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/tests/mcp/conftest.py

@@ -0,0 +1,196 @@
+"""
+Pytest fixtures for MCP server tests.
+
+Provides common fixtures for mocking dependencies and test data.
+"""
+
+import os
+from pathlib import Path
+from typing import Any, Dict, Generator
+from unittest.mock import AsyncMock, MagicMock, patch
+
+import pytest
+
+from mcp_config import MCPConfig
+
+
+@pytest.fixture
+def mock_env_with_api_key() -> Generator[Dict[str, str], None, None]:
+    """
+    Provide environment with MISTRAL_API_KEY set.
+
+    Yields:
+        Dictionary of environment variables.
+    """
+    env = {"MISTRAL_API_KEY": "test-api-key-12345"}
+    with patch.dict(os.environ, env, clear=True):
+        yield env
+
+
+@pytest.fixture
+def valid_config() -> MCPConfig:
+    """
+    Provide a valid MCPConfig instance for testing.
+
+    Returns:
+        MCPConfig with valid test values.
+    """
+    return MCPConfig(
+        mistral_api_key="test-api-key",
+        ollama_base_url="http://localhost:11434",
+        structure_llm_model="test-model",
+        structure_llm_temperature=0.2,
+        default_llm_provider="ollama",
+        weaviate_host="localhost",
+        weaviate_port=8080,
+        log_level="INFO",
+        output_dir=Path("test_output"),
+    )
+
+
+@pytest.fixture
+def mock_weaviate_client() -> Generator[MagicMock, None, None]:
+    """
+    Provide a mocked Weaviate client.
+
+    Yields:
+        MagicMock configured as a Weaviate client.
+    """
+    with patch("weaviate.connect_to_local") as mock_connect:
+        mock_client = MagicMock()
+        mock_connect.return_value = mock_client
+        yield mock_client
+
+
+# =============================================================================
+# Parsing Tools Fixtures
+# =============================================================================
+
+
+@pytest.fixture
+def sample_pdf_bytes() -> bytes:
+    """
+    Provide minimal valid PDF bytes for testing.
+
+    Returns:
+        Bytes representing a minimal valid PDF file.
+    """
+    # Minimal valid PDF structure
+    return b"""%PDF-1.4
+1 0 obj << /Type /Catalog /Pages 2 0 R >> endobj
+2 0 obj << /Type /Pages /Kids [3 0 R] /Count 1 >> endobj
+3 0 obj << /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >> endobj
+xref
+0 4
+0000000000 65535 f
+0000000009 00000 n
+0000000058 00000 n
+0000000115 00000 n
+trailer << /Size 4 /Root 1 0 R >>
+startxref
+193
+%%EOF"""
+
+
+@pytest.fixture
+def successful_pipeline_result() -> Dict[str, Any]:
+    """
+    Provide a successful pipeline result for mocking.
+
+    Returns:
+        Dictionary mimicking a successful process_pdf result.
+    """
+    return {
+        "success": True,
+        "document_name": "test-document",
+        "source_id": "test-document",
+        "pages": 10,
+        "chunks_count": 25,
+        "cost_ocr": 0.03,
+        "cost_llm": 0.05,
+        "cost_total": 0.08,
+        "output_dir": Path("output/test-document"),
+        "metadata": {
+            "title": "Test Document Title",
+            "author": "Test Author",
+            "language": "en",
+            "year": 2023,
+        },
+        "error": None,
+    }
+
+
+@pytest.fixture
+def failed_pipeline_result() -> Dict[str, Any]:
+    """
+    Provide a failed pipeline result for mocking.
+
+    Returns:
+        Dictionary mimicking a failed process_pdf result.
+    """
+    return {
+        "success": False,
+        "document_name": "failed-document",
+        "source_id": "failed-document",
+        "pages": 0,
+        "chunks_count": 0,
+        "cost_ocr": 0.0,
+        "cost_llm": 0.0,
+        "cost_total": 0.0,
+        "output_dir": "",
+        "metadata": {},
+        "error": "OCR processing failed: Invalid PDF structure",
+    }
+
+
+@pytest.fixture
+def mock_process_pdf() -> Generator[MagicMock, None, None]:
+    """
+    Provide a mocked process_pdf function.
+
+    Yields:
+        MagicMock for utils.pdf_pipeline.process_pdf.
+    """
+    with patch("mcp_tools.parsing_tools.process_pdf") as mock:
+        yield mock
+
+
+@pytest.fixture
+def mock_process_pdf_bytes() -> Generator[MagicMock, None, None]:
+    """
+    Provide a mocked process_pdf_bytes function.
+
+    Yields:
+        MagicMock for utils.pdf_pipeline.process_pdf_bytes.
+    """
+    with patch("mcp_tools.parsing_tools.process_pdf_bytes") as mock:
+        yield mock
+
+
+@pytest.fixture
+def mock_download_pdf() -> Generator[AsyncMock, None, None]:
+    """
+    Provide a mocked download_pdf function.
+
+    Yields:
+        AsyncMock for mcp_tools.parsing_tools.download_pdf.
+    """
+    with patch("mcp_tools.parsing_tools.download_pdf", new_callable=AsyncMock) as mock:
+        yield mock
+
+
+@pytest.fixture
+def temp_pdf_file(tmp_path: Path, sample_pdf_bytes: bytes) -> Path:
+    """
+    Create a temporary PDF file for testing.
+
+    Args:
+        tmp_path: Pytest tmp_path fixture.
+        sample_pdf_bytes: Sample PDF content.
+
+    Returns:
+        Path to the temporary PDF file.
+    """
+    pdf_path = tmp_path / "test_document.pdf"
+    pdf_path.write_bytes(sample_pdf_bytes)
+    return pdf_path