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/mcp_config.py

@@ -0,0 +1,123 @@
+"""
+Configuration management for Library RAG MCP Server.
+
+Loads and validates environment variables for the MCP server.
+"""
+
+import os
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Literal
+
+from dotenv import load_dotenv
+
+
+@dataclass
+class MCPConfig:
+    """
+    Configuration for Library RAG MCP Server.
+
+    Attributes:
+        mistral_api_key: API key for Mistral OCR and LLM services.
+        ollama_base_url: Base URL for Ollama local LLM server.
+        structure_llm_model: Model name for LLM processing.
+        structure_llm_temperature: Temperature for LLM generation.
+        weaviate_host: Weaviate server hostname.
+        weaviate_port: Weaviate server port.
+        log_level: Logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL).
+        default_llm_provider: Default LLM provider ("ollama" or "mistral").
+        output_dir: Base directory for processed files.
+    """
+
+    # Required
+    mistral_api_key: str
+
+    # LLM Configuration
+    ollama_base_url: str = "http://localhost:11434"
+    structure_llm_model: str = "deepseek-r1:14b"
+    structure_llm_temperature: float = 0.2
+    default_llm_provider: Literal["ollama", "mistral"] = "ollama"
+
+    # Weaviate Configuration
+    weaviate_host: str = "localhost"
+    weaviate_port: int = 8080
+
+    # Logging
+    log_level: str = "INFO"
+
+    # File System
+    output_dir: Path = Path("output")
+
+    @classmethod
+    def from_env(cls) -> "MCPConfig":
+        """
+        Load configuration from environment variables.
+
+        Returns:
+            MCPConfig instance populated from .env file.
+
+        Raises:
+            ValueError: If required environment variables are missing.
+        """
+        # Load .env file
+        load_dotenv()
+
+        # Required variables
+        mistral_api_key = os.getenv("MISTRAL_API_KEY")
+        if not mistral_api_key:
+            raise ValueError(
+                "MISTRAL_API_KEY environment variable is required. "
+                "Please set it in your .env file."
+            )
+
+        # Optional variables with defaults
+        return cls(
+            mistral_api_key=mistral_api_key,
+            ollama_base_url=os.getenv("OLLAMA_BASE_URL", "http://localhost:11434"),
+            structure_llm_model=os.getenv("STRUCTURE_LLM_MODEL", "deepseek-r1:14b"),
+            structure_llm_temperature=float(
+                os.getenv("STRUCTURE_LLM_TEMPERATURE", "0.2")
+            ),
+            default_llm_provider=os.getenv("DEFAULT_LLM_PROVIDER", "ollama"),  # type: ignore
+            weaviate_host=os.getenv("WEAVIATE_HOST", "localhost"),
+            weaviate_port=int(os.getenv("WEAVIATE_PORT", "8080")),
+            log_level=os.getenv("LOG_LEVEL", "INFO"),
+            output_dir=Path(os.getenv("OUTPUT_DIR", "output")),
+        )
+
+    @property
+    def weaviate_url(self) -> str:
+        """Get full Weaviate URL."""
+        return f"http://{self.weaviate_host}:{self.weaviate_port}"
+
+    def validate(self) -> None:
+        """
+        Validate configuration values.
+
+        Raises:
+            ValueError: If configuration is invalid.
+        """
+        # Validate LLM provider
+        if self.default_llm_provider not in ("ollama", "mistral"):
+            raise ValueError(
+                f"Invalid LLM provider: {self.default_llm_provider}. "
+                "Must be 'ollama' or 'mistral'."
+            )
+
+        # Validate log level
+        valid_log_levels = ("DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL")
+        if self.log_level.upper() not in valid_log_levels:
+            raise ValueError(
+                f"Invalid log level: {self.log_level}. "
+                f"Must be one of {valid_log_levels}."
+            )
+
+        # Validate temperature
+        if not 0.0 <= self.structure_llm_temperature <= 2.0:
+            raise ValueError(
+                f"Invalid temperature: {self.structure_llm_temperature}. "
+                "Must be between 0.0 and 2.0."
+            )
+
+        # Create output directory if it doesn't exist
+        self.output_dir.mkdir(parents=True, exist_ok=True)