🏗️ Convert to modern src-layout structure and cleanup project

- Move enhanced_mcp package to src/enhanced_mcp/ (Python best practice)
- Update pyproject.toml for src-layout configuration
- Fix test imports and paths for new structure
- Remove unnecessary directories: config/, scripts/
- Update CLAUDE.md documentation for src-layout
- Maintain full functionality with 50+ tools across 14 modules

Benefits:
- Better separation between source and development files
- Prevents accidental imports of development versions
- Follows modern Python packaging standards
- Improved testing isolation
- Professional package structure ready for distribution

config/claude_desktop_config.example.json

@@ -1,17 +0,0 @@
-{
-  "comment": "Example configuration for Claude Desktop",
-  "comment2": "Copy this to ~/Library/Application Support/Claude/claude_desktop_config.json (macOS)",
-  "comment3": "or %APPDATA%\\Claude\\claude_desktop_config.json (Windows)",
-  "mcpServers": {
-    "enhanced-tools": {
-      "command": "enhanced-mcp",
-      "cwd": "/home/rpm/claude/enhanced-mcp-tools"
-    },
-    "enhanced-tools-uv": {
-      "comment": "Alternative using uv (if enhanced-mcp not in PATH)",
-      "command": "uv",
-      "args": ["run", "enhanced-mcp"],
-      "cwd": "/home/rpm/claude/enhanced-mcp-tools"
-    }
-  }
-}

pyproject.toml

@@ -29,6 +29,7 @@ dependencies = [
 ]
 
 [tool.setuptools.packages.find]
+where = ["src"]
 include = ["enhanced_mcp*"]
 exclude = ["tests*", "docs*", "examples*", "scripts*", "config*"]
 
@@ -88,8 +89,8 @@ ignore = [
 
 # Additional ignore patterns for star imports in specific files
 [tool.ruff.lint.per-file-ignores]
-"enhanced_mcp/*/base.py" = ["F403", "F405"]
+"src/enhanced_mcp/*/base.py" = ["F403", "F405"]
-"enhanced_mcp/*" = ["F403", "F405"]  # Allow star imports throughout the enhanced_mcp package
+"src/enhanced_mcp/*" = ["F403", "F405"]  # Allow star imports throughout the enhanced_mcp package
 "tests/*" = ["E501", "F401", "F811", "F403", "F405"]
 
 [tool.pytest.ini_options]

scripts/README.md

@@ -1,32 +0,0 @@
-# Scripts
-
-This directory contains utility and analysis scripts for the Enhanced MCP Tools project.
-
-## Available Scripts
-
-- **analyze_essential_files.py** - Analyzes essential project files and dependencies
-- **compare_implementation.py** - Compares different implementation approaches
-
-## Usage
-
-Scripts can typically be run directly from the project root:
-
-```bash
-python scripts/analyze_essential_files.py
-python scripts/compare_implementation.py
-```
-
-Some scripts may require specific dependencies or the virtual environment:
-
-```bash
-uv sync  # Install dependencies first
-python scripts/analyze_essential_files.py
-```
-
-## Purpose
-
-These scripts are development utilities for:
-- Project analysis and validation
-- Implementation comparison
-- Development workflow automation
-- Code quality assessment

scripts/analyze_essential_files.py

@@ -1,181 +0,0 @@
-#!/usr/bin/env python3
-"""
-Essential Files Analysis for Enhanced MCP Tools
-
-This script analyzes which files are absolutely essential vs optional.
-"""
-
-import os
-from pathlib import Path
-
-
-def analyze_essential_files():
-    """Analyze which files are essential for running the server"""
-
-    print("📦 Enhanced MCP Tools - Essential Files Analysis")
-    print("=" * 60)
-
-    enhanced_mcp_dir = Path("enhanced_mcp")
-
-    # Core Infrastructure (ABSOLUTELY ESSENTIAL)
-    core_essential = [
-        "enhanced_mcp/__init__.py",
-        "enhanced_mcp/base.py",
-        "enhanced_mcp/mcp_server.py",
-    ]
-
-    print("\n🔴 ABSOLUTELY ESSENTIAL (Core Infrastructure):")
-    print("-" * 50)
-    for file_path in core_essential:
-        if os.path.exists(file_path):
-            size = os.path.getsize(file_path)
-            print(f"✅ {file_path:<35} ({size:,} bytes)")
-        else:
-            print(f"❌ {file_path:<35} (MISSING!)")
-
-    # Currently Required (due to imports in mcp_server.py)
-    currently_required = [
-        "enhanced_mcp/diff_patch.py",
-        "enhanced_mcp/intelligent_completion.py",
-        "enhanced_mcp/asciinema_integration.py",
-        "enhanced_mcp/sneller_analytics.py",
-        "enhanced_mcp/git_integration.py",
-        "enhanced_mcp/file_operations.py",
-        "enhanced_mcp/archive_compression.py",
-        "enhanced_mcp/workflow_tools.py",
-    ]
-
-    print("\n🟡 CURRENTLY REQUIRED (due to imports):")
-    print("-" * 50)
-    total_size = 0
-    for file_path in currently_required:
-        if os.path.exists(file_path):
-            size = os.path.getsize(file_path)
-            total_size += size
-            print(f"✅ {file_path:<35} ({size:,} bytes)")
-        else:
-            print(f"❌ {file_path:<35} (MISSING!)")
-
-    print(f"\nTotal size of ALL modules: {total_size:,} bytes")
-
-    # Potentially Optional (could be made optional with refactoring)
-    potentially_optional = [
-        ("asciinema_integration.py", "Terminal recording - specialized use case"),
-        ("sneller_analytics.py", "High-performance SQL - specialized use case"),
-        ("archive_compression.py", "Archive operations - can use standard tools"),
-        ("diff_patch.py", "Diff/patch - basic functionality, could be optional"),
-    ]
-
-    print("\n🟢 POTENTIALLY OPTIONAL (with refactoring):")
-    print("-" * 50)
-    for filename, description in potentially_optional:
-        file_path = f"enhanced_mcp/{filename}"
-        if os.path.exists(file_path):
-            size = os.path.getsize(file_path)
-            print(f"🔄 {filename:<35} - {description}")
-            print(f"   {file_path:<35} ({size:,} bytes)")
-
-    # Most Essential Core
-    most_essential = [
-        ("intelligent_completion.py", "AI-powered tool recommendations - core feature"),
-        ("git_integration.py", "Git operations - fundamental for development"),
-        ("file_operations.py", "File operations - basic functionality"),
-        ("workflow_tools.py", "Development workflow - essential utilities"),
-    ]
-
-    print("\n🔥 MOST ESSENTIAL (beyond core infrastructure):")
-    print("-" * 50)
-    essential_size = 0
-    for filename, description in most_essential:
-        file_path = f"enhanced_mcp/{filename}"
-        if os.path.exists(file_path):
-            size = os.path.getsize(file_path)
-            essential_size += size
-            print(f"⭐ {filename:<35} - {description}")
-            print(f"   {file_path:<35} ({size:,} bytes)")
-
-    # Calculate minimal vs full
-    core_size = sum(os.path.getsize(f) for f in core_essential if os.path.exists(f))
-
-    print("\n📊 SIZE ANALYSIS:")
-    print("-" * 50)
-    print(f"Core Infrastructure Only:    {core_size:,} bytes")
-    print(f"Minimal Essential:           {core_size + essential_size:,} bytes")
-    print(f"Full System (Current):       {core_size + total_size:,} bytes")
-
-    return {
-        "core_essential": core_essential,
-        "currently_required": currently_required,
-        "most_essential": [f"enhanced_mcp/{f}" for f, _ in most_essential],
-        "potentially_optional": [f"enhanced_mcp/{f}" for f, _ in potentially_optional],
-    }
-
-
-def show_minimal_server_example():
-    """Show how to create a minimal server"""
-
-    print("\n🚀 MINIMAL SERVER EXAMPLE:")
-    print("-" * 50)
-
-    minimal_example = '''
-# minimal_mcp_server.py - Example of absolute minimum files needed
-
-from enhanced_mcp.base import *
-from enhanced_mcp.intelligent_completion import IntelligentCompletion
-from enhanced_mcp.git_integration import GitIntegration  
-from enhanced_mcp.file_operations import EnhancedFileOperations
-
-class MinimalMCPServer(MCPMixin):
-    """Minimal MCP server with only essential tools"""
-    
-    def __init__(self, name: str = "Minimal MCP Server"):
-        super().__init__()
-        self.name = name
-        
-        # Only the most essential tools
-        self.completion = IntelligentCompletion()  # AI recommendations
-        self.git = GitIntegration()                # Git operations  
-        self.file_ops = EnhancedFileOperations()   # File operations
-        
-        self.tools = {
-            'completion': self.completion,
-            'git': self.git,
-            'file_ops': self.file_ops
-        }
-
-def create_minimal_server():
-    server = FastMCP("Minimal Enhanced MCP")
-    tool_server = MinimalMCPServer()
-    server.include_router(tool_server, prefix="tools")
-    return server
-
-if __name__ == "__main__":
-    server = create_minimal_server()
-    server.run()
-'''
-
-    print(minimal_example)
-
-
-if __name__ == "__main__":
-    os.chdir("/home/rpm/claude/enhanced-mcp-tools")
-    results = analyze_essential_files()
-    show_minimal_server_example()
-
-    print("\n🎯 SUMMARY:")
-    print("=" * 60)
-    print("✅ ABSOLUTE MINIMUM to run ANY server:")
-    for f in results["core_essential"]:
-        print(f"   - {f}")
-
-    print("\n✅ PRACTICAL MINIMUM for useful server:")
-    for f in results["most_essential"]:
-        print(f"   - {f}")
-
-    print("\n🔄 CURRENTLY ALL REQUIRED due to mcp_server.py imports:")
-    print("   - All 11 modules are imported and instantiated")
-
-    print("\n💡 TO MAKE MODULES OPTIONAL:")
-    print("   - Refactor mcp_server.py to use conditional imports")
-    print("   - Add configuration to enable/disable modules")
-    print("   - Use dependency injection pattern")

scripts/compare_implementation.py

@@ -1,91 +0,0 @@
-#!/usr/bin/env python3
-"""
-Comparison script to validate that all initial design functionality is implemented
-"""
-
-import re
-from pathlib import Path
-
-
-def extract_tool_names_from_file(file_path):
-    """Extract tool names from a Python file using regex"""
-    tools = []
-    try:
-        with open(file_path) as f:
-            content = f.read()
-
-        # Find all @mcp_tool decorators
-        tool_patterns = re.findall(r'@mcp_tool\(name="([^"]+)"', content)
-        tools.extend(tool_patterns)
-
-    except Exception as e:
-        print(f"Error reading {file_path}: {e}")
-
-    return tools
-
-
-def compare_implementations():
-    """Compare the initial design with current implementation"""
-
-    print("Enhanced MCP Tools - Implementation Validation")
-    print("=" * 60)
-
-    # Extract tools from initial design
-    initial_design_file = Path("/home/rpm/claude/enhanced-mcp-tools/.initial-design/scaffold.py")
-    initial_tools = extract_tool_names_from_file(initial_design_file)
-
-    # Extract tools from current implementation (enhanced_mcp modules)
-    enhanced_mcp_dir = Path("/home/rpm/claude/enhanced-mcp-tools/enhanced_mcp")
-    current_tools = []
-
-    # Extract tools from all enhanced_mcp modules
-    for module_file in enhanced_mcp_dir.glob("*.py"):
-        if module_file.name != "__init__.py":
-            module_tools = extract_tool_names_from_file(module_file)
-            current_tools.extend(module_tools)
-
-    print(f"\nInitial Design Tools: {len(initial_tools)}")
-    print(f"Current Implementation Tools: {len(current_tools)}")
-
-    # Compare tools
-    initial_set = set(initial_tools)
-    current_set = set(current_tools)
-
-    missing_tools = initial_set - current_set
-    extra_tools = current_set - initial_set
-    common_tools = initial_set & current_set
-
-    print(f"\nCommon Tools: {len(common_tools)}")
-    print(f"Missing from Implementation: {len(missing_tools)}")
-    print(f"Extra in Implementation: {len(extra_tools)}")
-
-    if missing_tools:
-        print("\n❌ Missing Tools:")
-        for tool in sorted(missing_tools):
-            print(f"  - {tool}")
-
-    if extra_tools:
-        print("\n✅ Extra Tools (improvements):")
-        for tool in sorted(extra_tools):
-            print(f"  - {tool}")
-
-    if common_tools:
-        print(f"\n✅ Implemented Tools ({len(common_tools)}):")
-        for tool in sorted(common_tools):
-            print(f"  - {tool}")
-
-    # Overall status
-    print("\n" + "=" * 60)
-    coverage = len(common_tools) / len(initial_tools) * 100 if initial_tools else 0
-    print(f"Implementation Coverage: {coverage:.1f}%")
-
-    if coverage >= 100:
-        print("✅ ALL initial design tools are implemented!")
-    elif coverage >= 80:
-        print("✅ Good coverage - most tools implemented")
-    else:
-        print("⚠️  Significant tools still need implementation")
-
-
-if __name__ == "__main__":
-    compare_implementations()

test_package_structure.py

@@ -11,11 +11,11 @@ def test_package_structure():
     """Test that the package structure is correct."""
     print("=== Package Structure Test ===")
     
-    # Check core files exist
+    # Check core files exist in src-layout
     required_files = [
-        "enhanced_mcp/__init__.py",
+        "src/enhanced_mcp/__init__.py",
-        "enhanced_mcp/base.py", 
+        "src/enhanced_mcp/base.py",
-        "enhanced_mcp/mcp_server.py",
+        "src/enhanced_mcp/mcp_server.py",
         "pyproject.toml"
     ]
     

tests/test_modular_structure.py

@@ -9,9 +9,9 @@ import os
 import sys
 from pathlib import Path
 
-# Add the project root to the Python path
+# With src-layout, the package should be properly installed in development mode
-project_root = Path(__file__).parent.parent  # Go up one more level to get to project root
+# project_root is still needed for file structure tests
-sys.path.insert(0, str(project_root))
+project_root = Path(__file__).parent.parent
 
 
 def test_imports():
@@ -118,8 +118,8 @@ def test_structure():
     print("\n🧪 Testing architecture structure...")
 
     try:
-        # Check that we have the expected file structure
+        # Check that we have the expected file structure in src-layout
-        enhanced_mcp_dir = project_root / "enhanced_mcp"
+        enhanced_mcp_dir = project_root / "src" / "enhanced_mcp"
         expected_files = [
             "__init__.py",
             "base.py",