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/.linear_project.json

@@ -0,0 +1,13 @@
+{
+  "initialized": true,
+  "created_at": "2025-12-24T14:34:02.791Z",
+  "team_id": "55c48386-0ed4-4f41-a963-c3d4bd2b9233",
+  "team_name": "linear_rag_philo",
+  "project_id": "c04bad18-7bda-44d0-a25c-51d5bf671734",
+  "project_name": "library_rag",
+  "project_url": "https://linear.app/philosophiatech/project/library-rag-mcp-server-pdf-ingestion-and-semantic-retrieval-5172487a22fc",
+  "meta_issue_id": "8ef2b8d5-662b-49da-83b3-ee8a98028d7f",
+  "meta_issue_identifier": "LRP-95",
+  "total_issues": 55,
+  "notes": "Project initialized by initializer agent. Extended by initializer bis with 12 new conversation interface issues (2025-12-29)."
+}