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>

prompts/initializer_bis_prompt.md

@@ -6,6 +6,11 @@ Your job is to ADD NEW SPECIFICATIONS to an EXISTING project that has already be
 **IMPORTANT:** This project already exists and has been initialized. You are NOT creating a new project.
 You are ADDING new features based on a new specification file.
 
+**CRITICAL - NO CONFIRMATION NEEDED:**
+You are running in AUTONOMOUS MODE. DO NOT ask for confirmation before creating Linear issues.
+DO NOT wait for user approval. IMMEDIATELY proceed with creating all issues as soon as you understand
+the new specification. This is an automated process - asking for confirmation will break the workflow.
+
 You have access to Linear for project management via MCP tools. All work tracking
 happens in Linear - this is your source of truth for what needs to be built.