Add Library RAG project and cleanup root directory

- Add complete Library RAG application (Flask + MCP server)
  - PDF processing pipeline with OCR and LLM extraction
  - Weaviate vector database integration (BGE-M3 embeddings)
  - Flask web interface with search and document management
  - MCP server for Claude Desktop integration
  - Comprehensive test suite (134 tests)

- Clean up root directory
  - Remove obsolete documentation files
  - Remove backup and temporary files
  - Update autonomous agent configuration

- Update prompts
  - Enhance initializer bis prompt with better instructions

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

generations/library_rag/init.sh

@@ -0,0 +1,131 @@
+#!/bin/bash
+# Library RAG - Type Safety & Documentation Enhancement
+# Initialization script for development environment
+
+set -e  # Exit on error
+
+echo "=========================================="
+echo "Library RAG - Development Environment Setup"
+echo "=========================================="
+echo ""
+
+# Check Python version
+echo "[1/5] Checking Python version..."
+python_version=$(python --version 2>&1)
+echo "  Found: $python_version"
+if ! python -c "import sys; assert sys.version_info >= (3, 10), 'Python 3.10+ required'" 2>/dev/null; then
+    echo "  ERROR: Python 3.10 or higher is required"
+    exit 1
+fi
+echo "  OK"
+echo ""
+
+# Create virtual environment if it doesn't exist
+echo "[2/5] Setting up virtual environment..."
+if [ ! -d "venv" ]; then
+    echo "  Creating virtual environment..."
+    python -m venv venv
+    echo "  Created venv/"
+else
+    echo "  Virtual environment already exists"
+fi
+
+# Activate virtual environment
+if [[ "$OSTYPE" == "msys" || "$OSTYPE" == "win32" ]]; then
+    source venv/Scripts/activate
+else
+    source venv/bin/activate
+fi
+echo "  Activated virtual environment"
+echo ""
+
+# Install dependencies
+echo "[3/5] Installing Python dependencies..."
+pip install --quiet --upgrade pip
+pip install --quiet -r requirements.txt
+# Install type checking tools
+pip install --quiet mypy types-Flask pydocstyle
+echo "  Installed all dependencies"
+echo ""
+
+# Start Docker containers
+echo "[4/5] Starting Weaviate with Docker Compose..."
+if command -v docker &> /dev/null; then
+    if docker compose version &> /dev/null; then
+        docker compose up -d
+        echo "  Weaviate is starting..."
+        echo "  Waiting for Weaviate to be ready..."
+        sleep 5
+
+        # Check if Weaviate is ready
+        max_attempts=30
+        attempt=0
+        while [ $attempt -lt $max_attempts ]; do
+            if curl -s http://localhost:8080/v1/.well-known/ready > /dev/null 2>&1; then
+                echo "  Weaviate is ready!"
+                break
+            fi
+            attempt=$((attempt + 1))
+            sleep 2
+        done
+
+        if [ $attempt -eq $max_attempts ]; then
+            echo "  WARNING: Weaviate may not be ready yet. Check 'docker compose logs'"
+        fi
+    else
+        echo "  WARNING: Docker Compose not found. Please install Docker Desktop."
+        echo "  Weaviate will need to be started manually: docker compose up -d"
+    fi
+else
+    echo "  WARNING: Docker not found. Please install Docker Desktop."
+    echo "  Weaviate will need to be started manually: docker compose up -d"
+fi
+echo ""
+
+# Create Weaviate schema if needed
+echo "[5/5] Initializing Weaviate schema..."
+python -c "
+import weaviate
+try:
+    client = weaviate.connect_to_local()
+    collections = client.collections.list_all()
+    if 'Chunk' in collections:
+        print('  Schema already exists')
+    else:
+        print('  Creating schema...')
+        import schema
+        print('  Schema created successfully')
+    client.close()
+except Exception as e:
+    print(f'  Note: Could not connect to Weaviate: {e}')
+    print('  Run this script again after Weaviate is ready, or run: python schema.py')
+" 2>/dev/null || echo "  Schema setup will be done on first Flask app run"
+echo ""
+
+# Print summary
+echo "=========================================="
+echo "Setup Complete!"
+echo "=========================================="
+echo ""
+echo "To start the Flask application:"
+echo "  python flask_app.py"
+echo ""
+echo "The application will be available at:"
+echo "  http://localhost:5000"
+echo ""
+echo "Useful commands:"
+echo "  - Run type checks:    mypy --strict ."
+echo "  - Run tests:          pytest tests/ -v"
+echo "  - Check docstrings:   pydocstyle --convention=google ."
+echo "  - View Weaviate:      http://localhost:8080/v1"
+echo ""
+echo "For development with Ollama (free LLM):"
+echo "  1. Install Ollama: https://ollama.ai"
+echo "  2. Pull model: ollama pull qwen2.5:7b"
+echo "  3. Start Ollama: ollama serve"
+echo ""
+echo "For MCP Server (Claude Desktop integration):"
+echo "  1. Run MCP server: python mcp_server.py"
+echo "  2. Configure Claude Desktop (see MCP_README.md)"
+echo "  3. Use parse_pdf and search tools from Claude"
+echo ""