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/__init__.py

@@ -0,0 +1,74 @@
+"""Utils - Pipeline de parsing PDF avec OCR Mistral et structuration LLM.
+
+Version 2.0 : Pipeline intelligent avec extraction LLM des métadonnées,
+TOC, classification des sections, chunking sémantique et validation.
+"""
+
+from .mistral_client import create_client, get_api_key, estimate_ocr_cost
+from .pdf_uploader import upload_pdf
+from .ocr_processor import run_ocr, serialize_ocr_response
+from .markdown_builder import build_markdown
+from .image_extractor import extract_images, create_image_writer
+from .hierarchy_parser import build_hierarchy
+from .llm_structurer import structure_with_llm, LLMStructureError
+
+# Nouveaux modules LLM v2
+from .llm_metadata import extract_metadata
+from .llm_toc import extract_toc
+from .llm_classifier import classify_sections, filter_indexable_sections
+from .llm_cleaner import clean_chunk, clean_page_markers, is_chunk_valid
+from .llm_chunker import chunk_section_with_llm, simple_chunk_by_paragraphs, extract_concepts_from_chunk, extract_paragraph_number
+from .llm_validator import validate_document, apply_corrections, enrich_chunks_with_concepts
+
+# Pipeline
+from .pdf_pipeline import process_pdf, process_pdf_v2, process_pdf_bytes
+from .weaviate_ingest import ingest_document, delete_document_chunks
+
+__all__ = [
+    # Client Mistral
+    "create_client",
+    "get_api_key", 
+    "estimate_ocr_cost",
+    # Upload
+    "upload_pdf",
+    # OCR
+    "run_ocr",
+    "serialize_ocr_response",
+    # Markdown
+    "build_markdown",
+    # Images
+    "extract_images",
+    "create_image_writer",
+    # Hiérarchie
+    "build_hierarchy",
+    # LLM Legacy
+    "structure_with_llm",
+    "LLMStructureError",
+    # LLM v2 - Métadonnées
+    "extract_metadata",
+    # LLM v2 - TOC
+    "extract_toc",
+    # LLM v2 - Classification
+    "classify_sections",
+    "filter_indexable_sections",
+    # LLM v2 - Nettoyage
+    "clean_chunk",
+    "clean_page_markers",
+    "is_chunk_valid",
+    # LLM v2 - Chunking
+    "chunk_section_with_llm",
+    "simple_chunk_by_paragraphs",
+    "extract_concepts_from_chunk",
+    "extract_paragraph_number",
+    # LLM v2 - Validation
+    "validate_document",
+    "apply_corrections",
+    "enrich_chunks_with_concepts",
+    # Pipeline
+    "process_pdf",
+    "process_pdf_v2",
+    "process_pdf_bytes",
+    # Weaviate
+    "ingest_document",
+    "delete_document_chunks",
+]