    skill_content += "**Analysis Performed:**\n"
    if build_api_reference:
        skill_content += "- ✅ API Reference (C2.5)\n"
    if build_dependency_graph:
        skill_content += "- ✅ Dependency Graph (C2.6)\n"
    if detect_patterns:
        skill_content += "- ✅ Design Patterns (C3.1)\n"
    if extract_test_examples:
        skill_content += "- ✅ Test Examples (C3.2)\n"
    if extract_config_patterns:
        skill_content += "- ✅ Configuration Patterns (C3.4)\n"
    skill_content += "- ✅ Architectural Analysis (C3.7)\n"
    if extract_docs:
        skill_content += "- ✅ Project Documentation (C3.9)\n"

    # Check if signal flow analysis was performed
    has_signal_analysis = (output_dir / "signals" / "signal_flow.json").exists()
    if has_signal_analysis:
        skill_content += "- ✅ Signal Flow Analysis (C3.10)\n"

    skill_content += "\n"

    # Add design patterns if available
    if detect_patterns:
        patterns_content = _format_patterns_section(output_dir)
        if patterns_content:
            skill_content += patterns_content

    # Add code examples if available
    if extract_test_examples:
        examples_content = _format_examples_section(output_dir)
        if examples_content:
            skill_content += examples_content

    # Add API reference if available
    if build_api_reference:
        api_content = _format_api_section(output_dir)
        if api_content:
            skill_content += api_content

    # Add architecture if available
    arch_content = _format_architecture_section(output_dir)
    if arch_content:
        skill_content += arch_content

    # Add configuration patterns if available
    if extract_config_patterns:
        config_content = _format_config_section(output_dir)
        if config_content:
            skill_content += config_content

    # Add signal flow analysis if available (C3.10)
    signal_content = _format_signal_flow_section(output_dir, results)
    if signal_content:
        skill_content += signal_content

    # Add project documentation if available
    if extract_docs and docs_data:
        docs_content = _format_documentation_section(output_dir, docs_data)
        if docs_content:
            skill_content += docs_content

    # Available references
    skill_content += "## 📚 Available References\n\n"
    skill_content += "This skill includes detailed reference documentation:\n\n"

    refs_added = False
    if build_api_reference and (output_dir / "api_reference").exists():
        skill_content += (
            "- **API Reference**: `references/api_reference/` - Complete API documentation\n"
        )
        refs_added = True
    if build_dependency_graph and (output_dir / "dependencies").exists():
        skill_content += (
            "- **Dependencies**: `references/dependencies/` - Dependency graph and analysis\n"
        )
        refs_added = True
    if detect_patterns and (output_dir / "patterns").exists():
        skill_content += "- **Patterns**: `references/patterns/` - Detected design patterns\n"
        refs_added = True
    if extract_test_examples and (output_dir / "test_examples").exists():
        skill_content += "- **Examples**: `references/test_examples/` - Usage examples from tests\n"
        refs_added = True
    if extract_config_patterns and (output_dir / "config_patterns").exists():
        skill_content += (
            "- **Configuration**: `references/config_patterns/` - Configuration patterns\n"
        )
        refs_added = True
    if (output_dir / "architecture").exists():
        skill_content += "- **Architecture**: `references/architecture/` - Architectural patterns\n"
        refs_added = True
    if extract_docs and (output_dir / "documentation").exists():
        skill_content += (
            "- **Documentation**: `references/documentation/` - Project documentation\n"
        )
        refs_added = True

    if not refs_added:
        skill_content += "No additional references generated (analysis features disabled).\n"

    skill_content += "\n"

    # Footer
    skill_content += "---\n\n"
    skill_content += "**Generated by Skill Seeker** | Codebase Analyzer with C3.x Analysis\n"

    # Write SKILL.md
    skill_path = output_dir / "SKILL.md"
    skill_path.write_text(skill_content, encoding="utf-8")

    line_count = len(skill_content.split("\n"))
    logger.info(f"✅ Generated SKILL.md: {skill_path} ({line_count} lines)")

    # Generate references/ directory structure
    _generate_references(output_dir)


def _get_language_stats(files: list[dict]) -> dict[str, int]:
    """Count files by language from analysis results."""
    stats = {}
    for file_data in files:
        # files is a list of dicts with 'language' key
        lang = file_data.get("language", "Unknown")
        if lang != "Unknown":
            stats[lang] = stats.get(lang, 0) + 1
    return stats


def _format_patterns_section(output_dir: Path) -> str:
    """Format design patterns section from patterns/detected_patterns.json."""
    patterns_file = output_dir / "patterns" / "detected_patterns.json"
    if not patterns_file.exists():
        return ""

    try:
        with open(patterns_file, encoding="utf-8") as f:
            patterns_data = json.load(f)
    except Exception:
        return ""

    if not patterns_data:
        return ""

    # Count patterns by type (deduplicate by class, keep highest confidence)
    pattern_counts = {}
    by_class = {}

    for pattern_file in patterns_data:
        for pattern in pattern_file.get("patterns", []):
            ptype = pattern.get("pattern_type", "Unknown")
            cls = pattern.get("class_name", "")
            confidence = pattern.get("confidence", 0)

            # Skip low confidence
            if confidence < 0.7:
                continue

            # Deduplicate by class
            key = f"{cls}:{ptype}"
            if key not in by_class or by_class[key]["confidence"] < confidence:
                by_class[key] = pattern

            # Count by type
            pattern_counts[ptype] = pattern_counts.get(ptype, 0) + 1

    if not pattern_counts:
        return ""

    content = "### 🎨 Design Patterns Detected\n\n"
    content += "*From C3.1 codebase analysis (confidence > 0.7)*\n\n"

    # Top 5 pattern types
    for ptype, count in sorted(pattern_counts.items(), key=lambda x: x[1], reverse=True)[:5]:
        content += f"- **{ptype}**: {count} instances\n"

    content += f"\n*Total: {len(by_class)} high-confidence patterns*\n\n"
    content += "*See `references/patterns/` for complete pattern analysis*\n\n"
    return content


def _format_examples_section(output_dir: Path) -> str:
    """Format code examples section from test_examples/test_examples.json."""
    examples_file = output_dir / "test_examples" / "test_examples.json"
    if not examples_file.exists():
        return ""

    try:
        with open(examples_file, encoding="utf-8") as f:
            examples_data = json.load(f)
    except Exception:
        return ""

    examples = examples_data.get("examples", [])
    if not examples:
        return ""

    # Filter high-value examples (complexity > 0.7)
    high_value = [ex for ex in examples if ex.get("complexity_score", 0) > 0.7]

    if not high_value:
        # If no high complexity, take any examples
        high_value = examples[:10]

    if not high_value:
        return ""

    content = "## 📝 Code Examples\n\n"
    content += "*High-quality examples extracted from test files (C3.2)*\n\n"

    # Top 10 examples
    for ex in sorted(high_value, key=lambda x: x.get("complexity_score", 0), reverse=True)[:10]:
        desc = ex.get("description", "Example")
        lang = ex.get("language", "python").lower()
        code = ex.get("code", "")
        complexity = ex.get("complexity_score", 0)

        content += f"**{desc}** (complexity: {complexity:.2f})\n\n"
        content += f"```{lang}\n{code}\n```\n\n"

    content += "*See `references/test_examples/` for all extracted examples*\n\n"
    return content


def _format_api_section(output_dir: Path) -> str:
    """Format API reference section."""
    api_dir = output_dir / "api_reference"
    if not api_dir.exists():
        return ""

    api_md = api_dir / "api_reference.md"
    if not api_md.exists():
        return ""

    try:
        api_content = api_md.read_text(encoding="utf-8")
    except Exception:
        return ""

    # Extract first section (up to 500 chars)
    preview = api_content[:500]
    if len(api_content) > 500:
        preview += "..."

    content = "## 🔧 API Reference\n\n"
    content += "*Extracted from codebase analysis (C2.5)*\n\n"
    content += preview + "\n\n"
    content += "*See `references/api_reference/` for complete API documentation*\n\n"
    return content


def _format_architecture_section(output_dir: Path) -> str:
    """Format architecture section from architecture/architectural_patterns.json."""
    arch_file = output_dir / "architecture" / "architectural_patterns.json"
    if not arch_file.exists():
        return ""

    try:
        with open(arch_file, encoding="utf-8") as f:
            arch_data = json.load(f)
    except Exception:
        return ""

    patterns = arch_data.get("patterns", [])
    if not patterns:
        return ""

    content = "## 🏗️ Architecture Overview\n\n"
    content += "*From C3.7 architectural analysis*\n\n"

    content += "**Detected Architectural Patterns:**\n\n"
    for pattern in patterns[:5]:
        name = pattern.get("pattern_name", "Unknown")
        confidence = pattern.get("confidence", 0)
        indicators = pattern.get("indicators", [])

        content += f"- **{name}** (confidence: {confidence:.2f})\n"
        if indicators:
            content += f"  - Indicators: {', '.join(indicators[:3])}\n"

    content += f"\n*Total: {len(patterns)} architectural patterns detected*\n\n"
    content += "*See `references/architecture/` for complete architectural analysis*\n\n"
    return content


def _format_config_section(output_dir: Path) -> str:
    """Format configuration patterns section."""
    config_file = output_dir / "config_patterns" / "config_patterns.json"
    if not config_file.exists():
        return ""

    try:
        with open(config_file, encoding="utf-8") as f:
            config_data = json.load(f)
    except Exception:
        return ""

    config_files = config_data.get("config_files", [])
    if not config_files:
        return ""

    total_settings = sum(len(cf.get("settings", [])) for cf in config_files)
    total_patterns = sum(len(cf.get("patterns", [])) for cf in config_files)

    content = "## ⚙️ Configuration Patterns\n\n"
    content += "*From C3.4 configuration analysis*\n\n"
    content += f"**Configuration Files Analyzed:** {len(config_files)}\n"
    content += f"**Total Settings:** {total_settings}\n"
    content += f"**Patterns Detected:** {total_patterns}\n\n"

    # List config file types found
    file_types = {}
    for cf in config_files:
        ctype = cf.get("config_type", "unknown")
        file_types[ctype] = file_types.get(ctype, 0) + 1

    if file_types:
        content += "**Configuration Types:**\n"
        for ctype, count in sorted(file_types.items(), key=lambda x: x[1], reverse=True):
            content += f"- {ctype}: {count} files\n"
        content += "\n"

    content += "*See `references/config_patterns/` for detailed configuration analysis*\n\n"
    return content


def _format_signal_flow_section(output_dir: Path, results: dict[str, Any]) -> str:
    """Format signal flow analysis section (C3.10 - Godot projects)."""
    signal_file = output_dir / "signals" / "signal_flow.json"
    if not signal_file.exists():
        return ""

    try:
        with open(signal_file, encoding="utf-8") as f:
            signal_data = json.load(f)
    except Exception:
        return ""

    stats = signal_data.get("statistics", {})
    patterns = signal_data.get("patterns", {})

    # Only show section if there are signals
    if stats.get("total_signals", 0) == 0:
        return ""

    content = "## 📡 Signal Flow Analysis\n\n"
    content += "*From C3.10 signal flow analysis (Godot Event System)*\n\n"

    # Statistics
    content += "**Signal Statistics:**\n"
    content += f"- **Total Signals**: {stats.get('total_signals', 0)}\n"
    content += f"- **Signal Connections**: {stats.get('total_connections', 0)}\n"
    content += f"- **Signal Emissions**: {stats.get('total_emissions', 0)}\n"
    content += f"- **Signal Density**: {stats.get('signal_density', 0):.2f} signals per file\n\n"

    # Most connected signals
    most_connected = stats.get("most_connected_signals", [])
    if most_connected:
        content += "**Most Connected Signals:**\n"
        for sig in most_connected[:5]:
            content += f"- `{sig['signal']}`: {sig['connection_count']} connections\n"
        content += "\n"

    # Detected patterns
    if patterns:
        content += "**Detected Event Patterns:**\n"
        for pattern_name, pattern_data in patterns.items():
            if pattern_data.get("detected"):
                confidence = pattern_data.get("confidence", 0)
                description = pattern_data.get("description", "")
                content += f"- **{pattern_name}** (confidence: {confidence:.2f})\n"
                content += f"  - {description}\n"
        content += "\n"

    # Test framework detection
    test_files = [f for f in results.get("files", []) if f.get("test_framework")]

    if test_files:
        frameworks = {}
        total_tests = 0
        for f in test_files:
            fw = f.get("test_framework")
            test_count = len(f.get("test_functions", []))
            frameworks[fw] = frameworks.get(fw, 0) + 1
            total_tests += test_count

        content += "**Test Framework Detection:**\n"
        for fw, count in frameworks.items():
            content += f"- **{fw}**: {count} test files, {total_tests} test cases\n"
        content += "\n"

    content += "*See `references/signals/` for complete signal flow analysis*\n\n"
    return content


def _format_documentation_section(_output_dir: Path, docs_data: dict[str, Any]) -> str:
    """Format project documentation section from extracted markdown files.

    Note: output_dir parameter is unused but kept for consistency with other _format_* functions.
    Documentation data is provided via docs_data parameter.
    """
    if not docs_data or docs_data.get("total_files", 0) == 0:
        return ""

    categories = docs_data.get("categories", {})
    files = docs_data.get("files", [])

    content = "## 📖 Project Documentation\n\n"
    content += "*Extracted from markdown files in the project (C3.9)*\n\n"
    content += f"**Total Documentation Files:** {docs_data['total_files']}\n"
    content += f"**Categories:** {len(categories)}\n\n"

    # List documents by category (most important first)
    priority_order = [
        "overview",
        "architecture",
        "guides",
        "workflows",
        "features",
        "api",
        "examples",
    ]

    # Sort categories by priority
    sorted_categories = []
    for cat in priority_order:
        if cat in categories:
            sorted_categories.append(cat)
    for cat in sorted(categories.keys()):
        if cat not in sorted_categories:
            sorted_categories.append(cat)

    for category in sorted_categories[:6]:  # Limit to 6 categories in SKILL.md
        cat_files = categories[category]
        content += f"### {category.title()}\n\n"

        # Get file details for this category
        cat_docs = [f for f in files if f.get("category") == category]

        for doc in cat_docs[:5]:  # Limit to 5 docs per category
            title = doc.get("title") or doc.get("filename", "Unknown")
            path = doc.get("path", "")

            # Add summary if available (deep/full depth)
            if doc.get("ai_description"):
                content += f"- **{title}**: {doc['ai_description']}\n"
            elif doc.get("summary"):
                # Extract first sentence from summary
                summary = doc["summary"].split("\n")[0]
                if len(summary) > 100:
                    summary = summary[:100] + "..."
                content += f"- **{title}**: {summary}\n"
            else:
                content += f"- **{title}** (`{path}`)\n"

        if len(cat_files) > 5:
            content += f"- *...and {len(cat_files) - 5} more*\n"

        content += "\n"

    # AI-enhanced topics if available
    all_topics = []
    for doc in files:
        all_topics.extend(doc.get("ai_topics", []))

    if all_topics:
        # Deduplicate and count
        from collections import Counter

        topic_counts = Counter(all_topics)
        top_topics = [t for t, _ in topic_counts.most_common(10)]
        content += f"**Key Topics:** {', '.join(top_topics)}\n\n"

    content += "*See `references/documentation/` for all project documentation*\n\n"
    return content


def _generate_references(output_dir: Path):
    """
    Generate references/ directory structure by symlinking analysis output.

    Creates a clean references/ directory that links to all analysis outputs.
    """
    references_dir = output_dir / "references"
    references_dir.mkdir(exist_ok=True)

    # Map analysis directories to reference names
    mappings = {
        "api_reference": "api_reference",
        "dependencies": "dependencies",
        "patterns": "patterns",
        "test_examples": "test_examples",
        "tutorials": "tutorials",
        "config_patterns": "config_patterns",
        "architecture": "architecture",
        "documentation": "documentation",
    }

    for source, target in mappings.items():
        source_dir = output_dir / source
        target_dir = references_dir / target

        if source_dir.exists() and source_dir.is_dir():
            # Copy directory to references/ (not symlink, for portability)
            import shutil

            if target_dir.exists():
                shutil.rmtree(target_dir)

            shutil.copytree(source_dir, target_dir)
            logger.debug(f"Copied {source} → references/{target}")

            # Clean up source directory to avoid duplication (Issue #279)
            # SKILL.md only references references/{target}, so source dir is redundant
            shutil.rmtree(source_dir)
            logger.debug(f"Cleaned up duplicate {source}/ directory")

    logger.info(f"✅ Generated references directory: {references_dir}")


def _check_deprecated_flags(args):
    """Check for deprecated flags and show migration warnings."""
    warnings = []

    # Deprecated: --depth
    if hasattr(args, "depth") and args.depth:
        preset_map = {
            "surface": "quick",
            "deep": "standard",
            "full": "comprehensive",
        }
        suggested_preset = preset_map.get(args.depth, "standard")
        warnings.append(
            f"⚠️  DEPRECATED: --depth {args.depth} → use --preset {suggested_preset} instead"
        )

    # Deprecated: --ai-mode
    if hasattr(args, "ai_mode") and args.ai_mode and args.ai_mode != "auto":
        if args.ai_mode == "api":
            warnings.append(
                "⚠️  DEPRECATED: --ai-mode api → use --enhance-level with ANTHROPIC_API_KEY set instead"
            )
        elif args.ai_mode == "local":
            warnings.append(
                "⚠️  DEPRECATED: --ai-mode local → use --enhance-level without API key instead"
            )
        elif args.ai_mode == "none":
            warnings.append("⚠️  DEPRECATED: --ai-mode none → use --enhance-level 0 instead")

    # Deprecated: --quick flag
    if hasattr(args, "quick") and args.quick:
        warnings.append("⚠️  DEPRECATED: --quick → use --preset quick instead")

    # Deprecated: --comprehensive flag
    if hasattr(args, "comprehensive") and args.comprehensive:
        warnings.append("⚠️  DEPRECATED: --comprehensive → use --preset comprehensive instead")

    # Show warnings if any found
    if warnings:
        print("\n" + "=" * 70)
        for warning in warnings:
            print(warning)
        print("\n💡 MIGRATION TIP:")
        print("   --preset quick          (1-2 min, basic features)")
        print("   --preset standard       (5-10 min, core features, DEFAULT)")
        print("   --preset comprehensive  (20-60 min, all features + AI)")
        print("   --enhance-level 0-3     (granular AI enhancement control)")
        print("\n⚠️  Deprecated flags will be removed in v4.0.0")
        print("=" * 70 + "\n")


def main():
    """Command-line interface for codebase analysis."""
    from skill_seekers.cli.arguments.analyze import add_analyze_arguments

    parser = argparse.ArgumentParser(
        description="Analyze local codebases and extract code knowledge",
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog="""
Examples:
  # Analyze current directory
  codebase-scraper --directory . --output output/codebase/

  # Deep analysis with API reference and dependency graph
  codebase-scraper --directory /path/to/repo --depth deep --build-api-reference --build-dependency-graph

  # Analyze only Python and JavaScript
  codebase-scraper --directory . --languages Python,JavaScript

  # Use file patterns
  codebase-scraper --directory . --file-patterns "*.py,src/**/*.js"

  # Full analysis with all features (default)
  codebase-scraper --directory . --depth deep

  # Surface analysis (fast, skip all analysis features)
  codebase-scraper --directory . --depth surface --skip-api-reference --skip-dependency-graph --skip-patterns --skip-test-examples

  # Skip specific features
  codebase-scraper --directory . --skip-patterns --skip-test-examples
""",
    )

    # Register all args from the shared definitions module
    add_analyze_arguments(parser)

    # Extra legacy arg only used by standalone CLI (not in arguments/analyze.py)
    parser.add_argument(
        "--ai-mode",
        choices=["auto", "api", "local", "none"],
        default="auto",
        help=(
            "AI enhancement mode for how-to guides: "
            "auto (auto-detect: API if ANTHROPIC_API_KEY set, else LOCAL), "
            "api (Claude API, requires ANTHROPIC_API_KEY), "
            "local (Claude Code Max, FREE, no API key), "
            "none (disable AI enhancement). "
            "💡 TIP: Use --enhance flag instead for simpler UX!"
        ),
    )

    # Check for deprecated flags
    deprecated_flags = {
        "--build-api-reference": "--skip-api-reference",
        "--build-dependency-graph": "--skip-dependency-graph",
        "--detect-patterns": "--skip-patterns",
        "--extract-test-examples": "--skip-test-examples",
        "--build-how-to-guides": "--skip-how-to-guides",
        "--extract-config-patterns": "--skip-config-patterns",
    }

    for old_flag, new_flag in deprecated_flags.items():
        if old_flag in sys.argv:
            logger.warning(
                f"⚠️  DEPRECATED: {old_flag} is deprecated. "
                f"All features are now enabled by default. "
                f"Use {new_flag} to disable this feature."
            )

    # Handle --preset-list flag BEFORE parse_args() to avoid required --directory validation
    if "--preset-list" in sys.argv:
        from skill_seekers.cli.presets import PresetManager

        print(PresetManager.format_preset_help())
        return 0

    args = parser.parse_args()

    # Check for deprecated flags and show warnings
    _check_deprecated_flags(args)

    # Handle presets using formal preset system
    preset_name = None
    if hasattr(args, "preset") and args.preset:
        # New --preset flag (recommended)
        preset_name = args.preset
    elif hasattr(args, "quick") and args.quick:
        # Legacy --quick flag (backward compatibility)
        preset_name = "quick"
    elif hasattr(args, "comprehensive") and args.comprehensive:
        # Legacy --comprehensive flag (backward compatibility)
        preset_name = "comprehensive"
    else:
        # Default preset if none specified
        preset_name = "standard"

    # Apply preset using PresetManager
    if preset_name:
        from skill_seekers.cli.presets import PresetManager

        try:
            preset_args = PresetManager.apply_preset(preset_name, vars(args))
            # Update args with preset values
            for key, value in preset_args.items():
                setattr(args, key, value)

            preset = PresetManager.get_preset(preset_name)
            logger.info(f"{preset.icon} {preset.name} analysis mode: {preset.description}")
        except ValueError as e:
            logger.error(f"❌ {e}")
            return 1

    # Apply default depth if not set by preset or CLI
    if args.depth is None:
        args.depth = "deep"  # Default depth

    setup_logging(verbose=args.verbose, quiet=getattr(args, "quiet", False))

    # Handle --dry-run
    if getattr(args, "dry_run", False):
        directory = Path(args.directory)
        print(f"\n{'=' * 60}")
        print(f"DRY RUN: Codebase Analysis")
        print(f"{'=' * 60}")
        print(f"Directory:    {directory.resolve()}")
        print(f"Output:       {args.output}")
        print(f"Preset:       {preset_name}")
        print(f"Depth:        {args.depth or 'deep (default)'}")
        print(f"Name:         {getattr(args, 'name', None) or directory.name}")
        print(f"Enhance:      level {args.enhance_level}")
        print(f"Skip flags:   ", end="")
        skips = []
        for flag in [
            "skip_api_reference",
            "skip_dependency_graph",
            "skip_patterns",
            "skip_test_examples",
            "skip_how_to_guides",
            "skip_config_patterns",
            "skip_docs",
        ]:
            if getattr(args, flag, False):
                skips.append(f"--{flag.replace('_', '-')}")
        print(", ".join(skips) if skips else "(none)")
        print(f"\n✅ Dry run complete")
        return 0

    # Validate directory
    directory = Path(args.directory)
    if not directory.exists():
        logger.error(f"Directory not found: {directory}")
        return 1

    if not directory.is_dir():
        logger.error(f"Not a directory: {directory}")
        return 1

    # Parse languages
    languages = None
    if args.languages:
        languages = [lang.strip() for lang in args.languages.split(",")]

    # Parse file patterns
    file_patterns = None
    if args.file_patterns:
        file_patterns = [p.strip() for p in args.file_patterns.split(",")]

    # Analyze codebase
    try:
        results = analyze_codebase(
            directory=directory,
            output_dir=Path(args.output),
            depth=args.depth,
            languages=languages,
            file_patterns=file_patterns,
            build_api_reference=not args.skip_api_reference,
            extract_comments=not args.no_comments,
            build_dependency_graph=not args.skip_dependency_graph,
            detect_patterns=not args.skip_patterns,
            extract_test_examples=not args.skip_test_examples,
            build_how_to_guides=not args.skip_how_to_guides,
            extract_config_patterns=not args.skip_config_patterns,
            extract_docs=not args.skip_docs,
            enhance_level=args.enhance_level,  # AI enhancement level (0-3)
            skill_name=getattr(args, "name", None),
            skill_description=getattr(args, "description", None),
            doc_version=getattr(args, "doc_version", ""),
        )

        # ============================================================
        # WORKFLOW SYSTEM INTEGRATION (Phase 2)
        # ============================================================
        from skill_seekers.cli.workflow_runner import run_workflows

        workflow_executed, workflow_names = run_workflows(args)

        # Print summary
        print(f"\n{'=' * 60}")
        print("CODEBASE ANALYSIS COMPLETE")
        if workflow_executed:
            print(f" + {len(workflow_names)} ENHANCEMENT WORKFLOW(S) EXECUTED")
        print(f"{'=' * 60}")
        print(f"Files analyzed: {len(results['files'])}")
        print(f"Output directory: {args.output}")
        if not args.skip_api_reference:
            print(f"API reference: {Path(args.output) / 'api_reference'}")
        if workflow_executed:
            print(f"Workflows applied: {', '.join(workflow_names)}")
        print(f"{'=' * 60}\n")

        return 0

    except KeyboardInterrupt:
        logger.error("\nAnalysis interrupted by user")
        return 130
    except Exception as e:
        logger.error(f"Analysis failed: {e}")
        import traceback

        traceback.print_exc()
        return 1


if __name__ == "__main__":
    sys.exit(main())