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_tools/__init__.py

@@ -0,0 +1,106 @@
+"""
+MCP Tools for Library RAG Server.
+
+This package contains all tool implementations for the Library RAG MCP server:
+- Parsing tools: PDF ingestion with optimal parameters
+- Retrieval tools: Semantic search and document management
+- Exceptions: Custom exception classes for structured error handling
+- Logging: Structured JSON logging configuration
+"""
+
+from mcp_tools.schemas import (
+    ParsePdfInput,
+    ParsePdfOutput,
+    SearchChunksInput,
+    SearchChunksOutput,
+    SearchSummariesInput,
+    SearchSummariesOutput,
+    GetDocumentInput,
+    GetDocumentOutput,
+    ListDocumentsInput,
+    ListDocumentsOutput,
+    GetChunksByDocumentInput,
+    GetChunksByDocumentOutput,
+    FilterByAuthorInput,
+    FilterByAuthorOutput,
+    DeleteDocumentInput,
+    DeleteDocumentOutput,
+)
+
+from mcp_tools.exceptions import (
+    MCPToolError,
+    WeaviateConnectionError,
+    PDFProcessingError,
+    DocumentNotFoundError,
+    ValidationError,
+    LLMProcessingError,
+    DownloadError,
+)
+
+from mcp_tools.logging_config import (
+    setup_mcp_logging,
+    get_tool_logger,
+    ToolInvocationLogger,
+    log_tool_invocation,
+    log_weaviate_query,
+    redact_sensitive_data,
+    redact_dict,
+)
+
+from mcp_tools.parsing_tools import parse_pdf_handler
+from mcp_tools.retrieval_tools import (
+    search_chunks_handler,
+    search_summaries_handler,
+    get_document_handler,
+    list_documents_handler,
+    get_chunks_by_document_handler,
+    filter_by_author_handler,
+    delete_document_handler,
+)
+
+__all__ = [
+    # Parsing tools
+    "parse_pdf_handler",
+    # Retrieval tools
+    "search_chunks_handler",
+    "search_summaries_handler",
+    "get_document_handler",
+    "list_documents_handler",
+    "get_chunks_by_document_handler",
+    "filter_by_author_handler",
+    "delete_document_handler",
+    # Parsing schemas
+    "ParsePdfInput",
+    "ParsePdfOutput",
+    # Retrieval schemas
+    "SearchChunksInput",
+    "SearchChunksOutput",
+    "SearchSummariesInput",
+    "SearchSummariesOutput",
+    "GetDocumentInput",
+    "GetDocumentOutput",
+    "ListDocumentsInput",
+    "ListDocumentsOutput",
+    "GetChunksByDocumentInput",
+    "GetChunksByDocumentOutput",
+    "FilterByAuthorInput",
+    "FilterByAuthorOutput",
+    "DeleteDocumentInput",
+    "DeleteDocumentOutput",
+    # Exceptions
+    "MCPToolError",
+    "WeaviateConnectionError",
+    "PDFProcessingError",
+    "DocumentNotFoundError",
+    "ValidationError",
+    "LLMProcessingError",
+    "DownloadError",
+    # Logging
+    "setup_mcp_logging",
+    "get_tool_logger",
+    "ToolInvocationLogger",
+    "log_tool_invocation",
+    "log_weaviate_query",
+    "redact_sensitive_data",
+    "redact_dict",
+]