Scaffold or audit an entire research project repository organized around its source library. Use whenever the user is starting, structuring, organizing, or reviewing a whole project — "set up a research repo", "how should I structure/organize this project", "initialize my sources folder", "new paper or literature-review project", "audit my repo structure", "is my sources folder set up right", "check my project layout". Builds the full tree from the sources spine outward — sources/{og,md,unprocessed}, references.bib, a PDF→Markdown convert script (OpenDataLoader PDF), a process-source intake command, CLAUDE.md/AGENTS.md, .gitignore, .venv — plus the analysis, manuscript, and review folders; or audits an existing repo and reports what is present, partial, or missing. NOT for intaking or converting a single PDF (use process-source) or building a publication replication package (use replication-package).
LLM token logprobs and calibration: per-decision confidence, ECE, Brier, reliability diagrams, low-confidence triage.
LLM council/panel voting: multi-model coders, consensus rules, inter-rater agreement (kappa, alpha), correlated-error diagnostics.
Compare OCR systems before a bulk run: candidate set, stratified ground truth, CER/WER, normalization, per-language and per-stratum accuracy.
Fact-check a manuscript's claims against the cited sources themselves: locate each source's knowledge-base Markdown file and verify the in-text claim is actually supported. Runs a pre-flight gate that refuses unless a per-source Markdown knowledge base exists and is clean (PDFs converted via process-source); then runs citation-check; then audits claim support, overclaiming, direction, scope, and misattribution.
Audit citation existence and fabrication risk, in-text/reference parity, DOIs, claim support, and style.
Typeset a working paper or journal submission in house-style LaTeX from any draft — Markdown, Word (.docx), TeX, ODT, RTF, or HTML. Convert with pandoc, wrap in an EB Garamond template, build the PDF with latexmk, and prepare for a specific journal (spacing, page limit, anonymization, disclosures, citation style). Use for "format/typeset/convert my paper to LaTeX", "make a working paper", "prepare this for submission to <journal>".
Clean and reshape Qualtrics conjoint exports to analysis-ready long format.