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/utils/mistral_client.py

@@ -0,0 +1,169 @@
+"""Mistral API Client Management.
+
+This module provides utilities for managing the Mistral API client,
+including API key retrieval and OCR cost estimation. It serves as the
+foundation for all Mistral API interactions in the Library RAG pipeline.
+
+Key Features:
+    - Automatic API key discovery from multiple sources
+    - Client instantiation with proper authentication
+    - OCR cost estimation for budget planning
+
+API Key Priority:
+    The module searches for the Mistral API key in this order:
+    1. Explicit argument passed to functions
+    2. MISTRAL_API_KEY environment variable
+    3. .env file in the project root
+
+Cost Estimation:
+    Mistral OCR pricing (as of 2024):
+    - Standard OCR: ~1 EUR per 1000 pages (0.001 EUR/page)
+    - OCR with annotations: ~3 EUR per 1000 pages (0.003 EUR/page)
+
+Example:
+    Basic client creation and usage::
+
+        from utils.mistral_client import create_client, estimate_ocr_cost
+
+        # Create authenticated client
+        client = create_client()
+
+        # Estimate cost for a 100-page document
+        cost = estimate_ocr_cost(100, use_annotations=False)
+        print(f"Estimated cost: {cost:.2f} EUR")  # Output: Estimated cost: 0.10 EUR
+
+    Using explicit API key::
+
+        client = create_client(api_key="your-api-key-here")
+
+See Also:
+    - :mod:`utils.ocr_processor`: OCR execution functions using this client
+    - :mod:`utils.pdf_uploader`: PDF upload utilities for OCR processing
+
+Note:
+    Ensure MISTRAL_API_KEY is set before using this module in production.
+    The API key can be obtained from the Mistral AI platform dashboard.
+"""
+
+import os
+from typing import Optional
+
+from dotenv import load_dotenv
+from mistralai import Mistral
+
+
+def get_api_key(api_key: Optional[str] = None) -> str:
+    """Retrieve the Mistral API key from available sources.
+
+    Searches for the API key in the following priority order:
+    1. Explicit argument passed to this function
+    2. MISTRAL_API_KEY environment variable
+    3. .env file in the project root
+
+    Args:
+        api_key: Optional API key to use directly. If provided and non-empty,
+            this value is used without checking other sources.
+
+    Returns:
+        The Mistral API key as a string.
+
+    Raises:
+        RuntimeError: If no API key is found in any of the checked sources.
+
+    Example:
+        >>> # Using environment variable
+        >>> key = get_api_key()
+        >>> len(key) > 0
+        True
+
+        >>> # Using explicit key
+        >>> key = get_api_key("my-api-key")
+        >>> key
+        'my-api-key'
+    """
+    # 1. Argument fourni
+    if api_key and api_key.strip():
+        return api_key.strip()
+
+    # 2. Variable d environnement
+    env_key = os.getenv("MISTRAL_API_KEY", "").strip()
+    if env_key:
+        return env_key
+
+    # 3. Fichier .env
+    load_dotenv()
+    env_key = os.getenv("MISTRAL_API_KEY", "").strip()
+    if env_key:
+        return env_key
+
+    raise RuntimeError(
+        "MISTRAL_API_KEY manquante. "
+        "Definissez la variable d environnement ou creez un fichier .env"
+    )
+
+
+def create_client(api_key: Optional[str] = None) -> Mistral:
+    """Create and return an authenticated Mistral client.
+
+    This is the primary entry point for obtaining a Mistral client instance.
+    The client can be used for OCR operations, chat completions, and other
+    Mistral API features.
+
+    Args:
+        api_key: Optional API key. If not provided, the key is automatically
+            retrieved from environment variables or .env file.
+
+    Returns:
+        An authenticated Mistral client instance ready for API calls.
+
+    Raises:
+        RuntimeError: If no API key is found (propagated from get_api_key).
+
+    Example:
+        >>> client = create_client()
+        >>> # Client is now ready for OCR or other operations
+        >>> response = client.ocr.process(...)  # doctest: +SKIP
+    """
+    key = get_api_key(api_key)
+    return Mistral(api_key=key)
+
+
+def estimate_ocr_cost(nb_pages: int, use_annotations: bool = False) -> float:
+    """Estimate the cost of OCR processing for a document.
+
+    Calculates the expected cost based on Mistral OCR pricing model.
+    This is useful for budget planning before processing large document
+    collections.
+
+    Pricing Model:
+        - Standard OCR: ~1 EUR per 1000 pages (0.001 EUR/page)
+        - OCR with annotations: ~3 EUR per 1000 pages (0.003 EUR/page)
+
+    The annotation mode is approximately 3x more expensive but provides
+    additional structural information useful for TOC extraction.
+
+    Args:
+        nb_pages: Number of pages in the document to process.
+        use_annotations: If True, uses the higher annotation pricing.
+            Annotations provide bounding box and structural data.
+
+    Returns:
+        Estimated cost in euros as a float.
+
+    Example:
+        >>> # Standard OCR for 100 pages
+        >>> estimate_ocr_cost(100)
+        0.1
+
+        >>> # OCR with annotations for 100 pages
+        >>> estimate_ocr_cost(100, use_annotations=True)
+        0.3
+
+        >>> # Large document collection
+        >>> estimate_ocr_cost(10000)
+        10.0
+    """
+    if use_annotations:
+        return nb_pages * 0.003  # 3 EUR / 1000 pages
+    else:
+        return nb_pages * 0.001  # 1 EUR / 1000 pages