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>

.claude/settings.local.json

@@ -63,7 +63,17 @@
       "Bash(docker info:*)",
       "Bash(docker stats:*)",
       "Bash(timeout:*)",
-      "Bash(docker inspect:*)"
+      "Bash(docker inspect:*)",
+      "Bash(mypy:*)",
+      "Bash(wc:*)",
+      "Bash(exit 0)",
+      "Bash(docker stop:*)",
+      "Bash(docker rm:*)",
+      "Bash(docker run:*)",
+      "Bash(docker compose:*)",
+      "Bash(cleanup_unused_files.bat)",
+      "Bash(cmd /c cleanup_unused_files.bat)",
+      "Bash(pytest:*)"
     ]
   }
 }