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Use when you need to audit a research project against the init-project-research template.
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Based on SOC occupation classification
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.
Use when you need to bootstrap a full research project with directory scaffold and Overleaf symlink.
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`.
Use when you need academic proofreading of a LaTeX paper (11 check categories).
Use when you need to assemble, anonymize, or audit a replication package.
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'.
| name | audit-project-research |
| description | Use when you need to audit a research project against the init-project-research template. |
| allowed-tools | Bash(ls*), Bash(readlink*), Bash(git*), Bash(diff*), Bash(jq*), Read, Glob, Grep |
| argument-hint | [project-path or no arguments for CWD] |
Compare a research project's directory structure against the current /init-project-research template and report gaps. Report-only.
/init-project-research/atlas-audit (this skill is per-project)| Invocation | Behaviour |
|---|---|
/audit-project-research (no args) | Audits CWD. Aborts if CWD is not a project directory. |
/audit-project-research <project-path> | Audits the given path. Resolves to absolute first. |
.gitkeep-stubbed mandatory template dirs (reviews/, correspondence/editorial/, correspondence/referee-reviews/, knowledge/, to-sort/), seeds reviews/INDEX.md and knowledge/_index.md with placeholders, and drops the canonical .latexmkrc into every directory containing *.tex that lacks one. These are decision-free safe defaults—no content choices are made, no existing files are touched. Every other "fix" action remains flag-only. Per rules/review-artefact-routing.md: never auto-create correspondence/internal-reviews/ (legacy dir, superseded; existing instances handled by /tidy-project-reviews).code/ in theoretical projects./init-project-research. Phases 2–8 below correspond 1:1 to init's Phases 3–9. When init adds a directory or convention, add the matching audit check here AND update /atlas-audit SA1.Ten phases, in order:
_index.md, papers/<short>.md, current-focus.md entries (mirrors init Phase 8).claude/audits/Resolve to absolute path (argument or CWD).
Determine project name from basename. Convention is kebab-case (matches the atlas slug, e.g. article40-access-as-mechanism). Title Case basenames (e.g. Article 40 Access As Mechanism) appear in older projects and are also valid — flag neither as a finding. Flag only basenames with non-conforming characters (spaces in kebab-case slugs, mixed-case-with-spaces, punctuation other than hyphens) as Info.
Check if git repo: git -C "<path>" rev-parse --is-inside-work-tree 2>/dev/null.
Detect project type:
| Indicator | Implies |
|---|---|
code/ or data/ | Experimental |
src/ or tests/ | Computational |
Only paper/, docs/, log/ | Theoretical |
| Mix of above | Mixed |
Read CLAUDE.md if it exists — extract declared metadata (type, venue, authors, slug).
Try to find an Atlas topic file matching the project: find ~/vault/atlas/ -name "<slug>.md". If found, note path for Phase 6.
Audits init's Phase 3 outputs. Sub-steps run in order; results aggregate into the Phase 9 report.
If no .context/ AND no .claude/, flag as pre-template project with consolidated remediation commands. Skip the rest of Phase 2 — this is a structural prerequisite. See references/pre-template-detection.md.
Record present / missing / degraded. Check: .context/, .claude/, docs/, docs/literature-review/, docs/readings/, docs/venues/, log/, paper*/, knowledge/ (required), reviews/ (required, per rules/review-artefact-routing.md), correspondence/referee-reviews/ (required), correspondence/editorial/ (required), to-sort/ (required).
Legacy flag: correspondence/internal-reviews/ — if present, flag as LEGACY and recommend running /tidy-project-reviews to migrate content to reviews/<source>/ (AI provenance) or correspondence/internal/ (human provenance) per the routing rule.
Check: CLAUDE.md (project root, non-empty), README.md, MEMORY.md, reviews/INDEX.md (required, per rules/review-artefact-routing.md), .gitignore (must include paper-*/backup/ and reviews/**/archived/), .context/current-focus.md, .context/project-recap.md, .claude/settings.local.json.
Legacy flag: REVIEW-STATE.md at project root — if present, flag as LEGACY and recommend running /tidy-project-reviews to move it to reviews/INDEX.md.
Dual-file flag (Gap A): if BOTH <project>/reviews/INDEX.md AND <project>/REVIEW-STATE.md exist, flag as DEGRADED — divergent state. This can happen if the post-Bug-1-fix review-state-log.sh (commit dcbcd9fb) hit a project where the rename Batch A missed (or where a fresh REVIEW-STATE.md was hand-created after retrofit). Recommend running /tidy-project-reviews to merge contents (its Phase 5.2 dedup-merges rows by (Check, Last Run) key) and remove REVIEW-STATE.md.
See references/review-consistency.md for canonical registry and legacy-location detection.
Experimental: code/, code/python/ or code/R/, data/, data/raw/, data/processed/, output/, output/figures/.
Computational: src/, tests/, experiments/, results/, pyproject.toml.
Python tooling: flag requirements.txt as Degraded.
Theoretical: no additional checks.
Compare .claude/settings.local.json allow against global ~/.claude/settings.json. Flag missing as Degraded. See references/permissions-sync.md.
Every hook entry must use object format {"type": "command", "command": "..."}, not bare strings. See references/hooks-schema.md.
Compare project's .claude/rules/ against global rules. Flag byte-identical duplicates as Redundant. See references/rules-sync.md.
Validate structure and hygiene. See references/github-release-repo.md.
Submission-ready projects without an artifact: flag when atlas outputs[] entry is Drafting/Submission-ready/Submitted/R&R and github-repo/ is absent or vault/atlas lack artifact_repo: fields. Recommend /anonymous-artifact. Do not auto-fix.
Skip for theoretical/qualitative projects: Skip artifact-missing check when (a) Project type detected as Theoretical in Phase 1, (b) No .py/.R/.jl/.do/.ipynb/.m files outside excluded dirs, AND (c) Atlas methods: contains only non-computational entries.
Classify items beyond scaffold as recognised growth or unrecognised (Info). See references/growth-patterns.md.
Create if absent: reviews/ with INDEX.md seeded from the routing-rule template (manifest only — per-source subdirs created lazily), correspondence/editorial/, correspondence/referee-reviews/, knowledge/ (with seed _index.md), to-sort/ (with .gitkeep), .latexmkrc in every dir with *.tex (detect via find -L). Record in audit log. Never overwrite existing files; flag drift as Degraded.
Per rules/review-artefact-routing.md: do NOT auto-create correspondence/internal-reviews/ — that legacy dir is superseded by the human-vs-AI provenance split (correspondence/internal/ for human collaborator feedback, reviews/<source>/ for AI output). If it exists in the project, flag as LEGACY rather than re-create it.
If .gitignore exists and lacks paper-*/backup/ or reviews/**/archived/, flag as DEGRADED and suggest adding (don't auto-edit).
Audits init's Phase 4 outputs. Beyond existence — verify meaningful content.
Must have: Project Overview (title, authors, venue, type), Research Questions (≥1), Setup/Overleaf, Folder Structure, Conventions. Flag placeholder text (<title>, TODO, TBD) and excessive length (>200 lines). Vault sync requires Project Overview fields for metadata extraction.
Title, authors, abstract/description, status checklist.
Per rules/review-artefact-routing.md, the manifest must have:
## Latest per source section (table or list of latest report per source slug)## Open issues section (aggregated from per-report headers)## Stale sources section (producers with no report in last 60 days)If the project still has a legacy REVIEW-STATE.md at root instead of reviews/INDEX.md, flag as LEGACY and direct to /tidy-project-reviews.
Legacy 10-column schema (Gap C). If reviews/INDEX.md exists but its content starts with the legacy 10-column REVIEW-STATE.md table header (| Paper | Check | Last Run | Verdict | Score | Open Issues | Source | Trigger | Report | Notes |), flag as DEGRADED — legacy schema. This is the Batch A (2026-05-17) retrofit pattern: 278 projects had their REVIEW-STATE.md renamed to reviews/INDEX.md verbatim without translating the content into the "Latest per source" manifest. The legacy schema is functional (rows continue to append correctly via the helper) but doesn't render the way /review-recap expects post-2026-05-17. Recommend running /review-recap to migrate content; do NOT auto-rewrite (audit is read-only here).
Must include: .DS_Store, __pycache__/, out/, paper/ (if Overleaf-managed), paper-*/backup/ (Overleaf snapshots, per routing rule), reviews/**/archived/ (archived reports, per routing rule).
Should be updated beyond "Project just initialised" if commits exist beyond the initial one.
Audits init's Phase 5 outputs. The nested-pattern paper directory is the cross-cutting concern.
Each paper*/ must contain a paper/ symlink → Overleaf with relative path (absolute paths break across machines). See references/paper-dir-conventions.md.
Scan all paper*/ directories for forbidden file types (code, data, package files). Hard rule — violations are Missing. See references/overleaf-separation.md.
Detect near-duplicate paper-*/ dirs and overlapping symlink targets. See references/paper-dir-conventions.md.
Each paper-{venue}/ should contain backup/ subdirectory. Flag root-level backup/ as wrong-convention. See references/paper-dir-conventions.md.
Every dir with .tex must have .latexmkrc with $out_dir = 'out'. Critical: use find -L to traverse Overleaf symlinks. Auto-scaffolded by Phase 2.11. See references/latex-build-config.md.
Verify paper-{venue}/correspondence/referee-reviews/ structure. See references/review-consistency.md.
If the project has a talk/deck (a paper-{venue}/talk/ dir, or a presentations/ dir, or any *-talk.tex/landing page), verify it follows the convention: the talk/ layout ({venue}-talk.tex, speaker-script.md, references.bib, .latexmkrc, figures/ incl. qr-{slug}.png, out/), a project-local links/{slug}/index.html as source of truth, and the correct folder pattern (archival → paper-{venue}/talk/; non-archival/seminar → presentations/). Flag deploy-only landing pages (no project copy), a missing speaker-script.md, a QR subtitle that over-promises resources the landing page lacks, and a local paper.pdf card that should be a DOI link. Report-only (these are talk artefacts, not init-scaffolded). See references/talk-dir-conventions.md.
Audits init's Phase 6 outputs. If not a git repo: flag as Missing (default since Feb 2026). If git repo, check: branch name (main or master), untracked files, remote status, nested repos (.git/ subdir → Missing; note: submodules have .git as file, use find -mindepth 2 -name .git), submodule tracking (if .gitmodules exists, verify checked out).
Audits init's Phase 7 outputs. Skip if no Atlas topic file found in Phase 1. Check drift on slug / status / venue / paper-dir / co-authors fields. See references/atlas-checks.md.
Audits init's Phase 8 outputs. Verify context library entries: 7.1 index row in .context/projects/_index.md; 7.2 paper file at .context/projects/papers/<short>.md with valid frontmatter; 7.3 mention in .context/current-focus.md. See references/task-management-integration.md.
Audits init's Phase 9 outputs.
knowledge/_index.md should exist if non-empty. If last updated > 90 days with recent activity, flag Degraded.
If project status > Idea: expect *-initial-review.md or literature_summary.md. If any paper-*/ has \cite{}, expect references.bib.
If reviews/ exists, verify structure follows the routing rule (rules/review-artefact-routing.md):
paper-critic/, domain-reviewer/, referee2-reviewer/, etc. — NOT variants like referee2/, peer-review/, fix/)YYYY-MM-DD.md, YYYY-MM-DD-HHMM.md (the timestamp-precision form review agents now write after the 5-agent patch commit 23ebcfff), OR YYYY-MM-DD-<descriptor>.md (manual descriptor form for same-day reruns)reviews/INDEX.md exists at the reviews/ root./CRITIC-REPORT.md and similar are rule violations)correspondence/internal-reviews/ (legacy)If any of these checks fail, flag as DEGRADED and recommend /tidy-project-reviews to retrofit. See references/review-agent-outputs.md for the legacy reference (now superseded by the routing rule).
Three severity levels:
| Level | Meaning |
|---|---|
| Missing | Expected by template, not present |
| Degraded | Present but incomplete or has issues |
| Info | May be intentional — no action needed unless it bothers you |
Full report format with severity markers and remediation lines: references/report-format.md.
After presenting the report, save a timestamped log to .claude/audits/ in the project:
.claude/audits/ if it doesn't exist (this is the only directory the skill creates — it's a self-contained audit trail, not a project-state mutation).YYYY-MM-DD-structure-audit.md with:
-2, -3, etc.Persistent audit trail so future sessions can see what was checked and when.
.claude/audits/ in Phase 10)/atlas-audit for that)/init-project-research — the template this skill audits against. Structural checks here mirror init's scaffold. When init adds a new directory or convention (e.g., github-repo/), add a matching audit check here AND update /atlas-audit SA1./atlas-audit — batch-audits all projects via SA1. SA1's structure checks must stay consistent with this skill's phases./sync-permissions — fixes Phase 2.5 permissions findings./project-safety — safety rules and folder guardrails./update-project-doc — fixes stale documentation (run after this audit)./compile-knowledge — fixes Phase 8.1 empty-knowledge-wiki findings.Per rules/submission-file-archive.md § Topic-folder layout, audit:
paper-<venue>/ — flag any docs/submission-history/, docs/venues/*/submission/, or root-level as-submitted PDFs.files:/submitted_files: pointer in the project's vault submissions + atlas outputs exists on disk under paper-<venue>/submission/archive/ (or published/, correspondence/, talk/, presentations/).PAPER-HISTORY.md freshness — run uv run "$(head -1 ~/.config/task-mgmt/path)/scripts/generate-paper-history.py" --project . --check; report stale/missing (fix = regenerate, one command).{surface}-{stage}[-{role}] (no exemptions).