Skill Claude CodeCodex
Read-only manuscript review, methodology review, re-review, and calibration workflow for template projects. USE WHEN the user asks for peer review, referee-style critique, methods/statistics review, or verification that revisions addressed prior comments.
Skill Claude CodeCodex
Template-native manuscript planning, outline, drafting, revision, formatting, citation check, and AI-use disclosure routing. USE WHEN the user asks to write, outline, revise, format, or prepare a paper inside the Research Project Template.
Skill Claude CodeCodex
Research-to-publication orchestrator for template projects: research, write, verify, review, revise, reproduce, validate, and finalize. USE WHEN the user wants the whole paper workflow or enters midstream with an existing paper or reviewer comments.
Skill Claude CodeCodex
Agentic-use and skill-routing workflow for the Research Project Template. USE WHEN discovering relevant skills, making template easier for agents to navigate, auditing docs/prompts skill coverage, checking .cursor/skillmanifest.json, evaluating external skills, reviewing external agentic operating models such as…
Skill Claude CodeCodex
Standards-compliant code for the Research Project Template — infrastructure or project src/, thin orchestrators, type hints, no mocks. USE WHEN implementing an algorithm, utility, analysis method, optimizer, new module in projects//src or infrastructure/, or user says add code following template architecture — even…
Skill Claude CodeCodex
Full checkout audit for the Research Project Template — tests, architecture, docs, manuscript, pipeline. USE WHEN user asks for comprehensive assessment, full repo review, health check across projects, audit everything, or pre-merge sanity sweep for template exemplars — even without naming docs/prompts or a skill. Not…
Skill Claude CodeCodex
Template-native research intake, literature search, source verification, synthesis, fact-checking, and systematic-review planning. USE WHEN the user asks to research a topic, build a literature corpus, fact-check claims, prepare a PRISMA-style review, or clarify a research question before manuscript work.
Skill Claude CodeCodex
Author or refresh AGENTS.md and README.md for template directories — accurate commands, Mermaid where helpful, link generated/activeprojects.md. USE WHEN folder needs AGENTS, README audit, doc contract fix, or signposting after code change — even without documentationcreation prompt.
Skill Claude CodeCodex
End-to-end feature work across src/, scripts/, tests/, manuscript, and docs for the Research Project Template. USE WHEN adding a pipeline-visible feature, new analysis stage, manuscript-facing output, or cross-layer integration — even without featureaddition prompt.
Skill Claude CodeCodex
Add or extend generic infrastructure/ packages — Layer 1 modules with SKILL.md, AGENTS.md, tests in tests/infratests/, 60% coverage. USE WHEN new reusable package under infrastructure/, extending validation/rendering/llm, or skill manifest entry — even without infrastructuremodule prompt.
Skill Claude CodeCodex
LLM prompt blocks for per-paper and corpus literature synthesis after a search pipeline. USE WHEN synthesizing arXiv/Crossref results, writing per-paper notes, thematic clusters, gap analysis from a literature corpus, or wiring templatesearchproject synthesis — even without naming infrastructure.llm templates.
Skill Claude CodeCodex
Triple-pass verification of every manuscript claim against code, data, refs, and renderer; repair prose while staying renderable. USE WHEN pre-submission, pre-Zenodo, pre-arXiv, abstract numbers disagree with CSV, citations do not support sentences, or user asks to triple-check / verify every claim — even without…
Skill Claude CodeCodex
Scaffold a research manuscript and project layout from a research brief — sections, config.yaml, src/, scripts/, tests. USE WHEN starting a new paper, new projects/ tree, manuscript from topic description, or aligning with templatecodeproject exemplar — even without copy-paste prompts.
Skill Claude CodeCodex
Audit or author registry-driven manuscript cross-refs — labels.yaml, [[FIG:]], [[THMREF:]], [[VAR:]] tokens. USE WHEN fixing figure/equation/theorem numbering, orphan registry keys, hard-coded "Theorem 7.3" in prose, or [[MISSING:]] injection failures — even for Pandoc projects that also use a YAML registry.
Skill Claude CodeCodex
Repo-wide methods orchestration workflow for the Research Project Template. USE WHEN the user asks to add, audit, improve, or validate methods, methodology, method contracts, stage-to-method wiring, artifact/evidence provenance, or orchestration across template projects.
Skill Claude CodeCodex
Systematic pipeline DAG failure triage for the Research Project Template. USE WHEN ./run.sh or executepipeline.py fails, a stage stalls (setup, tests, analysis, render, validate, LLM, copy), pytest/coverage gate fails mid-pipeline, PDF render or validate breaks, Project Analysis finishes too fast with no figures, or…
Skill Claude CodeCodex
End-to-end publication-readiness audit for public template exemplars — tests, no-mocks, methods contracts, claims, evidence, figures, references, rendered outputs, and deterministic regeneration. USE WHEN preparing a template or project for release, DOI deposit, peer review, or a publication sign-off.
Skill Claude CodeCodex
Clean-break refactors with migration for the Research Project Template — move logic to src/, split modules, rename APIs with test updates. USE WHEN restructuring code, extracting modules, removing duplication, or migration without behavior change.
Skill Claude CodeCodex
Deterministic reproducibility audit — fixed seeds, regenerate-from-clean, double-run diff before Zenodo/arXiv/release. USE WHEN outputs drift between runs, "worked on my machine", need regenerate-from-clean proof, or pre-release reproducibility check — even without naming docs/prompts.
Skill Claude CodeCodex
Full installation and validation workflow for a fresh clone of the Research Project Template. Installs dependencies, runs pre-commit hooks, executes the core pipeline against templatecodeproject, validates outputs, and reports a structured PASS / FAIL for each checkpoint. USE WHEN the user says "start", "set up the…
Skill Claude CodeCodex
Create pytest suites under the no-mocks policy — real data, temp files, subprocess, pytest-httpserver. USE WHEN adding tests, raising coverage, testing new src/ module, or user forbids mocks.
Skill Claude CodeCodex
Run validation CLI, prerender, markdown/PDF/integrity gates, and QA workflows for the Research Project Template. USE WHEN validate manuscript, check PDF for ?? refs, prerender gate, link checker, output integrity, or pre-commit validation — even without validationquality prompt.
Skill Claude CodeCodex
Top-level skill for the research template infrastructure layer. Use in Cursor, Claude Code, or similar agents when editing or importing anything under infrastructure/, understanding the two-layer architecture, or wiring build/validation/rendering/publishing. Covers module discovery, import patterns, thin…
Skill Claude CodeCodex
Skill for deterministic AutoResearch readiness planning. Use when adding, validating, or documenting opt-in autoresearch.yaml controls, stage-gate readiness, evidence-grounded claims, artifact readiness reports, or AutoResearchClaw-inspired workflow checks in template projects.