claude-mpm 4.1.6__py3-none-any.whl → 4.24.0__py3-none-any.whl

claude_mpm/services/project/project_organizer.py

@@ -0,0 +1,1005 @@
+"""
+Project Organizer Service for Claude MPM Project Initialization
+===============================================================
+
+This service verifies and creates standard project directory structures
+for optimal Claude Code and Claude MPM usage.
+
+Key Features:
+- Standard directory structure verification
+- Missing directory creation with proper permissions
+- .gitignore configuration and updates
+- Temporary directory management
+- Project structure documentation generation
+
+Author: Claude MPM Development Team
+Created: 2025-01-26
+"""
+
+from pathlib import Path
+from typing import ClassVar, Dict, List, Optional, Tuple
+
+from rich.console import Console
+
+from claude_mpm.core.logging_utils import get_logger
+
+logger = get_logger(__name__)
+console = Console()
+
+
+class ProjectOrganizer:
+    """Manages project directory structure and organization."""
+
+    # Standard directory structure for Claude MPM projects
+    STANDARD_DIRECTORIES: ClassVar[dict] = {
+        "tmp": "Temporary files, test outputs, and experiments",
+        "scripts": "Project scripts and automation tools",
+        "docs": "Project documentation",
+        "docs/_archive": "Archived documentation versions",
+        "tests": "Test suites and test fixtures",
+        ".claude-mpm": "Claude MPM configuration and data",
+        ".claude-mpm/memories": "Agent memory storage",
+        ".claude/agents": "Deployed agent configurations",
+        "src": "Source code (for libraries/packages)",
+    }
+
+    # Comprehensive gitignore patterns for Claude MPM projects
+    GITIGNORE_DIRS: ClassVar[dict] = {
+        # Temporary and cache directories
+        "tmp/",
+        "temp/",
+        "*.tmp",
+        "*.temp",
+        "*.cache",
+        ".claude-mpm/cache/",
+        ".claude-mpm/logs/",
+        ".claude/cache/",
+        # MCP service directories for local data
+        ".mcp-vector-search/",
+        ".kuzu-memory/",
+        "kuzu-memories/",  # kuzu-memory database directory
+        # Python artifacts
+        "__pycache__/",
+        "*.py[cod]",
+        "*$py.class",
+        "*.so",
+        ".Python",
+        "*.egg-info/",
+        "*.egg",
+        "dist/",
+        "build/",
+        "develop-eggs/",
+        ".eggs/",
+        "wheels/",
+        "pip-wheel-metadata/",
+        "*.manifest",
+        "*.spec",
+        # Testing and coverage
+        ".pytest_cache/",
+        ".coverage",
+        ".coverage.*",
+        "htmlcov/",
+        ".tox/",
+        ".nox/",
+        "*.cover",
+        ".hypothesis/",
+        ".pytype/",
+        "coverage.xml",
+        "*.pytest_cache",
+        # Virtual environments
+        ".env",
+        ".venv",
+        "env/",
+        "venv/",
+        "ENV/",
+        "env.bak/",
+        "venv.bak/",
+        "virtualenv/",
+        ".conda/",
+        "conda-env/",
+        # IDE and editor files
+        ".vscode/",
+        ".idea/",
+        "*.swp",
+        "*.swo",
+        "*~",
+        ".project",
+        ".pydevproject",
+        ".settings/",
+        "*.sublime-workspace",
+        "*.sublime-project",
+        # OS-specific files
+        ".DS_Store",
+        "Thumbs.db",
+        "ehthumbs.db",
+        "Desktop.ini",
+        "$RECYCLE.BIN/",
+        "*.cab",
+        "*.msi",
+        "*.msm",
+        "*.msp",
+        "*.lnk",
+        # Logs and databases
+        "*.log",
+        "*.sql",
+        "*.sqlite",
+        "*.sqlite3",
+        "*.db",
+        "logs/",
+        # Node/JavaScript
+        "node_modules/",
+        "npm-debug.log*",
+        "yarn-debug.log*",
+        "yarn-error.log*",
+        ".npm",
+        ".yarn/",
+        # Documentation builds
+        "_build/",
+        "site/",
+        "docs/_build/",
+        # Security and credentials
+        ".env.*",
+        "*.pem",
+        "*.key",
+        "*.cert",
+        "*.crt",
+        ".secrets/",
+        "credentials/",
+        # Claude MPM specific
+        ".claude-mpm/*.log",
+        ".claude-mpm/sessions/",
+        ".claude-mpm/tmp/",
+        ".claude/sessions/",
+        "*.mpm.tmp",
+        # Backup files
+        "*.bak",
+        "*.backup",
+        "*.old",
+        "backup/",
+        "backups/",
+    }
+
+    # Project type specific structures
+    PROJECT_STRUCTURES: ClassVar[dict] = {
+        "web": ["public", "src/components", "src/pages", "src/styles"],
+        "api": ["src/routes", "src/models", "src/middleware", "src/services"],
+        "cli": ["src/commands", "src/utils", "src/config"],
+        "library": ["src", "examples", "benchmarks"],
+        "mobile": ["src/screens", "src/components", "src/services", "assets"],
+        "fullstack": ["frontend", "backend", "shared", "infrastructure"],
+    }
+
+    def __init__(self, project_path: Path):
+        """Initialize the project organizer."""
+        self.project_path = project_path
+        self.gitignore_path = project_path / ".gitignore"
+        self.structure_report = {}
+
+    def verify_structure(self, project_type: Optional[str] = None) -> Dict:
+        """Verify project structure and identify missing components."""
+        report = {
+            "project_path": str(self.project_path),
+            "exists": [],
+            "missing": [],
+            "issues": [],
+            "recommendations": [],
+        }
+
+        # Check standard directories
+        for dir_name, description in self.STANDARD_DIRECTORIES.items():
+            dir_path = self.project_path / dir_name
+            if dir_path.exists():
+                report["exists"].append(
+                    {
+                        "path": dir_name,
+                        "description": description,
+                        "is_directory": dir_path.is_dir(),
+                    }
+                )
+            else:
+                report["missing"].append(
+                    {
+                        "path": dir_name,
+                        "description": description,
+                        "required": self._is_required_directory(dir_name, project_type),
+                    }
+                )
+
+        # Check project-type specific directories
+        if project_type and project_type in self.PROJECT_STRUCTURES:
+            for dir_name in self.PROJECT_STRUCTURES[project_type]:
+                dir_path = self.project_path / dir_name
+                if not dir_path.exists():
+                    report["missing"].append(
+                        {
+                            "path": dir_name,
+                            "description": f"{project_type} specific directory",
+                            "required": False,
+                        }
+                    )
+
+        # Check for common issues
+        report["issues"] = self._check_common_issues()
+
+        # Generate recommendations
+        report["recommendations"] = self._generate_recommendations(report)
+
+        self.structure_report = report
+        return report
+
+    def _is_required_directory(
+        self, dir_name: str, project_type: Optional[str]
+    ) -> bool:
+        """Determine if a directory is required for the project."""
+        # Always required directories
+        always_required = {"tmp", "scripts", "docs"}
+        if dir_name in always_required:
+            return True
+
+        # Type-specific requirements
+        if project_type:
+            if project_type in ["library", "package"] and dir_name == "src":
+                return True
+            if project_type in ["web", "api", "fullstack"] and dir_name == "tests":
+                return True
+
+        return False
+
+    def _check_common_issues(self) -> List[Dict]:
+        """Check for common project organization issues."""
+        issues = []
+
+        # Check for files in wrong locations
+        root_files = list(self.project_path.glob("*.py"))
+        test_files_in_root = [f for f in root_files if "test" in f.name.lower()]
+        if test_files_in_root:
+            issues.append(
+                {
+                    "type": "misplaced_tests",
+                    "description": "Test files found in project root",
+                    "files": [str(f.name) for f in test_files_in_root],
+                    "recommendation": "Move test files to tests/ directory",
+                }
+            )
+
+        script_files_in_root = [
+            f
+            for f in root_files
+            if f.name.lower().endswith((".sh", ".bash", ".py"))
+            and not f.name.startswith(".")
+            and f.name not in ["setup.py", "pyproject.toml"]
+        ]
+        if script_files_in_root:
+            issues.append(
+                {
+                    "type": "misplaced_scripts",
+                    "description": "Script files found in project root",
+                    "files": [
+                        str(f.name) for f in script_files_in_root[:5]
+                    ],  # Limit to 5
+                    "recommendation": "Move scripts to scripts/ directory",
+                }
+            )
+
+        # Check for missing .gitignore
+        if not self.gitignore_path.exists():
+            issues.append(
+                {
+                    "type": "missing_gitignore",
+                    "description": "No .gitignore file found",
+                    "recommendation": "Create .gitignore with standard patterns",
+                }
+            )
+        else:
+            # Check .gitignore completeness
+            gitignore_content = self.gitignore_path.read_text()
+            missing_patterns = []
+            for pattern in ["tmp/", "__pycache__", ".env", "*.log"]:
+                if pattern not in gitignore_content:
+                    missing_patterns.append(pattern)
+
+            if missing_patterns:
+                issues.append(
+                    {
+                        "type": "incomplete_gitignore",
+                        "description": "Common patterns missing from .gitignore",
+                        "patterns": missing_patterns,
+                        "recommendation": "Update .gitignore with missing patterns",
+                    }
+                )
+
+        # Check for large files that should be in tmp
+        large_files = []
+        for file in self.project_path.rglob("*"):
+            if file.is_file() and not any(part.startswith(".") for part in file.parts):
+                try:
+                    size_mb = file.stat().st_size / (1024 * 1024)
+                    if size_mb > 10:  # Files larger than 10MB
+                        if "tmp" not in str(file) and "node_modules" not in str(file):
+                            large_files.append(
+                                {
+                                    "path": str(file.relative_to(self.project_path)),
+                                    "size_mb": round(size_mb, 2),
+                                }
+                            )
+                except (OSError, PermissionError):
+                    continue
+
+        if large_files:
+            issues.append(
+                {
+                    "type": "large_files",
+                    "description": "Large files outside tmp/ directory",
+                    "files": large_files[:5],  # Limit to 5
+                    "recommendation": "Consider moving large files to tmp/ or adding to .gitignore",
+                }
+            )
+
+        return issues
+
+    def _generate_recommendations(self, report: Dict) -> List[str]:
+        """Generate recommendations based on verification report."""
+        recommendations = []
+
+        # Recommend creating missing required directories
+        required_missing = [d for d in report["missing"] if d.get("required")]
+        if required_missing:
+            recommendations.append(
+                f"Create {len(required_missing)} required directories: "
+                + ", ".join(d["path"] for d in required_missing)
+            )
+
+        # Recommend fixing issues
+        if report["issues"]:
+            for issue in report["issues"]:
+                recommendations.append(issue["recommendation"])
+
+        # Recommend documentation
+        if "docs" not in [d["path"] for d in report["exists"]]:
+            recommendations.append("Create docs/ directory for project documentation")
+
+        return recommendations
+
+    def create_missing_directories(self, force: bool = False) -> Dict:
+        """Create missing standard directories."""
+        created = []
+        skipped = []
+        errors = []
+
+        report = self.verify_structure()
+
+        for dir_info in report["missing"]:
+            dir_path = self.project_path / dir_info["path"]
+
+            # Skip non-required unless force
+            if not dir_info.get("required") and not force:
+                skipped.append(dir_info["path"])
+                continue
+
+            try:
+                dir_path.mkdir(parents=True, exist_ok=True)
+                created.append(dir_info["path"])
+                logger.info(f"Created directory: {dir_path}")
+
+                # Add README for certain directories
+                self._add_directory_readme(dir_path, dir_info["description"])
+
+            except Exception as e:
+                errors.append({"path": dir_info["path"], "error": str(e)})
+                logger.error(f"Failed to create {dir_path}: {e}")
+
+        return {
+            "created": created,
+            "skipped": skipped,
+            "errors": errors,
+        }
+
+    def _add_directory_readme(self, dir_path: Path, description: str) -> None:
+        """Add README file to newly created directory."""
+        readme_path = dir_path / "README.md"
+
+        # Only add README for certain directories
+        readme_dirs = ["tmp", "scripts", "docs/_archive", ".claude-mpm/memories"]
+        if any(str(dir_path).endswith(d) for d in readme_dirs):
+            if not readme_path.exists():
+                content = f"""# {dir_path.name}
+
+{description}
+
+## Purpose
+
+This directory is used for {description.lower()}.
+
+## Usage Guidelines
+
+"""
+                if "tmp" in str(dir_path):
+                    content += """- Place all temporary files and test outputs here
+- This directory is gitignored - contents will not be committed
+- Clean up old files periodically to save disk space
+- Use subdirectories to organize different types of temporary files
+"""
+                elif "scripts" in str(dir_path):
+                    content += """- All project scripts should be placed here
+- Use descriptive names for scripts
+- Include comments and usage instructions in scripts
+- Make scripts executable with `chmod +x script_name.sh`
+"""
+                elif "_archive" in str(dir_path):
+                    content += """- Archived documentation versions are stored here
+- Files are timestamped when archived
+- Preserve important historical documentation
+- Review and clean up old archives periodically
+"""
+                elif "memories" in str(dir_path):
+                    content += """- Agent memory files are stored here
+- Each agent can have its own memory file
+- Memories persist between sessions
+- Update memories when project knowledge changes
+"""
+
+                readme_path.write_text(content)
+                logger.debug(f"Created README in {dir_path}")
+
+    def update_gitignore(self, additional_patterns: Optional[List[str]] = None) -> bool:
+        """Update or create .gitignore file with standard patterns."""
+        try:
+            # Read existing content
+            existing_patterns = set()
+            if self.gitignore_path.exists():
+                content = self.gitignore_path.read_text()
+                existing_patterns = {
+                    line.strip()
+                    for line in content.splitlines()
+                    if line.strip() and not line.startswith("#")
+                }
+            else:
+                content = ""
+
+            # Combine all patterns
+            all_patterns = self.GITIGNORE_DIRS.copy()
+            if additional_patterns:
+                all_patterns.update(additional_patterns)
+
+            # Find missing patterns
+            missing = all_patterns - existing_patterns
+
+            if missing:
+                # Add section for new patterns
+                new_section = "\n# Added by Claude MPM /mpm-init\n"
+                for pattern in sorted(missing):
+                    new_section += f"{pattern}\n"
+
+                # Append to file
+                if content and not content.endswith("\n"):
+                    content += "\n"
+                content += new_section
+
+                # Write updated content
+                self.gitignore_path.write_text(content)
+                logger.info(f"Updated .gitignore with {len(missing)} patterns")
+                return True
+            logger.info(".gitignore already contains all standard patterns")
+            return False
+
+        except Exception as e:
+            logger.error(f"Failed to update .gitignore: {e}")
+            return False
+
+    def organize_misplaced_files(
+        self, dry_run: bool = True, auto_safe: bool = True
+    ) -> Dict:
+        """Organize misplaced files into proper directories.
+
+        Args:
+            dry_run: If True, only report what would be moved without moving
+            auto_safe: If True, only move files that are clearly safe to move
+        """
+        moves = []
+        skipped = []
+        errors = []
+
+        # Files that should never be moved from root
+        protected_root_files = {
+            "setup.py",
+            "pyproject.toml",
+            "package.json",
+            "package-lock.json",
+            "requirements.txt",
+            "Pipfile",
+            "Pipfile.lock",
+            "poetry.lock",
+            "Makefile",
+            "makefile",
+            "Dockerfile",
+            "docker-compose.yml",
+            ".gitignore",
+            ".gitattributes",
+            "LICENSE",
+            "README.md",
+            "README.rst",
+            "CHANGELOG.md",
+            "CONTRIBUTING.md",
+            "CODE_OF_CONDUCT.md",
+            "CLAUDE.md",
+            "CODE.md",
+            "DEVELOPER.md",
+            "STRUCTURE.md",
+            "OPS.md",
+            ".env.example",
+            ".env.sample",
+            "VERSION",
+            "BUILD_NUMBER",
+        }
+
+        # Scan root directory for misplaced files
+        root_files = list(self.project_path.glob("*"))
+        for file in root_files:
+            if file.is_file() and file.name not in protected_root_files:
+                target_dir = None
+                confidence = "low"  # low, medium, high
+                reason = ""
+
+                # Determine target directory based on file patterns
+                file_lower = file.name.lower()
+
+                # Test files (high confidence)
+                if "test" in file_lower and file.suffix == ".py":
+                    if file_lower.startswith("test_") or file_lower.endswith(
+                        "_test.py"
+                    ):
+                        target_dir = "tests"
+                        confidence = "high"
+                        reason = "Test file pattern detected"
+
+                # Script files (medium-high confidence)
+                elif file.suffix in [".sh", ".bash"]:
+                    target_dir = "scripts"
+                    confidence = "high"
+                    reason = "Shell script file"
+                elif file.suffix == ".py" and any(
+                    pattern in file_lower
+                    for pattern in ["script", "run", "cli", "tool"]
+                ):
+                    target_dir = "scripts"
+                    confidence = "medium"
+                    reason = "Python script pattern detected"
+
+                # Log and temporary files (high confidence)
+                elif file.suffix in [".log", ".tmp", ".temp", ".cache"]:
+                    target_dir = "tmp"
+                    confidence = "high"
+                    reason = "Temporary/log file"
+                elif file_lower.startswith(("tmp_", "temp_", "test_output", "debug_")):
+                    target_dir = "tmp"
+                    confidence = "high"
+                    reason = "Temporary file pattern"
+
+                # Documentation files (medium confidence)
+                elif (
+                    file.suffix in [".md", ".rst", ".txt"]
+                    and file.name not in protected_root_files
+                ):
+                    if any(
+                        pattern in file_lower
+                        for pattern in ["notes", "draft", "todo", "spec", "design"]
+                    ):
+                        target_dir = "docs"
+                        confidence = "medium"
+                        reason = "Documentation file pattern"
+
+                # Data files (medium confidence)
+                elif file.suffix in [".csv", ".json", ".xml", ".yaml", ".yml"]:
+                    if file.suffix in [".yaml", ".yml"] and any(
+                        pattern in file_lower for pattern in ["config", "settings"]
+                    ):
+                        # Config files might belong in root
+                        confidence = "low"
+                    else:
+                        target_dir = "data"
+                        confidence = "medium"
+                        reason = "Data file"
+
+                # Build artifacts (high confidence)
+                elif file.suffix in [".whl", ".tar.gz", ".zip"] and "dist" not in str(
+                    file.parent
+                ):
+                    target_dir = "dist"
+                    confidence = "high"
+                    reason = "Build artifact"
+
+                # Example files (medium confidence)
+                elif "example" in file_lower or "sample" in file_lower:
+                    target_dir = "examples"
+                    confidence = "medium"
+                    reason = "Example file pattern"
+
+                if target_dir:
+                    # Check if we should move based on confidence and auto_safe setting
+                    should_move = (
+                        (confidence == "high")
+                        if auto_safe
+                        else (confidence in ["high", "medium"])
+                    )
+
+                    if should_move:
+                        target_path = self.project_path / target_dir / file.name
+                        moves.append(
+                            {
+                                "source": str(file.relative_to(self.project_path)),
+                                "target": str(
+                                    target_path.relative_to(self.project_path)
+                                ),
+                                "reason": reason,
+                                "confidence": confidence,
+                            }
+                        )
+
+                        if not dry_run:
+                            try:
+                                # Create target directory if needed
+                                target_path.parent.mkdir(parents=True, exist_ok=True)
+                                # Move file
+                                file.rename(target_path)
+                                logger.info(
+                                    f"Moved {file.name} to {target_dir}/ ({reason})"
+                                )
+                            except Exception as e:
+                                errors.append({"file": str(file.name), "error": str(e)})
+                                logger.error(f"Failed to move {file.name}: {e}")
+                    else:
+                        skipped.append(
+                            {
+                                "file": str(file.name),
+                                "suggested_dir": target_dir,
+                                "confidence": confidence,
+                                "reason": "Low confidence move - skipped (use --no-auto-safe to include)",
+                            }
+                        )
+
+        # Also check for deeply nested test files that should be in tests/
+        if not auto_safe:  # Only in non-safe mode
+            for test_file in self.project_path.rglob("*test*.py"):
+                # Skip if already in tests directory
+                if "tests" in test_file.parts or "test" in test_file.parts:
+                    continue
+                # Skip if in node_modules or venv
+                if any(
+                    part in test_file.parts
+                    for part in ["node_modules", "venv", ".venv", "site-packages"]
+                ):
+                    continue
+
+                target_path = self.project_path / "tests" / test_file.name
+                moves.append(
+                    {
+                        "source": str(test_file.relative_to(self.project_path)),
+                        "target": str(target_path.relative_to(self.project_path)),
+                        "reason": "Test file found outside tests directory",
+                        "confidence": "medium",
+                    }
+                )
+
+                if not dry_run:
+                    try:
+                        target_path.parent.mkdir(parents=True, exist_ok=True)
+                        test_file.rename(target_path)
+                        logger.info(f"Moved {test_file.name} to tests/")
+                    except Exception as e:
+                        errors.append(
+                            {
+                                "file": str(test_file.relative_to(self.project_path)),
+                                "error": str(e),
+                            }
+                        )
+
+        return {
+            "dry_run": dry_run,
+            "auto_safe": auto_safe,
+            "proposed_moves": moves if dry_run else [],
+            "completed_moves": [] if dry_run else moves,
+            "skipped": skipped,
+            "errors": errors,
+            "total": len(moves),
+            "total_skipped": len(skipped),
+            "total_errors": len(errors),
+        }
+
+    def generate_structure_documentation(self) -> str:
+        """Generate markdown documentation of project structure."""
+        doc = """# Project Structure Report
+
+## Structure Validation
+
+"""
+        # Add validation summary
+        validation = self.validate_structure()
+        doc += f"**Overall Grade:** {validation.get('grade', 'Not evaluated')}\n"
+        doc += f"**Score:** {validation.get('score', 0)}/100\n\n"
+
+        if validation["errors"]:
+            doc += "### 🔴 Critical Issues\n"
+            for error in validation["errors"]:
+                doc += f"- {error}\n"
+            doc += "\n"
+
+        if validation["warnings"]:
+            doc += "### ⚠️  Warnings\n"
+            for warning in validation["warnings"]:
+                doc += f"- {warning}\n"
+            doc += "\n"
+
+        doc += "## Directory Organization\n\n"
+
+        # Document existing structure
+        for dir_name, description in self.STANDARD_DIRECTORIES.items():
+            dir_path = self.project_path / dir_name
+            if dir_path.exists():
+                doc += f"### ✅ `{dir_name}/`\n{description}\n\n"
+
+                # List some contents
+                try:
+                    contents = list(dir_path.iterdir())[:5]
+                    if contents:
+                        doc += "**Contents:**\n"
+                        for item in contents:
+                            if item.is_dir():
+                                doc += f"- {item.name}/ (directory)\n"
+                            else:
+                                doc += f"- {item.name}\n"
+                        if len(list(dir_path.iterdir())) > 5:
+                            doc += f"- ... and {len(list(dir_path.iterdir())) - 5} more items\n"
+                        doc += "\n"
+                except PermissionError:
+                    doc += "*Permission denied to list contents*\n\n"
+            else:
+                doc += f"### ❌ `{dir_name}/` (Missing)\n{description}\n\n"
+
+        # Document misplaced files
+        organize_result = self.organize_misplaced_files(dry_run=True, auto_safe=True)
+        if organize_result["proposed_moves"]:
+            doc += "## 📦 Files to Reorganize\n\n"
+            doc += "The following files could be better organized:\n\n"
+            for move in organize_result["proposed_moves"][:10]:  # Limit to 10
+                doc += f"- `{move['source']}` → `{move['target']}`\n"
+                doc += f"  - Reason: {move['reason']}\n"
+                doc += f"  - Confidence: {move['confidence']}\n"
+            if len(organize_result["proposed_moves"]) > 10:
+                doc += f"\n... and {len(organize_result['proposed_moves']) - 10} more files\n"
+            doc += "\n"
+
+        # Document gitignore status
+        doc += "## .gitignore Configuration\n\n"
+        if self.gitignore_path.exists():
+            gitignore_content = self.gitignore_path.read_text()
+            critical_patterns = [
+                "tmp/",
+                "__pycache__",
+                ".env",
+                "*.log",
+                ".claude-mpm/cache/",
+            ]
+            doc += "### Critical Patterns Status:\n"
+            for pattern in critical_patterns:
+                status = "✅" if pattern in gitignore_content else "❌"
+                doc += f"- {status} `{pattern}`\n"
+            doc += "\n"
+        else:
+            doc += "❌ No .gitignore file found\n\n"
+
+        # Add recommendations
+        if self.structure_report and self.structure_report.get("recommendations"):
+            doc += "## 💡 Recommendations\n\n"
+            for rec in self.structure_report["recommendations"]:
+                doc += f"- {rec}\n"
+            doc += "\n"
+
+        # Add quick fix commands
+        doc += "## 🛠️ Quick Fix Commands\n\n"
+        doc += "```bash\n"
+        doc += "# Run complete initialization\n"
+        doc += "claude-mpm mpm-init --organize\n\n"
+        doc += "# Review without changes\n"
+        doc += "claude-mpm mpm-init --review\n\n"
+        doc += "# Update existing documentation\n"
+        doc += "claude-mpm mpm-init --update\n"
+        doc += "```\n"
+
+        return doc
+
+    def generate_structure_report_json(self) -> Dict:
+        """Generate a comprehensive JSON structure report."""
+        validation = self.validate_structure()
+        organize_result = self.organize_misplaced_files(dry_run=True, auto_safe=True)
+
+        report = {
+            "timestamp": str(Path.cwd()),
+            "project_path": str(self.project_path),
+            "validation": validation,
+            "directories": {},
+            "misplaced_files": organize_result,
+            "gitignore": {
+                "exists": self.gitignore_path.exists(),
+                "patterns_status": {},
+            },
+            "statistics": {
+                "total_directories": 0,
+                "total_files": 0,
+                "misplaced_files": len(organize_result.get("proposed_moves", [])),
+                "structure_score": validation.get("score", 0),
+            },
+        }
+
+        # Check directory status
+        for dir_name, description in self.STANDARD_DIRECTORIES.items():
+            dir_path = self.project_path / dir_name
+            report["directories"][dir_name] = {
+                "exists": dir_path.exists(),
+                "description": description,
+                "file_count": len(list(dir_path.glob("*"))) if dir_path.exists() else 0,
+                "is_directory": dir_path.is_dir() if dir_path.exists() else None,
+            }
+            if dir_path.exists():
+                report["statistics"]["total_directories"] += 1
+
+        # Check gitignore patterns
+        if self.gitignore_path.exists():
+            gitignore_content = self.gitignore_path.read_text()
+            critical_patterns = [
+                "tmp/",
+                "__pycache__",
+                ".env",
+                "*.log",
+                ".claude-mpm/cache/",
+            ]
+            for pattern in critical_patterns:
+                report["gitignore"]["patterns_status"][pattern] = (
+                    pattern in gitignore_content
+                )
+
+        # Count total files
+        for item in self.project_path.rglob("*"):
+            if item.is_file():
+                report["statistics"]["total_files"] += 1
+
+        return report
+
+    def ensure_project_ready(
+        self, auto_organize: bool = False, safe_mode: bool = True
+    ) -> Tuple[bool, List[str]]:
+        """Ensure project is ready for Claude MPM usage.
+
+        Args:
+            auto_organize: Automatically organize misplaced files
+            safe_mode: Only perform safe operations
+        """
+        actions_taken = []
+        issues_found = []
+
+        # Verify structure first
+        self.verify_structure()
+
+        # Create required directories
+        result = self.create_missing_directories(force=False)
+        if result["created"]:
+            actions_taken.append(f"Created {len(result['created'])} directories")
+
+        # Create tmp directory with proper README if it doesn't exist
+        tmp_dir = self.project_path / "tmp"
+        if not tmp_dir.exists():
+            tmp_dir.mkdir(parents=True, exist_ok=True)
+            self._add_directory_readme(
+                tmp_dir, "Temporary files, test outputs, and experiments"
+            )
+            actions_taken.append("Created tmp/ directory with README")
+
+        # Update .gitignore with comprehensive patterns
+        if self.update_gitignore():
+            actions_taken.append("Updated .gitignore with comprehensive patterns")
+
+        # Check if organization is needed
+        organize_result = self.organize_misplaced_files(
+            dry_run=True, auto_safe=safe_mode
+        )
+        if organize_result["proposed_moves"]:
+            if auto_organize:
+                # Perform the organization
+                actual_result = self.organize_misplaced_files(
+                    dry_run=False, auto_safe=safe_mode
+                )
+                if actual_result["completed_moves"]:
+                    actions_taken.append(
+                        f"Organized {len(actual_result['completed_moves'])} files into proper directories"
+                    )
+                if actual_result["errors"]:
+                    issues_found.append(
+                        f"Failed to move {len(actual_result['errors'])} files"
+                    )
+            else:
+                actions_taken.append(
+                    f"Identified {len(organize_result['proposed_moves'])} files to reorganize (use --organize to move)"
+                )
+                if organize_result["skipped"]:
+                    actions_taken.append(
+                        f"Skipped {len(organize_result['skipped'])} low-confidence moves"
+                    )
+
+        # Check for remaining issues
+        if self.structure_report.get("issues"):
+            for issue in self.structure_report["issues"]:
+                if issue["type"] not in [
+                    "misplaced_scripts",
+                    "misplaced_tests",
+                ]:  # These may be handled
+                    issues_found.append(issue["description"])
+
+        # Generate structure validation report
+        validation_report = self.validate_structure()
+        if not validation_report["is_valid"]:
+            issues_found.extend(validation_report["errors"])
+
+        ready = len(issues_found) == 0
+        return ready, actions_taken
+
+    def validate_structure(self) -> Dict:
+        """Validate the project structure meets Claude MPM standards."""
+        validation = {
+            "is_valid": True,
+            "errors": [],
+            "warnings": [],
+            "score": 100,
+        }
+
+        # Check critical directories exist
+        critical_dirs = ["tmp", "scripts", "docs"]
+        for dir_name in critical_dirs:
+            if not (self.project_path / dir_name).exists():
+                validation["is_valid"] = False
+                validation["errors"].append(f"Missing critical directory: {dir_name}/")
+                validation["score"] -= 10
+
+        # Check .gitignore completeness
+        if not self.gitignore_path.exists():
+            validation["is_valid"] = False
+            validation["errors"].append("No .gitignore file found")
+            validation["score"] -= 15
+        else:
+            gitignore_content = self.gitignore_path.read_text()
+            critical_patterns = ["tmp/", "__pycache__", ".env", "*.log"]
+            for pattern in critical_patterns:
+                if pattern not in gitignore_content:
+                    validation["warnings"].append(
+                        f"Missing gitignore pattern: {pattern}"
+                    )
+                    validation["score"] -= 2
+
+        # Check for files in wrong locations
+        root_files = list(self.project_path.glob("*"))
+        misplaced_count = 0
+        for file in root_files:
+            if file.is_file() and (
+                ("test" in file.name.lower() and file.suffix == ".py")
+                or (file.suffix in [".sh", ".bash"] and file.name not in ["Makefile"])
+                or file.suffix in [".log", ".tmp", ".cache"]
+            ):
+                misplaced_count += 1
+
+        if misplaced_count > 0:
+            validation["warnings"].append(
+                f"{misplaced_count} files potentially misplaced in root"
+            )
+            validation["score"] -= min(misplaced_count * 2, 20)
+
+        # Score interpretation
+        if validation["score"] >= 90:
+            validation["grade"] = "A - Excellent structure"
+        elif validation["score"] >= 80:
+            validation["grade"] = "B - Good structure"
+        elif validation["score"] >= 70:
+            validation["grade"] = "C - Acceptable structure"
+        elif validation["score"] >= 60:
+            validation["grade"] = "D - Needs improvement"
+        else:
+            validation["grade"] = "F - Poor structure"
+
+        return validation