Skills guide

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Describe your research task in the Host, or select a visible Qiongli Skill. In Codex, use $qiongli or a shortcut such as $qiongli-paper-read. The shared guidance helps the model choose the relevant work; it does not require every stage to run. Task IDs identify research activities, not native CLI commands.

The tables below list the internal research Skills. They are not all separate Host entries. Supplemental cards and subject profiles support these Skills; they do not create additional agents or MCP tools.

The descriptions and use cases below come from the same registry in both languages.

Stage Overview

Stage	Focus	Skill count	Typical user intent
A_framing	topic framing, questions, theory, gap, venue	6	"What exactly is my contribution?"
B_literature	search, screen, extract, cite, map	9	"What does the literature say, and how do I build a corpus?"
C_design	design, variables, robustness, datasets	9	"How should this study be designed and operationalized?"
D_ethics	IRB, privacy, governance	3	"What ethics and data-protection materials do I need?"
E_synthesis	evidence synthesis, quality, bias	5	"How do I combine and rate evidence?"
F_writing	manuscript building, tables, figures, results writing	8	"How do I turn analysis into publishable text?"
G_compliance	reporting checklists, tone, PRISMA	3	"Is this compliant and submission-ready?"
J_proofread	AI detection, humanization, similarity, final polish	4	"How do I de-AI and finalize the manuscript?"
H_submission	submission package, rebuttal, review simulation	8	"How do I package, defend, and stress-test the paper?"
I_code	academic code, stats, reproducibility	10	"How do I implement and verify research code?"
K_presentation	academic talks, slide planning, Slidev, Beamer	4	"How do I turn the paper into a defensible talk?"
L_coursework	assignment briefs, rubrics, learning outcomes, coursework revision	4	"How do I satisfy this assignment honestly and clearly?"
M_dissertation	dissertation planning, chapter maps, supervisor feedback, defense prep	4	"How do I plan, draft, revise, and defend this dissertation?"
Z_cross_cutting	metadata, model collaboration, self-critique	5	"How do I improve quality across stages?"

Canonical Skills By Stage

A. Framing

Use Stage A when you are still defining the research question, contribution, theory anchor, or venue positioning.

Skill	Display Name	When to use	Produces
question-refiner	Question Refiner	Use when you need to transform vague topics into structured rqs via pico/peo + finer evaluation.	RQSet
contribution-crafter	Contribution Crafter	When framing the pitch for a manuscript introduction	ContributionStatement
hypothesis-generator	Hypothesis Generator	Use when you need to translate rqs into testable hypotheses with mechanisms and boundary conditions.	HypothesisSet
theory-mapper	Theory Mapper	Use when you need to map theoretical concepts, relationships, and frameworks with mermaid diagrams.	TheoreticalFramework
gap-analyzer	Gap Analyzer	Use when you need to identify and categorize research gaps using 5-type taxonomy with finer prioritization.	GapAnalysis
venue-analyzer	Venue Analyzer	Explore venues before a draft or adapt a manuscript to a chosen journal or conference.	VenueAnalysis

B. Literature

Use Stage B when you are building or maintaining the literature base for a topic, especially systematic or reproducible reviews.

Skill	Display Name	When to use	Produces
academic-searcher	Academic Searcher	Use when a B1 search needs reproducible provider execution, search_diagnostics.md, dedup logs, or review-grade coverage checks.	SearchQueryPlan, SearchResults, SearchLog, DedupLog, SearchDiagnostics
paper-screener	Paper Screener	Use when candidate records need include/exclude decisions, diagnostic flags preserved, or PRISMA flow counts.	ScreeningDecisionLog, FullTextScreening, PRISMAFlowData
paper-extractor	Paper Extractor	Use when included papers need notes or extraction_table.md without overclaiming metadata-only or abstract-only evidence.	ExtractionTable, PaperNotes
citation-snowballer	Citation Snowballer	Use when B3 needs forward/backward citation expansion, known-item follow-up, or coverage repair after search diagnostics.	SnowballLog, SearchResults, DedupLog
fulltext-fetcher	Full-text Fetcher	Use when reports need retrieval_manifest.csv, controlled full-text statuses, or Zotero/OA resolver handoff.	FullTextStatus, RetrievalManifest
citation-formatter	Citation Formatter	Use when B5 needs citekey cleanup, DOI normalization, duplicate handling, or export-ready bibliography.bib.	Bibliography
concept-extractor	Concept Extractor	Use after Stage A when B1 search terms, controlled vocabulary, excluded ambiguous terms, or seed recall are unsettled.	ConceptMap
literature-mapper	Literature Mapper	Use when extracted papers need a defensible non-chronological map for related work or novelty positioning.	LiteratureMap
reference-manager-bridge	Reference Manager Bridge	Use when B5 needs Zotero local sync, import-file fallback, RIS/CSL-JSON export, or bibliography exchange.	Bibliography, RISExport, CSLJSONExport, ZoteroImportReport

C. Design

Use Stage C when the question is already clear and the next problem is design validity, data feasibility, and operationalization.

Skill	Display Name	When to use	Produces
study-designer	Study Designer	After /find-gap and /build-framework, when you want to run an empirical, qualitative, or mixed-methods study.	DesignSpec, AnalysisPlan, DataManagementPlan, Instruments, Preregistration
rival-hypothesis-designer	Rival Hypothesis Designer	After hypotheses (A1_5) and study design (C1) are drafted	RivalHypotheses
robustness-planner	Robustness Planner	After analysis plan (C3) is drafted	RobustnessPlan
dataset-finder	Dataset Finder	After study design specifies what data is needed	DatasetPlan
variable-constructor	Variable Constructor	After study design is finalized	VariableSpec
data-dictionary-builder	Data Dictionary Builder	After study design is finalized and instruments are selected	DataDictionary
data-management-plan	Data Management Plan	Use when you need to generate fair-compliant data management plans specifying storage, backup, retention, sharing, and archival.	DataManagementPlan
prereg-writer	Pre-registration Writer	After study design and analysis plan are finalized	Preregistration
variable-operationalizer	Variable Operationalizer	After theoretical framework is established	OperationalizationMap

D. Ethics

Use Stage D when the study touches human participants, sensitive data, governance, or data-release constraints.

Skill	Display Name	When to use	Produces
ethics-irb-helper	Ethics & IRB Helper	Before data collection involving human participants or sensitive data	EthicsPackage
statement-generator	Statement Generator	When finalizing a manuscript for submission and ensuring compliance with journal statement requirements (e.g., PLOS, Nature, Elsevier).	Manuscript
deidentification-planner	Deidentification Planner	When handling any dataset containing identifiable information	DeidentificationPlan

E. Synthesis

Use Stage E when the evidence base already exists and the task is to combine, rate, or stress-test that evidence.

Skill	Display Name	When to use	Produces
effect-size-calculator	Effect Size Calculator	When preparing data for a quantitative meta-analysis	EffectSizeTable, AnalysisCode
evidence-synthesizer	Evidence Synthesizer	Use after you have:	EvidenceTable, SynthesisMatrix
quality-assessor	Quality Assessor	Use when you need to assess risk of bias and certainty via rob 2, robins-i, grade.	QualityTable, GRADESummary
publication-bias-checker	Publication Bias Checker	After completing meta-analysis (E3) with ≥5 studies	PublicationBiasReport
qualitative-coding	Qualitative Coding	Use after raw qualitative data has been collected or extracted, but before the final synthesis narrative is drafted. Ideal for Grounded Theory, Thematic Analysis, or Interpretative Phenomenological Analysis (IPA).	DataDictionary, ThematicCodebook

F. Writing

Use Stage F when the main question is turning evidence and analysis into sections, tables, figures, and readable claims.

Skill	Display Name	When to use	Produces
manuscript-architect	Manuscript Architect	You want to draft a paper from an existing RESEARCH/[topic]/ project folder (empirical study or systematic review).	ManuscriptOutline, Manuscript, ClaimGraph, FiguresTablesPlan
proposal-writer	Proposal Writer	When preparing a research proposal, opening report, prospectus, study plan, or 开题报告 before results-focused manuscript drafting.	ResearchProposal
analysis-interpreter	Analysis Interpreter	After primary analysis is complete	ResultInterpretation
effect-size-interpreter	Effect Size Interpreter	After primary analysis is complete	EffectInterpretation
table-generator	Table Generator	After primary analysis is complete	FormattedTables
figure-specifier	Figure Specifier	After primary analysis is complete	FigureSpecs
meta-optimizer	Meta Optimizer	After manuscript draft is complete (F2/F3/F4)	MetaOptimization
discussion-writer	Discussion Writer	Use after the Results section has been drafted and the primary findings are finalized. Provide the core contribution statement and literature framing to ensure alignment.	DiscussionDraft, StorySpine

G. Compliance

Use Stage G when the paper exists and now needs formal checklist coverage, tone cleanup, or reporting verification.

Skill	Display Name	When to use	Produces
prisma-checker	PRISMA Checker	Use when you need to verify prisma 2020 flow diagram and all 27 checklist items.	PRISMAChecklist
reporting-checker	Reporting Checker	Before submission (final quality assurance pass)	ReportingChecklist
tone-normalizer	Tone Normalizer	After manuscript draft is complete (but before final submission)	ToneNormalization

J. Proofread

Use Stage J when the draft is substantively complete and needs AI-fingerprint review, human-voice rewriting, similarity screening, or final proofreading before submission.

Skill	Display Name	When to use	Produces
ai-fingerprint-scanner	AI Fingerprint Scanner	Use for a requested language-pattern diagnosis; grammar-only correction can enter final-proofreader directly.	AIDetectionReport
human-voice-rewriter	Human-Voice Rewriter	Use for requested expression or voice revision; reuse supplied text and any existing findings.	HumanizedManuscript
similarity-checker	Similarity Checker	Use for requested source-overlap or attribution checks; prior rewriting is not an automatic prerequisite.	SimilarityReport
final-proofreader	Final Proofreader	Use for requested scholarly grammar/consistency corrections or a formal final proofreading pass.	ProofreadChecklist

H. Submission

Use Stage H when the manuscript is near submission or already under review.

Skill	Display Name	When to use	Produces
submission-packager	Submission Packager	You have a near-final manuscript draft ready for submission	SubmissionPackage
rebuttal-assistant	Rebuttal Assistant	After receiving a Revise & Resubmit (R&R) decision	ResponseToReviewers, ResponseLetter
peer-review-simulation	Peer Review Simulation	Use for a requested referee-style manuscript review or formal H3 task; a focused check needs only relevant lenses.	PeerReviewSimulation
fatal-flaw-detector	Fatal Flaw Detector	Before final submission (last quality gate)	FatalFlawAnalysis
journal-fit-recommender	Journal Fit Recommender	Use when an existing manuscript needs manuscript-first reverse journal fit before submission.	JournalFitRecommendation
reviewer-empathy-checker	Reviewer Empathy Checker	After drafting the response letter (from rebuttal-assistant H2) but BEFORE submitting	EmpathyCheck
credit-taxonomy-helper	CRediT Taxonomy Helper	During submission packaging (H1)	CRediTStatement
limitation-auditor	Limitation Auditor	Use during the late drafting or pre-submission phase when the Methods and Discussion sections are complete, to ensure the manuscript demonstrates scholarly humility and self-awareness before peer reviewers point out the flaws.	LimitationSection, MitigationStrategy

I. Code

Use Stage I for academic code, data workflows, statistical execution, and reproducibility. This lane is stricter than general engineering prompts.

The core strict sequence is:

1. code-specification
2. code-planning
3. code-execution
4. code-review
5. reproducibility-auditor

That sequence is what code-build --focus full is designed to reinforce.

Skill	Display Name	When to use	Produces
code-builder	Code Builder	Use when you need to convert academic methods into executable code with domain-profile library selection.	AnalysisCode
data-cleaning-planner	Data Cleaning Planner	After dataset is obtained, before any analysis	CleaningPlan
data-merge-planner	Data Merge Planner	When analysis requires combining multiple data sources	MergePlan
code-specification	Code Specification	Use when you need to generate strict opsx-style constraint sets before coding.	CodeSpec
code-planning	Code Planning	Use when you need to transform specs into parallelizable, zero-decision execution plans.	CodePlan
code-execution	Code Execution	Use when you need to execute code plans with cprofile performance profiling and optimization.	PerformanceProfile
code-review	Code Review	Use when you need to secondary model reviews code logic, security, and statistical validity.	CodeReview
reproducibility-auditor	Reproducibility Auditor	Use when you need to verify seeds, containerization, and fail-graceful contingencies.	ReproducibilityReport
release-packager	Release Packager	When preparing for manuscript submission (data/code availability statement)	ReleasePackage
stats-engine	Stats Engine	You need to execute modeling/testing for synthesis (E3/E3_5) or empirical results (F stage) with a clear report of assumptions and uncertainty.	StatsReport

K. Presentation

Use Stage K when the paper already exists and the next task is to turn it into a talk, seminar deck, or conference presentation.

Skill	Display Name	When to use	Produces
presentation-planner	Presentation Planner	After manuscript is substantially complete (or results are available)	PresentationPlan
slide-architect	Slide Architect	After presentation-planner has produced a slide blueprint	SlideDeckSpec
slidev-scholarly-builder	Slidev Scholarly Builder	When Slidev + scholarly is chosen as the output backend	SlidevDeck, BibTeXFile
beamer-builder	Beamer Builder	When LaTeX Beamer is the chosen backend	BeamerDeck, BibTeXFile

L. Coursework

Use Stage L when the task is coursework, an assignment brief, marking rubric, learning outcomes, a case analysis, reflective writing, portfolio, or capstone coursework.

Skill	Display Name	When to use	Produces
assignment-brief-analyzer	Assignment Brief Analyzer	Use when a coursework, capstone, or dissertation brief needs parsing before planning or drafting.	AssignmentBrief, AcademicIntegrityNotes
rubric-mapper	Rubric Mapper	Use when coursework must be planned or revised against a rubric or learning outcomes.	RubricMap, LearningOutcomeMap
coursework-architect	Coursework Architect	Use before drafting coursework essays, reports, cases, reflections, portfolios, or capstone components.	CourseworkOutline, CourseworkClaimEvidencePlan
coursework-reviser	Coursework Reviser	Use when a coursework draft needs rubric-facing revision or final submission readiness checks.	CourseworkRevisionPlan, CourseworkSubmissionChecklist

M. Dissertation

Use Stage M when the task is a dissertation, thesis, capstone, major project, supervisor feedback integration, or viva/defense preparation.

Skill	Display Name	When to use	Produces
dissertation-planner	Dissertation Planner	Use when starting or restructuring a dissertation, thesis, capstone, or major project.	DissertationPlan
chapter-architect	Chapter Architect	Use when a dissertation needs chapter architecture, chapter status, or word-count allocation.	DissertationChapterMap
supervisor-feedback-integrator	Supervisor Feedback Integrator	Use when supervisor or committee feedback must become a traceable dissertation revision plan.	DissertationFeedbackLog
dissertation-readiness-checker	Dissertation Readiness Checker	Use before dissertation submission, viva, or defense preparation.	DissertationReadinessReport

Z. Cross-Cutting

Use Stage Z when the need cuts across stages rather than belonging to one paper section.

Skill	Display Name	When to use	Produces
metadata-enricher	Metadata Enricher	Use when you need to normalize and enrich doi, venue, year, author metadata across artifacts.	Bibliography
academic-context-maintainer	Academic Context Maintainer	Use for research-state continuity, detailed stage consolidation, progress tracking, or a file-by-file review for the user's own manual cleanup.	ResearchStateSnapshot, ResearchDecisionLog, StageSummary
boundary-interviewer	Boundary Interviewer	Use during brainstorms, Stage A framing, gap finding, or before high-risk study design, writing, submission, research code, and handoff work when research scope, claim strength, evidence threshold, validity risk, generalizability, or reviewer expectations remain unclear.	AcademicIdeaFunnel, BoundaryReview
model-collaborator	Model Collaborator	Use when literature screening, peer review simulation, rebuttal drafting, qualitative coding, or code/statistics validation benefits from independent multi-model passes before synthesis.	CollaborationTrace
self-critique	Self-Critique	Use for a requested research review or a required quality check; repeat only for affected fixes or the formal review contract.	CritiqueLog

Subject guidance

Describe the field, method and protocol in your request. The Host can read relevant bundled profiles; the 1.x --domain switch is not a native 2.x CLI option. Profiles guide the work, but do not establish evidence or current journal policy.

Available profiles:

• accounting
• biomedical
• business-management
• cs-ai
• ecology-environmental
• economics
• education
• epidemiology
• finance
• geoeconomics
• political-economy
• political-science
• psychology

Continue

Use task examples, the CLI guide or collaboration guidance. For changes to the framework, see Extend Qiongli.