Scholarly Research MCP Server

# Clean Project Structure ## Overview This document shows the cleaned and organized project structure after removing unnecessary files and consolidating the MCP tools. ## Directory Structure ``` mcp-for-research/ ├── 📁 src/ # Source code │ ├── 📄 index.ts # Main consolidated MCP server (5 tools) │ ├── 📁 adapters/ # Data source connectors │ │ ├── 📄 pubmed.ts # PubMed API integration │ │ ├── 📄 google-scholar.ts # Google Scholar web scraping │ │ ├── 📄 google-scholar-firecrawl.ts # Firecrawl integration │ │ ├── 📄 arxiv.ts # ArXiv integration │ │ ├── 📄 unified-search.ts # Basic multi-source search │ │ ├── 📄 enhanced-unified-search.ts # Advanced multi-source search │ │ └── 📄 preference-aware-unified-search.ts # User preference integration │ └── 📁 preferences/ # User preference management │ └── 📄 user-preferences.ts # Preference storage and retrieval ├── 📁 docs/ # Documentation │ ├── 📄 API_REFERENCE.md # Complete API documentation │ ├── 📄 ARCHITECTURE.md # Technical system design │ ├── 📄 DATA_MODELS.md # Data structure definitions │ ├── 📄 DEVELOPMENT.md # Developer setup guide │ └── 📄 TROUBLESHOOTING.md # Problem-solving guide ├── 📁 tests/ # Test files │ ├── 📄 test-preferences.js # Preference system tests │ ├── 📄 test-all-tools-simple.sh # Bash test runner (recommended) │ ├── 📄 test_all_tools.py # Python test runner │ ├── 📄 test-all-tools.js # JavaScript test runner │ ├── 📄 test-arxiv-*.js # ArXiv-specific tests │ ├── 📄 test-google-scholar-*.js # Google Scholar tests │ ├── 📄 test-firecrawl-*.js # Firecrawl integration tests │ ├── 📄 test-unified-*.js # Unified search tests │ ├── 📄 test-build.js # Build verification tests │ ├── 📄 test-citations.js # Citation tests │ ├── 📄 jest.setup.js # Jest configuration │ ├── 📄 README.md # Test documentation │ └── 📄 run-arxiv-tests.sh # ArXiv test runner script ├── 📁 scripts/ # Build and utility scripts │ ├── 📄 test-mcp-tool.js # MCP tool testing utility │ ├── 📄 publish-both.js # Publishing script │ └── 📄 version.js # Version management script ├── 📁 .github/ # GitHub configuration ├── 📁 .cursor/ # Cursor editor configuration (gitignored) ├── 📁 dist/ # Built output (gitignored) ├── 📁 node_modules/ # Dependencies (gitignored) ├── 📄 .gitignore # Git ignore rules (includes .cursor/) ├── 📄 .npmrc # NPM configuration ├── 📄 .npmignore # NPM ignore rules ├── 📄 package.json # Project configuration and dependencies ├── 📄 package-lock.json # Locked dependency versions ├── 📄 tsconfig.json # TypeScript configuration ├── 📄 README.md # Main project documentation ├── 📄 README-consolidated.md # Consolidated approach documentation ├── 📄 TOOL_CONSOLIDATION.md # Tool consolidation reference ├── 📄 PROJECT_STRUCTURE_CLEAN.md # This file ├── 📄 PROJECT_STRUCTURE.md # Legacy structure documentation ├── 📄 CHANGELOG.md # Version history and changes └── 📄 LICENSE # MIT license ``` ## What Was Cleaned Up ### ❌ Removed Files - `ion` - Unrelated file (appeared to be a man page) - `cholarly-research-mcp version` - Git log output file - `test-search_arxiv-1756073254017.js` - Temporary test file with timestamp - `src/index-consolidated.ts` - Merged into main index.ts ### ✅ Added to .gitignore - `.cursor/` - Cursor editor configuration files - `*.cursor` - Any cursor-specific files ### 🔄 Consolidated Tools - **Before**: 24 individual MCP tools - **After**: 5 powerful, multi-functional tools - **Reduction**: 80% fewer tools to manage ## Key Benefits of Clean Structure ### **Organization** - Clear separation of concerns - Logical grouping of related files - Consistent naming conventions ### **Maintainability** - Easier to find specific functionality - Reduced code duplication - Centralized tool definitions ### **User Experience** - Fewer tools to remember - More powerful functionality - Consistent interface patterns ### **Development** - Simpler testing setup - Easier debugging - Better error handling ## File Purposes ### **Core Source Files** - `src/index.ts` - Main MCP server with 5 consolidated tools - `src/adapters/` - Database and API connectors - `src/preferences/` - User preference management ### **Documentation** - `README.md` - Main project overview and setup - `README-consolidated.md` - Detailed consolidation explanation - `TOOL_CONSOLIDATION.md` - Quick reference for tool mapping - `docs/` - Technical documentation ### **Testing** - `tests/` - Comprehensive test suite - `test-all-tools-simple.sh` - Recommended test runner - Multiple test runners for different environments ### **Configuration** - `package.json` - Project metadata and scripts - `tsconfig.json` - TypeScript compilation settings - `.gitignore` - Version control exclusions ## Development Workflow ### **Building** ```bash npm run build # Compile TypeScript to JavaScript npm run dev # Development mode with hot reload npm start # Run production build ``` ### **Testing** ```bash npm run test:all-tools-bash # Run all tests (recommended) npm run test:all-tools-python # Python test runner npm run test:all-tools-js # JavaScript test runner ``` ### **Version Management** ```bash npm run version:patch # Increment patch version npm run version:minor # Increment minor version npm run version:major # Increment major version ``` ## Future Improvements ### **Planned Enhancements** - Plugin system for new data sources - Advanced caching and optimization - Better error handling and logging - Enhanced user preference system ### **Extensibility** - Modular adapter system - Custom tool definitions - API versioning support - Backward compatibility ## Conclusion The cleaned project structure provides a much more maintainable and user-friendly codebase. The consolidation from 24 tools to 5 powerful tools reduces complexity while maintaining all functionality. The organized directory structure makes it easier for developers to contribute and for users to understand the system.