qiongli-workflow

Research Paper Workflow

Run a model-agnostic paper workflow using shared Task IDs and artifact contracts.

This is a self-contained skill package. All assets needed for execution — workflows, skill specifications, output templates, standards, and agent roles — are bundled in subdirectories of this package. No external repo access is needed.

Quick Start

1. Ask for paper_type: empirical, qualitative, systematic-review, methods, or theory.
2. Ask for task_id from the contract (for example F3 or G1).
3. Execute the task and write outputs to RESEARCH/[topic]/ using the exact file paths.
4. Apply quality gates before submission tasks (H1, H2).
5. For orchestrator task-run, declare controller ownership when relevant with --execution-mode, --controller, --primary, --reviewer, --verifier, and --solo-role-gates.

Available Workflow Commands

These commands map to the same behavior across Codex, Claude Code, and Gemini:

/paper [topic] [venue]                # Master router — choose paper type + task ID
/lit-review [topic] [year range]     # Systematic literature review (PRISMA)
/paper-read [URL or DOI]             # Deep paper analysis
/find-gap [research area]            # Identify research gaps
/build-framework [theory/concept]    # Build theoretical framework
/academic-write [section] [topic]    # Academic writing assistance
/synthesize [topic] [outcome_id]     # Evidence synthesis / meta-analysis
/paper-write [topic] [type] [venue]  # Full manuscript drafting
/study-design [topic]                # Empirical study design
/ethics-check [topic]                # Ethics / IRB pack
/submission-prep [topic] [venue]     # Submission package
/rebuttal [topic]                    # Rebuttal / response to reviewers
/code-build [method] --domain ...    # Build academic research code
/proofread [topic]                   # AI de-trace / final proofreading
/academic-present [topic]            # Academic presentation preparation

Bundled Workflows

Full workflow definitions are included in the workflows/ subdirectory of this skill package. When a user invokes any command above (e.g. /paper, /lit-review), read the corresponding file from workflows/<command-name>.md for the complete execution instructions.

The workflows/paper.md file is the master router — it maps every Task ID (A1–K4) to the correct sub-workflow or skill card. Start there for any task-ID-based request.

Skill Directory Structure

The skill system covers the full research lifecycle across 11 stages:

skills/
├── A_framing/       (question-refiner, contribution-crafter, hypothesis-generator, theory-mapper, gap-analyzer, venue-analyzer)
├── B_literature/    (academic-searcher, paper-screener, paper-extractor, citation-snowballer, fulltext-fetcher, citation-formatter, concept-extractor, literature-mapper, reference-manager-bridge)
├── C_design/        (study-designer, rival-hypothesis-designer, robustness-planner, dataset-finder, variable-constructor, data-dictionary-builder, data-management-plan, prereg-writer, variable-operationalizer)
├── D_ethics/        (ethics-irb-helper, statement-generator, deidentification-planner)
├── E_synthesis/     (effect-size-calculator, evidence-synthesizer, quality-assessor, publication-bias-checker, qualitative-coding)
├── F_writing/       (manuscript-architect, analysis-interpreter, effect-size-interpreter, table-generator, figure-specifier, meta-optimizer, discussion-writer)
├── G_compliance/    (prisma-checker, reporting-checker, tone-normalizer)
├── J_proofread/     (ai-fingerprint-scanner, human-voice-rewriter, similarity-checker, final-proofreader)
├── H_submission/    (submission-packager, rebuttal-assistant, peer-review-simulation, fatal-flaw-detector, reviewer-empathy-checker, credit-taxonomy-helper, limitation-auditor)
├── I_code/          (code-builder, data-cleaning-planner, data-merge-planner, code-specification, code-planning, code-execution, code-review, reproducibility-auditor, stats-engine)
├── K_presentation/  (presentation-planner, slide-architect, slidev-scholarly-builder, beamer-builder)
├── Z_cross_cutting/ (academic-context-maintainer, metadata-enricher, model-collaborator, self-critique)
└── domain-profiles/ (economics, finance, psychology, biomedical, education, cs-ai, ...)

Output Structure

RESEARCH/[topic]/
├── context/                 # Project-level research state + decision log
├── framing/                 # A-stage outputs (RQ, hypothesis, contribution, venue)
├── protocol.md              # Research protocol
├── search_log.md            # Reproducible search records
├── screening/               # Screening logs + PRISMA flow
├── notes/                   # Individual paper notes
├── extraction_table.md      # Data extraction table
├── synthesis.md             # Final synthesis report
├── manuscript/              # Outline, draft, claims map, figures plan
├── proofread/               # AI detection, humanization, similarity, final proofread
├── submission/              # Cover letter, checklist, statements
├── revision/                # Rebuttal + response materials
├── analysis/                # Code + data pipelines
├── presentation/            # Slide deck spec, slides.md / slides.tex
└── bibliography.bib         # BibTeX references

Required Behavior

• Use the canonical task and output definitions in references/workflow-contract.md.
• Keep stage labels and task IDs unchanged across models.
• Do not infer stage order alphabetically when the contract exposes explicit ordering metadata.
• When self-critique is one of the required skills, preserve critique history across revision rounds and treat review/self_critique_log.md as the canonical issue register for the loop.
• If a requested output is missing prerequisites, create a gap note and ask whether to:
  1. continue with placeholders, or
  2. run the prerequisite task first.
• Keep claims, methods, and evidence aligned (run integrity checks for stage G).
• Track central claims in RESEARCH/[topic]/evidence/claim-evidence-ledger.csv using references/evidence-ledger-contract.md; unsupported central claims become gap notes, not invented citations.
• Before final writing, proofread, submission, rebuttal, or presentation-facing outputs, apply references/citation-risk-policy.md when citation support is material.
• At high-risk stage transitions, write RESEARCH/[topic]/context/stage_handoff.md using references/stage-handoff-contract.md.
• Use venue-profiles/ when a target venue profile is available; otherwise create a venue gap note instead of assuming community-specific expectations.
• Apply references/academic-output-rubric.md whenever producing scholarly prose, synthesis, design, review, or submission artifacts.
• Treat controller-mode metadata as audit-relevant: task-run accepts only solo|duo|triad for --execution-mode, only runtime agents for --controller / --primary / --reviewer / --verifier, and only strict|standard|off for --solo-role-gates.
• Use --mcp-strict and --skills-strict for authoritative controller-aware runs; avoid --skip-validation for submission-facing, Stage-I code, or final manuscript outputs.
• In solo mode, record role-specific gate intent: Codex-only writing should cover evidence ledger, citation risk, claim calibration, and scholarly voice checks; Claude-only engineering should cover implementation intent, declared write set, failing-test-first discipline, command evidence, and rollback notes. Current offline audits hard-block missing claim-map artifacts for Codex-only writing and missing implementation-intent artifacts for Claude-only code unless solo gates are off.
• In Codex-Claude duo mode, record blocking disagreements with a disagreement matrix and resolve them by evidence, method risk, implementation validity, and downstream publication impact.
• When a workflow references templates/<name>.md, load the template from the templates/ subdirectory of this package.

Skill Loading Strategy

Three-tier loading for token efficiency. All paths are relative to this skill package directory:

1. Quick lookup (~6KB): Use skills-summary.md — skill names + one-line descriptions per stage. Use this to identify which skill to invoke.
2. Default reference (~19KB): Use skills-core.md — consolidated process descriptions, templates, and output formats. Use this when executing a skill.
3. Full specification: Load skills/[stage]/[skill-name].md — detailed edge cases, error recovery, quality bars, and verbose templates. Use this only when the core reference is insufficient.

Bundled Assets

This package includes the following subdirectories:

Directory	Contents
workflows/	16 workflow definitions (slash commands)
references/	Stage playbooks + workflow contract
skills/	71 detailed skill spec files across 13 stage directories
skills-summary.md	Quick-reference skill index (~3KB)
skills-core.md	Consolidated skill reference (~19KB)
templates/	50+ output templates for manuscripts, submissions, ethics, evidence, and handoffs
standards/	Canonical contract YAML + capability map + agent profiles
roles/	10 agent role definitions for orchestrator execution
venue-profiles/	Venue expectation profiles for CHI, ACL, NeurIPS, Nature, JAMA, and AOM

References

• Task model + outputs: references/workflow-contract.md
• Platform routing map: references/platform-routing.md
• Coverage matrix: references/coverage-matrix.md
• Academic output rubric: references/academic-output-rubric.md
• Evidence ledger contract: references/evidence-ledger-contract.md
• Citation risk policy: references/citation-risk-policy.md
• Stage handoff contract: references/stage-handoff-contract.md
• Method diagnostic contract: references/method-diagnostic-contract.md
• Stage playbooks:
  • references/stage-A-framing.md (tasks A1–A5)
  • references/stage-B-literature.md (tasks B1–B6)
  • references/stage-C-design.md (tasks C1–C5)
  • references/stage-D-ethics.md (tasks D1–D3)
  • references/stage-E-synthesis.md (tasks E1–E5)
  • references/stage-F-writing.md (tasks F1–F6)
  • references/stage-G-compliance.md (tasks G1–G4)
  • references/stage-J-proofread.md (tasks J1–J4)
  • references/stage-H-submission.md (tasks H1–H4)
  • references/stage-I-code.md (tasks I1–I9)
  • references/stage-K-presentation.md (tasks K1–K4)