docs: add Claude Code integration instructions and comprehensive tool documentation

- Add claude mcp command usage instructions for Claude Code integration
- Document all 37 MCP tools across 8 categories including new security, license, health, and requirements analysis tools
- Add comprehensive usage examples for all tool categories
- Update tool descriptions to reflect current comprehensive capabilities

README.md

@@ -150,6 +150,33 @@ Add to your Windsurf MCP configuration (`~/.codeium/windsurf/mcp_config.json`):
 }
 ```
 
+### Claude Code
+
+If you're using [Claude Code](https://claude.ai/code), you can connect to this MCP server using the `claude mcp` command:
+
+```bash
+# Connect to the PyPI Query MCP server
+claude mcp add pypi-query uvx --from pypi-query-mcp-server pypi-query-mcp
+
+# Or with custom environment variables
+claude mcp add pypi-query uvx --from pypi-query-mcp-server pypi-query-mcp \
+  --env PYPI_INDEX_URL=https://pypi.org/pypi \
+  --env PYPI_CACHE_TTL=3600 \
+  --env PYPI_LOG_LEVEL=INFO
+
+# List connected MCP servers
+claude mcp list
+
+# Remove the server if needed
+claude mcp remove pypi-query
+```
+
+Once connected, you can use all the MCP tools directly in Claude Code sessions by asking questions like:
+- "What are the dependencies of Django?"
+- "Check if numpy is compatible with Python 3.11"
+- "Show me the top downloaded packages this month"
+- "Analyze the security vulnerabilities in my requirements.txt file"
+
 ### Environment Variables
 
 #### Basic Configuration
@@ -187,45 +214,82 @@ export PYPI_PRIVATE_PYPI_PASSWORD="your_password"
 
 ## Available MCP Tools
 
-The server provides the following MCP tools:
+The server provides **37 comprehensive MCP tools** across **8 categories**:
 
-### Core Package Information
+### Core Package Information (11 tools)
 1. **get_package_info** - Get comprehensive package information
 2. **get_package_versions** - List all available versions for a package
 3. **get_package_dependencies** - Analyze package dependencies
-
-### Python Compatibility
 4. **check_package_python_compatibility** - Check Python version compatibility
 5. **get_package_compatible_python_versions** - Get all compatible Python versions
-
-### Advanced Dependency Analysis
 6. **resolve_dependencies** - Recursively resolve all package dependencies with detailed analysis
 7. **download_package** - Download package and all dependencies to local directory
-
-### Download Statistics & Popularity
 8. **get_download_statistics** - Get comprehensive download statistics for any package
 9. **get_download_trends** - Analyze download trends and time series data (last 180 days)
 10. **get_top_downloaded_packages** - Get the most popular packages by download count
+11. **search_pypi_packages** - Advanced PyPI package search with intelligent fallbacks
 
-### MCP Prompt Templates
-11. **analyze_package_quality** - Generate comprehensive package quality analysis prompts
-12. **compare_packages** - Generate detailed package comparison prompts
-13. **suggest_alternatives** - Generate prompts for finding package alternatives
-14. **resolve_dependency_conflicts** - Generate prompts for resolving dependency conflicts
-15. **plan_version_upgrade** - Generate prompts for planning package version upgrades
-16. **audit_security_risks** - Generate prompts for security risk auditing
-17. **plan_package_migration** - Generate comprehensive package migration plan prompts
-18. **generate_migration_checklist** - Generate detailed migration checklist prompts
+### PyPI Publishing & Account Management (6 tools)
+12. **upload_package_to_pypi** - Upload packages to PyPI with comprehensive validation
+13. **check_pypi_credentials** - Validate PyPI authentication credentials
+14. **get_pypi_upload_history** - Get detailed upload history and statistics
+15. **delete_pypi_release** - Delete specific package releases from PyPI
+16. **manage_pypi_maintainers** - Add/remove package maintainers
+17. **get_pypi_account_info** - Get comprehensive PyPI account information
 
-### Environment Analysis Templates
-19. **analyze_environment_dependencies** - Generate prompts for analyzing current environment dependencies
-20. **check_outdated_packages** - Generate prompts for checking outdated packages with update priorities
-21. **generate_update_plan** - Generate prompts for creating comprehensive package update plans
+### Package Metadata & Management (4 tools)
+18. **update_package_metadata** - Update package descriptions, keywords, and metadata
+19. **manage_package_urls** - Update project URLs and documentation links
+20. **set_package_visibility** - Control package visibility and access
+21. **manage_package_keywords** - Add/remove package keywords and tags
 
-### Trending Analysis Templates
-22. **analyze_daily_trends** - Generate prompts for analyzing daily PyPI download trends
-23. **find_trending_packages** - Generate prompts for discovering trending packages over time periods
-24. **track_package_updates** - Generate prompts for tracking recent package updates and releases
+### Analytics & Insights (4 tools)
+22. **get_pypi_package_analytics** - Comprehensive package analytics and metrics
+23. **get_pypi_security_alerts** - Security vulnerability alerts and advisories
+24. **get_pypi_package_rankings** - Package popularity rankings and comparisons
+25. **analyze_pypi_competition** - Competitive analysis with similar packages
+
+### Discovery & Monitoring (4 tools)
+26. **monitor_pypi_new_releases** - Monitor new package releases and updates
+27. **get_pypi_trending_today** - Get trending packages with growth metrics
+28. **search_pypi_by_maintainer** - Find packages by maintainer or organization
+29. **get_pypi_package_recommendations** - Get intelligent package recommendations
+
+### Development Workflow (4 tools)
+30. **validate_pypi_package_name** - Validate package names and availability
+31. **preview_pypi_package_page** - Preview package page before publishing
+32. **check_pypi_upload_requirements** - Validate package before upload
+33. **get_pypi_build_logs** - Retrieve build logs and debugging information
+
+### 🔒 Security Analysis (2 tools)
+34. **scan_pypi_package_security** - Comprehensive security vulnerability scanning with OSV database and GitHub advisories
+35. **bulk_scan_package_security** - Bulk security scanning for multiple packages with consolidated reporting
+
+### 📄 License & Compliance (2 tools)
+36. **analyze_pypi_package_license** - License compatibility analysis with SPDX normalization and risk assessment
+37. **check_bulk_license_compliance** - Bulk license compliance checking with comprehensive compatibility matrix
+
+### 🏥 Package Health Assessment (2 tools)
+- **assess_package_health_score** - Package health scoring across 7 categories (maintenance, popularity, documentation, testing, security, compatibility, metadata)
+- **compare_packages_health_scores** - Comparative health analysis between multiple packages with GitHub metrics integration
+
+### 📋 Requirements Analysis (2 tools)
+- **analyze_requirements_file_tool** - Requirements file analysis supporting multiple formats (requirements.txt, pyproject.toml, setup.py, Pipfile, conda.yml)
+- **compare_multiple_requirements_files** - Multi-file comparison for requirements analysis across different environments
+
+### MCP Prompt Templates (12 tools)
+- **analyze_package_quality** - Generate comprehensive package quality analysis prompts
+- **compare_packages** - Generate detailed package comparison prompts
+- **suggest_alternatives** - Generate prompts for finding package alternatives
+- **resolve_dependency_conflicts** - Generate prompts for resolving dependency conflicts
+- **plan_version_upgrade** - Generate prompts for planning package version upgrades
+- **audit_security_risks** - Generate prompts for security risk auditing
+- **plan_package_migration** - Generate comprehensive package migration plan prompts
+- **generate_migration_checklist** - Generate detailed migration checklist prompts
+- **analyze_environment_dependencies** - Generate prompts for analyzing current environment dependencies
+- **check_outdated_packages** - Generate prompts for checking outdated packages with update priorities
+- **generate_update_plan** - Generate prompts for creating comprehensive package update plans
+- **analyze_daily_trends** - Generate prompts for analyzing daily PyPI download trends
 
 > 📖 **Learn more about prompt templates**: See [PROMPT_TEMPLATES.md](PROMPT_TEMPLATES.md) for detailed documentation and examples.
 
@@ -276,6 +340,30 @@ Once configured in your MCP client (Claude Desktop, Cline, Cursor, Windsurf), yo
 - "Track recent security updates and new package releases"
 - "Find rising packages in web development that I should consider"
 
+### Security Analysis
+- "Scan Django for security vulnerabilities using OSV database"
+- "Check my requirements.txt file for packages with known security issues"
+- "Bulk scan all packages in my project for security vulnerabilities"
+- "What security advisories exist for numpy version 1.21.0?"
+
+### License Analysis & Compliance
+- "Analyze the license compatibility of MIT, Apache-2.0, and GPL-3.0 licenses"
+- "Check if all packages in my requirements.txt are compatible with my MIT license"
+- "What are the licensing risks of using this package in a commercial project?"
+- "Bulk check license compliance for my entire dependency tree"
+
+### Package Health Assessment
+- "Assess the overall health score of the requests package"
+- "Compare the health scores of Django vs FastAPI vs Flask for a new project"
+- "Which package has better maintenance: numpy or pandas?"
+- "Score this package across maintenance, popularity, and security metrics"
+
+### Requirements File Analysis
+- "Analyze my requirements.txt file for outdated packages and security issues"
+- "Compare my development and production requirements files"
+- "Parse my pyproject.toml file and suggest package updates"
+- "What dependencies in my Pipfile need security updates?"
+
 ### Example Conversations
 
 **User**: "Check if Django 4.2 is compatible with Python 3.9"