Reproducible Literature Synthesis with infrastructure/search and infrastructure/reference

This paper documents template search project, the literature-search exemplar shipped with the Research Project Template (https://github.com/docxology/template). The project demonstrates two configurable, reproducible pipelines sharing the same configuration file and the same infrastructure/search/ + infrastructure/reference/ modules. The standard pipeline (scripts/run search pipeline.py) handles a single SearchQuery end-to-end. The deep-search pipeline (scripts/run deep search.py, see ) fans out across a list of keywords (each capped at 100 papers per keyword from deep search.max results per keyword in manuscript/config.yaml), fully enriches every paper with its abstract and PDF fulltext, and (optionally) uses the local LLM to write a multi-section reading note for every paper. When a deep-search aggregate exists, the latest run covered 3 keyword(s) with unique paper(s) after cross-keywo