What problem does it solve? Journal submissions require a standalone reproducibility repository with a Zenodo DOI, but paper code often lives inside a larger monorepo with internal imports and restricted data. This Skill automates extracting a paper's code, results, and scripts into a clean standalone repository ready for GitHub and Zenodo archiving. ## Core Features & Use Cases - Dependency Tracing and Manifest Creation: Traces imports from paper entry scripts and records source files, scripts, results, and dependencies in a repo-manifest.yaml file. - Standalone Repo Scaffolding: Creates a complete repository structure with src/, data/synthetic/, results/, scripts/, and tests/, rewriting all internal imports from trajectory_tda.* to src.*. - Synthetic Data Generation and Smoke Tests: Generates synthetic data matching statistical properties (never real BHPS/USoc data) and smoke tests that pass without the monorepo installed. - Use Case: Before submitting paper P01-B to a journal, run the extraction to produce ../p01-b-[slug]/ with passing tests, then push to GitHub, tag v1.0.0, and let Zenodo mint the DOI cited in submission statements. ## Quick Start Ask the AI to run /paper-repo-extract for paper P01-B and confirm the target directory and operation list when prompted.
