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/.env.example

@@ -0,0 +1,51 @@
+# ============================================================================
+# Library RAG MCP Server - Environment Configuration
+# ============================================================================
+# Copy this file to .env and fill in your values.
+# Required variables are marked with [REQUIRED].
+# ============================================================================
+
+# [REQUIRED] Mistral API Key for OCR and LLM services
+# Get your key at: https://console.mistral.ai/
+MISTRAL_API_KEY=your-mistral-api-key-here
+
+# ============================================================================
+# LLM Configuration
+# ============================================================================
+
+# Ollama base URL for local LLM (default: http://localhost:11434)
+OLLAMA_BASE_URL=http://localhost:11434
+
+# LLM model for structure extraction (default: deepseek-r1:14b)
+STRUCTURE_LLM_MODEL=deepseek-r1:14b
+
+# Temperature for LLM generation (0.0-2.0, default: 0.2)
+STRUCTURE_LLM_TEMPERATURE=0.2
+
+# Default LLM provider: "ollama" (local, free) or "mistral" (API, paid)
+# For MCP server, always uses "mistral" with mistral-medium-latest
+DEFAULT_LLM_PROVIDER=ollama
+
+# ============================================================================
+# Weaviate Configuration
+# ============================================================================
+
+# Weaviate server hostname (default: localhost)
+WEAVIATE_HOST=localhost
+
+# Weaviate server port (default: 8080)
+WEAVIATE_PORT=8080
+
+# ============================================================================
+# Logging
+# ============================================================================
+
+# Log level: DEBUG, INFO, WARNING, ERROR, CRITICAL (default: INFO)
+LOG_LEVEL=INFO
+
+# ============================================================================
+# File System
+# ============================================================================
+
+# Base directory for processed files (default: output)
+OUTPUT_DIR=output