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Docs Index

Start here if you're new to FLS:

  • INSTALL.md — installation options and verification steps.
  • USAGE.md — the main workflow (--delta, integrity checks, summarization).
  • docs/API_KEYS.md — Semantic Scholar key + Unpaywall email setup (and .env.local).
  • docs/RAG.md — local/offline RAG (index + query), plus OCR option for scanned PDFs.
  • docs/UNPAYWALL.md — Unpaywall endpoint details and usage notes.
  • docs/CUSTOMIZATION.md — tuning keywords/categories/research context.
  • docs/AGENT_INTEGRATION.md — agent session protocol (model-agnostic) and templates.
  • templates/AGENT.template.md — copy/paste protocol for any agent instructions file (model-agnostic).

Typical loop:

  1. fls.py (optional convenience runner; confirms config then runs scan + index)
  2. literature_scan.py --delta (fetch + download PDFs)
  3. rag_index.py (build/update local index)
  4. rag_query.py (retrieve evidence/snippets for synthesis)
  5. orchestrate_summarization.py (agents read PDFs and store structured notes)