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.bat

@@ -0,0 +1,154 @@
+@echo off
+REM ============================================================================
+REM Library RAG MCP Server - Development Environment Setup (Windows)
+REM ============================================================================
+REM This script sets up and starts the development environment for the
+REM Library RAG MCP Server project.
+REM
+REM Usage:
+REM   init.bat           - Full setup (venv, deps, docker, verify)
+REM   init.bat --quick   - Quick start (docker only, assumes deps installed)
+REM
+REM Requirements:
+REM   - Python 3.10+
+REM   - Docker Desktop
+REM   - Git
+REM ============================================================================
+
+setlocal enabledelayedexpansion
+
+echo.
+echo ============================================
+echo Library RAG MCP Server - Setup
+echo ============================================
+echo.
+
+REM Check for quick mode
+set QUICK_MODE=false
+if "%1"=="--quick" set QUICK_MODE=true
+
+REM Check prerequisites
+echo Checking prerequisites...
+
+where python >nul 2>&1
+if %errorlevel% neq 0 (
+    echo [ERROR] Python is not installed or not in PATH
+    exit /b 1
+)
+echo [OK] Python is installed
+
+where docker >nul 2>&1
+if %errorlevel% neq 0 (
+    echo [ERROR] Docker is not installed or not in PATH
+    exit /b 1
+)
+echo [OK] Docker is installed
+
+REM Check Docker is running
+docker info >nul 2>&1
+if %errorlevel% neq 0 (
+    echo [ERROR] Docker is not running. Please start Docker Desktop.
+    exit /b 1
+)
+echo [OK] Docker is running
+
+if "%QUICK_MODE%"=="false" (
+    echo.
+    echo Setting up Python virtual environment...
+
+    if not exist "venv" (
+        echo Creating virtual environment...
+        python -m venv venv
+    )
+    echo [OK] Virtual environment exists
+
+    REM Activate venv
+    call venv\Scripts\activate.bat
+    echo [OK] Virtual environment activated
+
+    echo.
+    echo Installing Python dependencies...
+    pip install --upgrade pip -q
+    pip install -r requirements.txt -q
+    echo [OK] Dependencies installed
+)
+
+REM Check for .env file
+echo.
+echo Checking environment configuration...
+if not exist ".env" (
+    if exist ".env.example" (
+        echo [WARN] .env file not found. Copying from .env.example...
+        copy .env.example .env >nul
+        echo [WARN] Please edit .env and add your MISTRAL_API_KEY
+    ) else (
+        echo [ERROR] .env file not found. Create it with MISTRAL_API_KEY=your-key
+        exit /b 1
+    )
+) else (
+    echo [OK] .env file exists
+)
+
+REM Start Docker services
+echo.
+echo Starting Docker services (Weaviate + Transformers)...
+docker compose up -d
+
+REM Wait for Weaviate to be ready
+echo.
+echo Waiting for Weaviate to be ready...
+set RETRY_COUNT=0
+set MAX_RETRIES=30
+
+:wait_loop
+curl -s http://localhost:8080/v1/.well-known/ready >nul 2>&1
+if %errorlevel% equ 0 (
+    echo [OK] Weaviate is ready!
+    goto weaviate_ready
+)
+
+set /a RETRY_COUNT+=1
+if %RETRY_COUNT% geq %MAX_RETRIES% (
+    echo [ERROR] Weaviate failed to start. Check docker compose logs.
+    exit /b 1
+)
+
+echo|set /p="."
+timeout /t 2 /nobreak >nul
+goto wait_loop
+
+:weaviate_ready
+
+REM Initialize Weaviate schema
+if exist "schema_v2.py" (
+    echo.
+    echo Initializing Weaviate schema...
+    python schema_v2.py 2>nul
+    echo [OK] Schema initialized
+)
+
+echo.
+echo ============================================
+echo Setup Complete!
+echo ============================================
+echo.
+echo Services running:
+echo   - Weaviate:     http://localhost:8080
+echo   - Transformers: Running (internal)
+echo.
+echo Quick commands:
+echo   - Run MCP server:    python mcp_server.py
+echo   - Run Flask app:     python flask_app.py
+echo   - Run tests:         pytest tests\ -v
+echo   - Type check:        mypy . --strict
+echo   - Stop services:     docker compose down
+echo.
+echo Configuration:
+echo   - Edit .env file to configure API keys and settings
+echo   - See MCP_README.md for MCP server documentation
+echo.
+echo Note: For MCP server, configure Claude Desktop with:
+echo   %%APPDATA%%\Claude\claude_desktop_config.json
+echo.
+
+endlocal