PaperQA2 is an agentic retrieval-augmented generation (RAG) system for scientific literature. It answers questions by searching, indexing, and analyzing PDFs, text documents, and clinical trials using a multi-step agent workflow. The system integrates with multiple scholarly metadata providers (Crossref, Semantic Scholar, OpenAlex, Unpaywall) for DOI resolution, citation counts, retraction detection, and journal quality scoring. It supports multiple LLM backends via LiteLLM, pluggable PDF readers (pypdf, PyMuPDF, Docling, Nemotron), and vector stores (Numpy, Qdrant). The architecture is a Python library with a CLI (`pqa`), featuring a hierarchical Pydantic settings system, an agent framework with tool selection and memory, and a plugin-based document parsing pipeline. While primarily an application, it is research-backed with published benchmarks (LitQA2, LFRQA) and includes config presets for different quality/performance trade-offs.