Hybrid RAG Project MCP Server

# Project Restructuring Options ## Current Problem **Root directory has 18 files** (13 MD, 4 SH, 1 PY), making it cluttered and hard to navigate. ### Current Root Files: ``` 📄 Documentation (13 files): - ARCHITECTURE.md - BOUNDARY_TESTING_SUGGESTIONS.md - CHANGELOG.md - CONTRIBUTING.md - CONVERSATION_MEMORY.md - DEMO_CHEAT_SHEET.md - GITHUB_SETUP.md - MARKDOWN_FIX.md (temp file) - QUICK_START.md - README.md - TESTING_RESULTS.md - TEST_PLAN.md (temp file) - USAGE_COMPARISON.md 🔧 Scripts (4 files): - ask.sh - package.sh - setup.sh - restructure.sh (temp file) ⚙️ Setup (1 file): - setup.py ``` --- ## Option 1: Minimal Reorganization (CONSERVATIVE) ⭐ **Goal:** Keep it simple, minimal changes, GitHub-friendly ### Structure: ``` hybrid-rag-project/ ├── README.md # Keep in root (GitHub requirement) ├── LICENSE # Keep in root (standard) ├── CHANGELOG.md # Keep in root (standard) ├── setup.py # Keep in root (Python standard) ├── requirements.txt # Keep in root (Python standard) │ ├── docs/ # Move most documentation here │ ├── getting-started/ │ │ ├── QUICK_START.md │ │ ├── DEMO_CHEAT_SHEET.md │ │ └── CONVERSATION_MEMORY.md │ ├── technical/ │ │ ├── ARCHITECTURE.md │ │ └── TESTING_RESULTS.md │ ├── guides/ │ │ ├── BOUNDARY_TESTING_SUGGESTIONS.md │ │ ├── USAGE_COMPARISON.md │ │ └── GITHUB_SETUP.md │ └── contributing/ │ └── CONTRIBUTING.md │ ├── scripts/ # Keep scripts here │ ├── demo/ │ │ ├── conversational_demo.py │ │ ├── interactive_demo.py │ │ └── run_demo.py │ ├── tools/ │ │ ├── boundary_testing.py │ │ ├── generate_large_dataset.py │ │ ├── ask.sh → ../conversational_demo.py │ │ ├── setup.sh │ │ └── package.sh │ └── servers/ │ ├── mcp_server.py │ └── mcp_server_claude.py │ ├── src/hybrid_rag/ # Core code (no change) ├── config/ # Configuration (no change) ├── data/ # Data files (no change) ├── tests/ # Tests (no change) └── .gitignore DELETE: - MARKDOWN_FIX.md (temp file) - TEST_PLAN.md (temp file) - restructure.sh (temp file) ``` ### Changes: - ✅ Root has only 5 essential files - ✅ All docs in `docs/` with logical grouping - ✅ Scripts organized by purpose - ✅ GitHub-friendly (README, LICENSE, CHANGELOG in root) - ✅ Python-standard (setup.py, requirements.txt in root) - ⚠️ Need to update some import paths ### Pros: - Clean root directory - Professional organization - GitHub conventions followed - Easy to navigate - Minimal code changes ### Cons: - Users need to look in `docs/` for guides - Script paths change (update documentation) --- ## Option 2: Flat Documentation (SIMPLE) **Goal:** Simplest change, just move docs to one folder ### Structure: ``` hybrid-rag-project/ ├── README.md ├── LICENSE ├── CHANGELOG.md ├── CONTRIBUTING.md ├── setup.py ├── requirements.txt │ ├── docs/ # All docs here (flat) │ ├── ARCHITECTURE.md │ ├── BOUNDARY_TESTING_SUGGESTIONS.md │ ├── CONVERSATION_MEMORY.md │ ├── DEMO_CHEAT_SHEET.md │ ├── GITHUB_SETUP.md │ ├── QUICK_START.md │ ├── TESTING_RESULTS.md │ └── USAGE_COMPARISON.md │ ├── scripts/ # Scripts stay as-is │ ├── ask.sh │ ├── boundary_testing.py │ ├── conversational_demo.py │ ├── generate_large_dataset.py │ ├── interactive_demo.py │ ├── mcp_server.py │ ├── mcp_server_claude.py │ ├── package.sh │ ├── run_demo.py │ └── setup.sh │ ├── src/hybrid_rag/ ├── config/ ├── data/ └── tests/ ``` ### Changes: - ✅ Move 8 docs to `docs/` - ✅ Keep 4 standard files in root (README, LICENSE, CHANGELOG, CONTRIBUTING) - ✅ Scripts unchanged - ✅ No code changes needed ### Pros: - Simplest change (just move files) - No code modifications - No import path changes - Quick to implement ### Cons: - `docs/` folder not organized - Scripts still mixed in one folder - Moderately cluttered docs directory --- ## Option 3: Full Reorganization (COMPREHENSIVE) **Goal:** Professional, enterprise-grade structure ### Structure: ``` hybrid-rag-project/ ├── README.md # Overview + quick start ├── LICENSE ├── CHANGELOG.md ├── pyproject.toml # Modern Python packaging │ ├── docs/ # Organized documentation │ ├── index.md # Documentation hub │ ├── user-guide/ │ │ ├── installation.md │ │ ├── quick-start.md │ │ ├── usage.md │ │ └── conversation-memory.md │ ├── reference/ │ │ ├── architecture.md │ │ ├── api-reference.md │ │ └── configuration.md │ ├── guides/ │ │ ├── boundary-testing.md │ │ ├── mcp-setup.md │ │ └── github-workflow.md │ ├── tutorials/ │ │ ├── basic-queries.md │ │ ├── advanced-queries.md │ │ └── custom-retrievers.md │ └── development/ │ ├── contributing.md │ ├── testing.md │ └── performance.md │ ├── examples/ # Example scripts │ ├── basic_demo.py │ ├── conversational_demo.py │ └── custom_retriever_example.py │ ├── tools/ # Development tools │ ├── cli.py # Unified CLI entry point │ ├── benchmarks/ │ │ └── boundary_testing.py │ └── generators/ │ └── generate_dataset.py │ ├── servers/ # Server implementations │ ├── mcp/ │ │ ├── __init__.py │ │ ├── server.py │ │ └── tools.py │ └── api/ │ └── rest_server.py │ ├── bin/ # Executable scripts │ ├── ask # No .sh extension │ ├── setup │ └── package │ ├── src/hybrid_rag/ # Core library │ ├── __init__.py │ ├── __main__.py # Entry point: python -m hybrid_rag │ ├── cli/ # CLI implementation │ ├── retrievers/ │ ├── loaders/ │ └── chains/ │ ├── tests/ │ ├── unit/ │ ├── integration/ │ └── performance/ │ ├── config/ │ └── config.yaml │ ├── data/ │ ├── sample/ # Sample data │ └── user/ # User data (gitignored) │ └── .github/ # GitHub workflows └── workflows/ └── tests.yml ``` ### Changes: - ✅ Professional structure - ✅ Docs organized by audience - ✅ Clear separation of concerns - ✅ Modern Python practices - ✅ CLI as package entry point - ⚠️ Significant refactoring needed ### Pros: - Enterprise-grade structure - Scales well for large projects - Clear purpose for each directory - Great for teams - Documentation is well-organized ### Cons: - Major refactoring required - Learning curve for contributors - Import paths change significantly - May be overkill for this project --- ## Option 4: Hybrid Approach (RECOMMENDED) ⭐⭐ **Goal:** Balance cleanliness with practicality ### Structure: ``` hybrid-rag-project/ ├── README.md # Overview + installation ├── LICENSE ├── CHANGELOG.md ├── CONTRIBUTING.md ├── setup.py ├── requirements.txt │ ├── docs/ │ ├── README.md # Documentation index │ ├── getting-started/ │ │ ├── quick-start.md │ │ ├── conversation-memory.md │ │ └── demo-cheat-sheet.md │ ├── architecture/ │ │ ├── system-design.md # (was ARCHITECTURE.md) │ │ ├── testing-results.md │ │ └── boundary-testing.md │ └── guides/ │ ├── usage-comparison.md │ ├── github-setup.md │ └── contributing.md # Link to root CONTRIBUTING.md │ ├── scripts/ │ ├── demos/ │ │ ├── conversational.py # Main demo │ │ ├── interactive.py # Simple demo │ │ └── basic.py # run_demo.py renamed │ ├── mcp/ │ │ ├── server.py # mcp_server.py renamed │ │ └── server_claude.py # Legacy version │ ├── tools/ │ │ ├── boundary_test.py # Testing tool │ │ └── dataset_generator.py # Data generation │ └── bin/ # Executable wrappers │ ├── ask.sh # Main launcher │ ├── setup.sh │ └── package.sh │ ├── src/hybrid_rag/ # No change ├── config/ # No change ├── data/ # No change └── tests/ # No change ``` ### Changes: - ✅ Root has 6 essential files - ✅ Docs organized but not over-structured - ✅ Scripts categorized by purpose - ✅ Minimal code changes - ✅ Easy to navigate - ✅ Room to grow ### Pros: - Clean root directory - Logical organization - Not over-engineered - Easy migration path - Maintains simplicity - Professional appearance ### Cons: - Still some navigation required - Need to update references in docs - Script paths change --- ## Comparison Matrix | Aspect | Option 1 (Minimal) | Option 2 (Flat) | Option 3 (Full) | Option 4 (Hybrid) | |--------|-------------------|-----------------|-----------------|-------------------| | **Root Cleanliness** | ⭐⭐⭐⭐⭐ (5 files) | ⭐⭐⭐⭐ (6 files) | ⭐⭐⭐⭐⭐ (4 files) | ⭐⭐⭐⭐⭐ (6 files) | | **Ease of Migration** | ⭐⭐⭐⭐ | ⭐⭐⭐⭐⭐ | ⭐⭐ | ⭐⭐⭐⭐ | | **Findability** | ⭐⭐⭐⭐⭐ | ⭐⭐⭐ | ⭐⭐⭐⭐⭐ | ⭐⭐⭐⭐⭐ | | **Professional Look** | ⭐⭐⭐⭐ | ⭐⭐⭐ | ⭐⭐⭐⭐⭐ | ⭐⭐⭐⭐⭐ | | **Scalability** | ⭐⭐⭐⭐ | ⭐⭐⭐ | ⭐⭐⭐⭐⭐ | ⭐⭐⭐⭐ | | **Simplicity** | ⭐⭐⭐⭐ | ⭐⭐⭐⭐⭐ | ⭐⭐ | ⭐⭐⭐⭐ | | **Code Changes** | Small | None | Large | Small | | **Time to Implement** | 30 min | 10 min | 3 hours | 45 min | --- ## My Recommendation ### **Option 4 (Hybrid Approach)** ⭐⭐ **Why:** - ✅ Cleans up root effectively - ✅ Professional without being over-engineered - ✅ Easy to implement (45 minutes) - ✅ Logical organization that scales - ✅ Minimal code changes - ✅ Great for a UCSC project portfolio ### Quick wins: 1. Root goes from 18 files → 6 files 2. Docs organized by purpose 3. Scripts categorized clearly 4. Still simple to navigate 5. Professional appearance --- ## Alternative Recommendation for Different Goals ### If you want **simplicity above all**: **Option 2 (Flat)** - 10-minute change - No code modifications - Good enough for most users ### If you want **maximum cleanliness**: **Option 1 (Minimal)** - Most organized docs structure - GitHub best practices - 30-minute change ### If this becomes **production/team project**: **Option 3 (Full)** - Enterprise-grade - Room for growth - Clear conventions --- ## Files to Delete (All Options) These are temporary/obsolete files that should be removed: ```bash rm MARKDOWN_FIX.md # Temporary troubleshooting file rm TEST_PLAN.md # Temporary planning file rm restructure.sh # Temporary script rm BOUNDARY_TESTING_REPORT.md # If exists (generated file) ``` Add to `.gitignore`: ``` # Generated reports *_REPORT.md BOUNDARY_TESTING_REPORT.md # Temporary files TEST_PLAN.md MARKDOWN_FIX.md ``` --- ## Implementation Steps (for Option 4) ### Phase 1: Prepare (5 min) ```bash # Backup current state git add -A git commit -m "Backup before restructure" # Create new directories mkdir -p docs/{getting-started,architecture,guides} mkdir -p scripts/{demos,mcp,tools,bin} ``` ### Phase 2: Move Documentation (10 min) ```bash # Move to appropriate locations mv QUICK_START.md docs/getting-started/quick-start.md mv CONVERSATION_MEMORY.md docs/getting-started/conversation-memory.md mv DEMO_CHEAT_SHEET.md docs/getting-started/demo-cheat-sheet.md mv ARCHITECTURE.md docs/architecture/system-design.md mv TESTING_RESULTS.md docs/architecture/testing-results.md mv BOUNDARY_TESTING_SUGGESTIONS.md docs/architecture/boundary-testing.md mv USAGE_COMPARISON.md docs/guides/usage-comparison.md mv GITHUB_SETUP.md docs/guides/github-setup.md # Delete temp files rm MARKDOWN_FIX.md TEST_PLAN.md restructure.sh ``` ### Phase 3: Reorganize Scripts (10 min) ```bash # Move scripts mv scripts/conversational_demo.py scripts/demos/conversational.py mv scripts/interactive_demo.py scripts/demos/interactive.py mv scripts/run_demo.py scripts/demos/basic.py mv scripts/mcp_server.py scripts/mcp/server.py mv scripts/mcp_server_claude.py scripts/mcp/server_claude.py mv scripts/boundary_testing.py scripts/tools/boundary_test.py mv scripts/generate_large_dataset.py scripts/tools/dataset_generator.py # Move shell scripts mv ask.sh scripts/bin/ask.sh mv setup.sh scripts/bin/setup.sh mv package.sh scripts/bin/package.sh ``` ### Phase 4: Update References (15 min) - Update README.md with new paths - Update script imports - Update documentation cross-references - Create docs/README.md as index ### Phase 5: Test & Commit (5 min) ```bash # Test that demos still work python scripts/demos/conversational.py # Commit changes git add -A git commit -m "Restructure project for better organization" ``` --- ## Your Decision **Which option do you prefer?** 1. **Option 1 (Minimal)** - Clean, GitHub-standard 2. **Option 2 (Flat)** - Simplest, fastest 3. **Option 3 (Full)** - Enterprise-grade 4. **Option 4 (Hybrid)** - Recommended balance ⭐⭐ 5. **Custom** - Mix and match features **Or do you want to:** - See a detailed implementation plan for your choice? - Discuss trade-offs more? - Keep current structure? Let me know and I'll implement your preferred option!