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/test_config.py

@@ -0,0 +1,133 @@
+"""
+Unit tests for MCP configuration management.
+
+Tests the MCPConfig class for proper loading, validation, and defaults.
+"""
+
+import os
+import pytest
+from pathlib import Path
+from unittest.mock import patch
+
+from mcp_config import MCPConfig
+
+
+class TestMCPConfigFromEnv:
+    """Test MCPConfig.from_env() method."""
+
+    def test_loads_with_required_key(self) -> None:
+        """Test config loads when MISTRAL_API_KEY is present."""
+        with patch.dict(os.environ, {"MISTRAL_API_KEY": "test-key-123"}, clear=True):
+            config = MCPConfig.from_env()
+            assert config.mistral_api_key == "test-key-123"
+
+    def test_raises_without_api_key(self) -> None:
+        """Test ValueError is raised when MISTRAL_API_KEY is missing."""
+        with patch("mcp_config.load_dotenv"):  # Prevent reading .env file
+            with patch.dict(os.environ, {}, clear=True):
+                with pytest.raises(ValueError) as exc_info:
+                    MCPConfig.from_env()
+                assert "MISTRAL_API_KEY" in str(exc_info.value)
+
+    def test_default_values_applied(self) -> None:
+        """Test all default values are applied correctly."""
+        with patch.dict(os.environ, {"MISTRAL_API_KEY": "test-key"}, clear=True):
+            config = MCPConfig.from_env()
+
+            # Check all defaults
+            assert config.ollama_base_url == "http://localhost:11434"
+            assert config.structure_llm_model == "deepseek-r1:14b"
+            assert config.structure_llm_temperature == 0.2
+            assert config.default_llm_provider == "ollama"
+            assert config.weaviate_host == "localhost"
+            assert config.weaviate_port == 8080
+            assert config.log_level == "INFO"
+            assert config.output_dir == Path("output")
+
+    def test_custom_values_loaded(self) -> None:
+        """Test custom environment values are loaded correctly."""
+        custom_env = {
+            "MISTRAL_API_KEY": "custom-key",
+            "OLLAMA_BASE_URL": "http://custom:1234",
+            "STRUCTURE_LLM_MODEL": "custom-model",
+            "STRUCTURE_LLM_TEMPERATURE": "0.7",
+            "DEFAULT_LLM_PROVIDER": "mistral",
+            "WEAVIATE_HOST": "weaviate.example.com",
+            "WEAVIATE_PORT": "9999",
+            "LOG_LEVEL": "DEBUG",
+            "OUTPUT_DIR": "/custom/output",
+        }
+        with patch.dict(os.environ, custom_env, clear=True):
+            config = MCPConfig.from_env()
+
+            assert config.mistral_api_key == "custom-key"
+            assert config.ollama_base_url == "http://custom:1234"
+            assert config.structure_llm_model == "custom-model"
+            assert config.structure_llm_temperature == 0.7
+            assert config.default_llm_provider == "mistral"
+            assert config.weaviate_host == "weaviate.example.com"
+            assert config.weaviate_port == 9999
+            assert config.log_level == "DEBUG"
+            assert config.output_dir == Path("/custom/output")
+
+
+class TestMCPConfigValidation:
+    """Test MCPConfig.validate() method."""
+
+    def test_valid_config_passes(self) -> None:
+        """Test valid configuration passes validation."""
+        config = MCPConfig(
+            mistral_api_key="test-key",
+            default_llm_provider="ollama",
+            log_level="INFO",
+            structure_llm_temperature=0.5,
+        )
+        # Should not raise
+        config.validate()
+
+    def test_invalid_llm_provider_fails(self) -> None:
+        """Test invalid LLM provider raises ValueError."""
+        config = MCPConfig(
+            mistral_api_key="test-key",
+            default_llm_provider="invalid",  # type: ignore
+        )
+        with pytest.raises(ValueError) as exc_info:
+            config.validate()
+        assert "Invalid LLM provider" in str(exc_info.value)
+
+    def test_invalid_log_level_fails(self) -> None:
+        """Test invalid log level raises ValueError."""
+        config = MCPConfig(
+            mistral_api_key="test-key",
+            log_level="INVALID",
+        )
+        with pytest.raises(ValueError) as exc_info:
+            config.validate()
+        assert "Invalid log level" in str(exc_info.value)
+
+    def test_invalid_temperature_fails(self) -> None:
+        """Test temperature outside 0-2 range raises ValueError."""
+        config = MCPConfig(
+            mistral_api_key="test-key",
+            structure_llm_temperature=2.5,
+        )
+        with pytest.raises(ValueError) as exc_info:
+            config.validate()
+        assert "Invalid temperature" in str(exc_info.value)
+
+
+class TestMCPConfigProperties:
+    """Test MCPConfig properties."""
+
+    def test_weaviate_url_property(self) -> None:
+        """Test weaviate_url property returns correct URL."""
+        config = MCPConfig(
+            mistral_api_key="test-key",
+            weaviate_host="my-host",
+            weaviate_port=9090,
+        )
+        assert config.weaviate_url == "http://my-host:9090"
+
+
+if __name__ == "__main__":
+    pytest.main([__file__, "-v"])