Use when you need to validate a paper's bibliography — cross-references \cite{} keys against .bib files or embedded \bibitem entries, finds missing/unused/typo'd keys, and checks every key against the Paperpile library via the local resolver. Deep verification mode spawns parallel agents for DOI/metadata validation at scale. Fix mode rekeys drifted keys to canonical and stages missing entries for Paperpile.

2026-07-09113

init-project-research

flonat/claude-research

Use when you need to bootstrap a full research project with directory scaffold and Overleaf symlink.

2026-07-09113

preprint

flonat/claude-research

Use when you need to create a preprint / working-paper variant of a paper currently in conference or journal format. Forks the existing Overleaf project — adds a `preprint/` subfolder using the user's `your-template` Template, ports the body content from the source paper. The preprint is accessed locally via the existing `paper-{venue}/paper/preprint/` path (subfolder under the conference paper's symlink); no separate `paper-wp/` directory. Trigger on "set up a working paper", "create a preprint", "WP version", "arXiv-ready version", "ready to preprint". Never creates a new top-level Overleaf project — always nests inside the existing one. Never uses the conference's own style (.sty / .cls); always swaps to `your-template`.

2026-07-09113

proofread

flonat/claude-research

Use when you need academic proofreading of a LaTeX paper (11 check categories).

2026-07-09113

review-cluster

flonat/claude-research

Use when you need a mid-draft adversarial review of a paper — runs paper-critic + domain-reviewer + claim-verify + blindspot in parallel, then auto-synthesises into a prioritised revision plan. Distinct from /pre-submission-report (final-gate kitchen sink, 13 sub-agents) — this is the active-drafting feedback loop. Triggers: 'review my draft', 'adversarial review', 'cluster review', 'mid-draft critique', 'feedback before pre-submission'.

2026-07-09113

name	replication-package
description	Use when you need to assemble, anonymize, or audit a replication package.
allowed-tools	Bash(cp), Bash(rm), Bash(mkdir), Bash(ls), Bash(git), Bash(find), Bash(sed), Bash(grep), Bash(du), Bash(wc), Bash(dirname), Bash(basename), Bash(readlink), Bash(rsync), Bash(mv*), Read, Write, Edit, Glob, Grep, AskUserQuestion, Skill
argument-hint	[project-path] [--mode assemble\|blind\|audit]

Replication Package — Assemble, Anonymize, and Audit

Build publication-ready replication packages, optionally anonymize for double-blind review, or audit an existing package for reproducibility. The original project is never modified.

Modes

Mode	What it does	Use case
Assemble	Clean copy + AI trace removal + AEA-style README	Sharing, Zenodo deposit, journal supplementary
Blind	Everything in Assemble + identity anonymization	Double-blind conference/journal submission
Audit	Read-only 11-check reproducibility validation	Pre-deposit quality gate, self-check

Default mode: Assemble. Infer Blind if the user says "anonymize", "double-blind", or "blind review". Infer Audit if the user says "audit", "check reproducibility", or "validate package".

When to Use

Submitting supplementary materials or replication files to a journal
Depositing a package on Zenodo, Dataverse, or ICPSR
Sharing a project repo publicly (GitHub, institutional repository)
Preparing for double-blind submission (Blind mode)
Self-checking reproducibility before deposit (Audit mode)

When NOT to Use

Quick one-off cleanup of a single file — do it manually
Removing a single AI artifact — just delete it directly
Projects with no empirical or computational component

Critical Rules

Never modify the original project. All work happens on a copy in a sibling folder.
Dry-run mandatory. Always show what will be removed/changed and get user confirmation before any deletions.
Binary files are never modified. Warn the user to manually check PDFs (Document Properties), images (EXIF data), and datasets for embedded metadata.
Self-citations are always interactive. Never auto-remove or auto-anonymize a citation. Flag each potential self-citation and let the user decide per citation. In Blind mode, surface every self-citation against the loaded submission author list and require a per-citation decision (third-person OK / blind the entry). When the cited paper's author list is a subset of the submission's, third-person is structurally insufficient and the bib entry MUST be blinded — see _shared/double-blind-anonymity-checklist.md §P4–P5.
Resolve symlinks. Use rsync -aL so symlinked content (e.g., Overleaf paper/ symlinks) becomes real files in the copy.
Preserve compilability. The output must still compile/run — only infrastructure and identity are removed, not project functionality.
Blind mode runs the structured-metadata field check (A2) before reporting clean. pyproject.toml [project] authors, package.json author/contributors, Cargo.toml [package] authors, CITATION.cff, LICENSE holder, etc. — see _shared/double-blind-anonymity-checklist.md §"Structured-metadata field check (A2)" for the full target list. This was the CCS 2026 #1328 desk-reject trigger and is now non-skippable.

Assemble Mode (Non-Blind)

Phases 1-7: Scan → Copy → Scrub AI Traces → Generate README → Verify → Fresh Git → Report.

Full workflow: references/assemble-workflow.md

Blind Mode (Assemble + Anonymization)

Runs all Assemble phases, then continues with Phases 8-12: Collect Identity → Anonymize LaTeX → Anonymize Other Files → Anonymous Git → Leak Check Report.

Full workflow: references/blind-workflow.md

Audit Mode (Read-Only)

11-check reproducibility validation: Compilation, Script order, Output presence, Dependencies, Data provenance, README, File sizes, End-to-end clarity, AI traces, Identity leaks, Numeric reproduction.

Full workflow: references/audit-workflow.md

Check 11 (Numeric reproduction) is N/A unless an expected_values.json (the manuscript's reported numbers) sits at the package root. When present, the audit parses the package's committed output files and scores them against that ground truth within tolerance — catching paper-vs-output drift. It is read-only and never re-runs scripts. Convention + scoring rubric: references/expected-values-schema.md.

HPC-run results

If the project used [HPC cluster] (hpc/ directory with *.sbatch), the results in out/<jobid>/ should include git-sha.txt + git-status.txt (written by the sbatch templates before srun). Audit must verify these exist and the SHA matches a commit in the repo — this is the compute-reproducibility equivalent of Script order + Dependencies for HPC runs. The Assemble README should document the hpc/ entry point and the HF/conda env-setup script alongside code/ + data/. See Task Management docs/guides/hpc.md.

What This Skill Does NOT Do

Does not modify the original project — all changes are in the sibling folder (Assemble/Blind) or purely read-only (Audit).
Does not modify binary files — PDFs, images, datasets are copied as-is. User must check these manually for embedded metadata.
Does not auto-handle self-citations — every potential self-citation requires user decision.
Does not anonymize the paper title — titles are generally not considered identifying (but some venues disagree; user should check).
Does not strip PDF metadata — if a compiled PDF exists, its Document Properties may contain author info. User should recompile from the anonymized source or use exiftool to strip metadata.
Does not run scripts — it verifies their presence and order but does not execute them (too risky without a controlled environment). Check 11 (Numeric reproduction) likewise compares the package's already-committed output files against the manuscript; it never re-runs the pipeline, so it catches paper-vs-output drift, not full fresh-run reproduction.

Examples

Assemble mode (default)

"Build a replication package for my research paper"

Runs Assemble mode on the current project, creates ../mcdm-paper-replication/.

Blind mode

"Anonymize my paper for AAAI double-blind submission"

Runs Blind mode, creates ../mcdm-paper-replication-blind/.

Audit mode

"Audit the reproducibility of my replication package"

Runs Audit mode (read-only) on the specified package directory.

Explicit path and mode

"/replication-package ~/papers/negotiation-model --mode blind"

Runs Blind mode on the specified project path.

Cross-References

data-sensitivity rule — raw data is read-only; replication packages must document data provenance without modifying data/raw/
overleaf-separation rule — paper/ structure is preserved; symlinks resolved by rsync
shared/multi-language-conventions.md — dependency detection patterns for Python, R, Julia, MATLAB
shared/publication-output.md — output file verification and freshness checks
/latex — compilation check in Audit mode
references/aea-readme-template.md — AEA-style README template for Assemble mode
references/figure-table-crosswalk.md — per-figure/table crosswalk (with LaTeX Label) + paper-consistency check, appended to the README (Phase 4)
references/logging-skeletons.md — per-script logging + master-script skeletons (R/Python/Julia/Stata) offered in Phase 5
references/release-readiness-checklist.md — 14-point PASS/FAIL pre-release gate emitted at Phase 7 (RELEASE-READINESS.md)
references/rules.dropboxignore — Dropbox-sync ignore file for Dropbox-synced packages (Phase 6)
references/anonymization-patterns.md — replacement tables for Blind mode
references/audit-rubric.md — 11-check scoring rubric for Audit mode
references/expected-values-schema.md — expected_values.json convention + numeric-reproduction scoring rubric (Check 11)
references/deposit-checklist.md — platform-specific deposit completeness checklist
references/report-template.md — report format for Blind mode
_shared/double-blind-anonymity-checklist.md — authoritative paper+artifact anonymity matrix (P1–P8, A1–A9). Blind mode must run all artifact-side checks (A1–A9) before reporting clean.

Note: This skill replaces the former /export-project-clean and /export-project-anon skills. All their functionality is preserved in Assemble and Blind modes respectively.

Output Verification (Guard)

This skill writes files. Before any auto-commit, emit an outputs manifest and run the shared verifier. See skills/_shared/verify-outputs.md for the full protocol.

Required tail steps (before git commit):

Write manifest to <project>/.claude/state/outputs-manifest-<UTC-timestamp>.json listing every file this skill claims to have written in this invocation (paths relative to the project root).

Run:

python3 "$HOME/.claude/skills/_shared/verify_outputs.py" \
    --manifest "$MANIFEST" \
    --project-root "$PROJECT_ROOT"

If the verifier exits non-zero, do not commit — surface the missing-files list to the user and stop. The verifier has already logged an error entry to ~/.claude/ecc/skill-outcomes.jsonl, which feeds the launcher dashboard.

Why: closes the "hallucinated outputs" failure class (commit b2cff75, 2026-04-18).