Skills Usage

This file explains how the installed Codex skills are used in this repository.

Why these skills

  • The project is literature-heavy and Markdown-first.
  • The current stage emphasizes review synthesis, citation hygiene, structured prompting, and early conceptual design.
  • The skill set is intentionally small and focused on research throughput rather than automation breadth.

The repository currently uses two layers of skills:

  • installed general-purpose research skills copied into the project from external skill packs
  • project-local custom dgm- skills for reusable paper workflow actions
  • a tracked repo-local paper skill pack under codex/paper_skills/ for sharing and reuse

Practical usage

Skill Role in this repo Typical use
literature-review first-pass synthesis run structured reconnaissance and theme extraction across a topic cluster
bgpt-paper-search paper discovery find additional papers when the remote MCP path is configured
citation-management reference hygiene verify metadata, correct author-year drift, and update references/library.bib
markitdown document conversion turn supported source files into Markdown-friendly text when needed
markdown-mermaid-writing Markdown-native writing draft notes, diagrams, and lightweight visual explanations
hypothesis-generation conceptual framing compare gap framings, competing explanations, and narrower thesis variants
exploratory-data-analysis future empirical support inspect pilot data or experiment artifacts when the project becomes empirical
networkx graph-modeling support sketch graph schemas and relationship structures for later method work
dgm-research-positioning paper positioning workflow turn literature notes into a narrow problem framing, candidate gap, thesis variants, and contribution statements
dgm-citation-audit manuscript trust and reference hygiene identify unsupported claims, separate strong vs weak sources, and conservatively update references/library.bib
dgm-method-design paper-first method workflow convert substrate analysis plus literature findings into a narrow, conceptual Method section without drifting into system-writeup language
dgm-md-to-pdf-chapter-polisher chapter assembly and export workflow merge modular Markdown chapter files into a polished chapter draft and export a single-chapter PDF

High-frequency skills

  • literature-review
  • citation-management
  • hypothesis-generation
  • dgm-research-positioning
  • dgm-citation-audit
  • dgm-method-design
  • dgm-md-to-pdf-chapter-polisher

Lower-frequency or future-stage skills

  • markitdown
  • exploratory-data-analysis
  • networkx

Shareable skill pack

  • Repo-tracked custom skills now live in codex/paper_skills/custom/.
  • Zip packages for transfer or reuse live in codex/skill_packages/.
  • The external paper-workflow skill list is documented in codex/paper_skills/manifests/external_skills_manifest.md.

Caveat

  • bgpt-paper-search is part of the intended workflow, but it still depends on external MCP configuration before it becomes fully usable in Codex.
  • The active installed skills still live in local .codex/skills/ and machine-level Codex directories.
  • The repo copies under codex/paper_skills/ are the shareable project version for collaborators and download.