Refactor code structure for improved readability and maintainability

fix: resolve indexer loop indentation and implement topic-aware DB routing

feat: Update Milvus search to allow for a configurable top K results and add new research papers to the database summary

feat: Add single-command pipeline for end-to-end processing and update README with new usage instructions

feat: Create runbook for processing new PDFs into Milvus with detailed commands and outcomes

feat: Add File Agent for accessing project files and enhance root agent with file retrieval capabilities

feat: Integrate summarizer agent and enhance agent instructions for structured responses

feat: Add internet search agent to enhance query capabilities and integrate with google_search tool

feat: Enhance Milvus RAG agent with metadata querying and update instruction set

feat: Add indexing functionality for -RAG.md files into Milvus with chunking and embedding

Remove obsolete image files and references, implement RAG preparation and metadata addition scripts

feat: Add 'md-with-images' command to generate Markdown with images for each paper

feat: Implement project orchestrator CLI with subcommands for PDF ingestion and output preparation

chore: Update .gitignore to include additional environment and cache files

Implement code changes to enhance functionality and improve performance