Imported from aspi6246/Claude-Code-Skills-for-Academics (code-sweep/SKILL.md). Install upstream with npx skills add aspi6246/Claude-Code-Skills-for-Academics --skill code-sweep. Copyright stays with the author.

Code Sweep

Audit a research project for drift between scripts, outputs, raw data, and the paper. Propose fixes one at a time; the user confirms each. This skill extends script-registry — it reuses that skill's YAML schema, builder, and folder conventions. The only YAML additions Code Sweep introduces are status: and seed:.

Invocation

• /code-sweep — full sweep (all checks)
• /code-sweep --quick — structural checks only; skips dry-run + paper cross-ref
• /code-sweep --sample N — override dry-run sample size (default 1000)
• /code-sweep --no-dryrun — skip just the dry-run step
• /code-sweep --no-paper — skip just the paper cross-ref step

If invoked via trigger phrase, default to full sweep unless the user qualifies ("quick code sweep", etc.).

Step 1 — Layout detection

Read the project's CLAUDE.md (in the current working directory) for folder paths. Default conventions (inherited from script-registry):

If the project's CLAUDE.md declares different paths, use those. If no Code/ folder exists, abort with: "This doesn't look like a research project (no Code/ folder). Code Sweep is designed for empirical-finance research projects."

Step 2 — YAML schema extensions

script-registry already defines the registry: block (purpose, inputs, outputs, paper_target, notes). Code Sweep adds two optional fields:

registry:
  purpose: "..."
  inputs:
    - Data/Processed/foo.parquet
  outputs:
    - Output/Figures/fig_descriptive_stats.pdf
    - Output/Tables/tab_main_results.tex
  paper_target: "Table 1, Figure 3"
  notes: "..."
  status: active           # NEW — active | deprecated. Default: active if absent.
  seed: 42                 # NEW — required iff script uses randomness.

produces_figures / produces_tables are not added — they're derivable from outputs: by extension (.pdf/.png → figure, .tex → table).

Step 3 — Naming patterns

Inherit script-registry's convention:

• Scripts: ^\d+[a-z]?\. Claude_[A-Za-z0-9_]+\.Rmd$ (e.g. 3. Claude_Clean_Data.Rmd, 12b. Claude_Run_Models.Rmd)
• Figures: ^fig_[a-z0-9_]+\.(pdf|png|jpg)$ in Output/Figures/
• Tables: ^tab_[a-z0-9_]+\.tex$ in Output/Tables/

If the project's existing files don't follow these patterns, prefer the project's actual convention — sample a few existing files to infer the pattern and check the rest against that, rather than rigidly enforcing the default.

Step 4 — Checks

Run in this order. Tag each finding MUST-FIX or SUGGESTED. Skip checks gated by --quick / --no-dryrun / --no-paper.

MUST-FIX (paper can't reproduce / pipeline broken)

M1. registry: block completeness — for every .Rmd in Code/ (non-recursive, excluding _Archive/):

• registry: block exists
• purpose, inputs, outputs are present (inputs/outputs may be empty lists)
• All inputs: paths actually exist on disk
• All outputs: paths actually exist on disk (the script may not have been run yet — if status is active and outputs are missing, flag MUST-FIX; if status: deprecated, demote to SUGGESTED)

M2. Paper cross-reference (skip on --quick or --no-paper) — parse the paper:

1. Start with Paper/main.tex (or whatever CLAUDE.md designates).
2. Recursively follow \input{...} and \include{...} to sub-files.
3. Resolve \graphicspath{{path1/}{path2/}} if present.
4. Extract every \includegraphics[...]{stem} and \input{...} reference (ignore commented lines).
5. For each referenced figure stem, the file must exist in Output/Figures/ (try .pdf, .png, .jpg) AND some active script's outputs: must list it.
6. For each referenced table stem, the file must exist in Output/Tables/ (.tex) AND some active script's outputs: must list it.

Missing file OR missing producing script → MUST-FIX. Don't compile the paper — this is parse-based.

M3. Dry-run viability (skip on --quick or --no-dryrun) — for each status: active script:

1. Purl: Rscript -e "knitr::purl('Code/<script>.Rmd', output=tempfile(fileext='.R'), quiet=TRUE)"
2. Wrap the purled code with a header that sets:

   options(.codesweep_sample = <N from --sample>)
   options(.codesweep_dryrun = TRUE)

3. Run the wrapped script via Rscript --vanilla with a 120s timeout.
4. Capture stderr; any non-zero exit or timeout → MUST-FIX with the error message.

Scripts that respect .codesweep_sample should sample their data loads. Scripts that don't will run on full data — slower but still informative. Document this convention in the project's CLAUDE.md if it's not already.

M4. Registry sync — run Rscript "Code/_Claude Scripts/build_registry.R" (or whatever the project uses). After it completes:

• Check the "Drift Warnings" section in the rebuilt Code/REGISTRY.md.
• Each drift warning (undeclared inputs/outputs, unused inputs/outputs) → MUST-FIX with the proposed YAML fix.
• Check the "Scripts Without Registry Metadata" section — any entries → MUST-FIX (propose adding the block).

If build_registry.R doesn't exist, suggest invoking the script-registry skill to set it up, then abort this check.

M5. Reproducibility — set.seed() — grep each active .Rmd for randomness markers: sample(, rnorm(, runif(, rbinom(, rpois(, rbeta(, rgamma(, kmeans(, boot(, bootstrap(, Sys.setenv.*SEED. If any are present:

• seed: must be declared in the registry: block
• The script must call set.seed(<the registry seed>) somewhere before the randomness

Missing seed OR mismatched seed → MUST-FIX.

SUGGESTED (housekeeping)

S1. Stale outputs — for each declared output, compare its mtime to each declared input's mtime. If any input is newer than this output → flag staleness. Report only ("fig_x.pdf is older than data/raw_y.parquet"). Don't propose re-running. The user knows whether the staleness matters.

S2. Orphan outputs — files in Output/Figures/, Output/Tables/, Output/Processed Data/ not declared in any active script's outputs: → SUGGESTED. Propose: move to Output/_Archive/ (create if missing) OR delete (only if user explicitly says delete).

S3. Orphan inputs — files under Data/ not referenced in any active script's inputs: → SUGGESTED. Don't propose deletion (raw data is precious); just flag.

S4. Naming-convention violations — files in Code/, Output/Figures/, Output/Tables/ that don't match the patterns in Step 3 → SUGGESTED with proposed rename. Do not auto-rename — every rename also requires updating outputs: declarations and possibly the paper's \includegraphics references. Propose the rename and the corresponding YAML/paper edits as one bundle.

S5. Deprecated or DAG-orphan scripts — flag a script as a candidate for Code/_Archive/ if:

• status: deprecated, OR
• No other active script's inputs: references any of its outputs, AND none of its outputs appear in the paper cross-ref set from M2

→ SUGGESTED move to Code/_Archive/. Per project rule: move, never delete.

S6. Loose .R files in Code/ — any .R file directly under Code/ (not in _Claude Scripts/) that isn't the pipeline orchestrator (Code/00_run_pipeline.R or whatever CLAUDE.md designates) → SUGGESTED move to Code/_Claude Scripts/. Likely a purled or temp script that didn't get filed.

S7. TODO/FIXME inventory — grep \b(TODO|FIXME|XXX|HACK)\b across Code/ (excluding _Archive/). Report each match as file:line:text, grouped by file. Informational only — no proposed fix.

S8. Environment manifest sync — collect every library(pkg), require(pkg), and pkg::fn reference across Code/ (excluding _Archive/). Compare to renv.lock if present, or DESCRIPTION / requirements.txt. Packages referenced but not in the lockfile → SUGGESTED. If no lockfile exists, suggest creating one with renv::init().

Step 5 — Report

Append the sweep results to today's session log at Code/_Claude Session Logs/YYYY-MM-DD.md (the same convention as wrap-up: one file per day, multiple sessions append with a horizontal-rule separator). If the project's CLAUDE.md designates a different log path or filename pattern, follow that instead. Create the log file if it does not exist.

If the day's log already contains content, append with a leading horizontal rule (---) and timestamped section header. The sweep does not replace any prior content.

Format:

---

## Code Sweep — <YYYY-MM-DD HH:MM>

**Invocation:** `/code-sweep <args>`
**Mode:** full | quick | partial (note skipped checks)

### Summary
- MUST-FIX: <N> findings
- SUGGESTED: <M> findings

### MUST-FIX

#### M1.a — `registry:` block missing `inputs:` in `3. Claude_Clean_Data.Rmd`
**Issue:** YAML block missing required field.
**Proposed fix:** add `inputs: [Data/raw/firms.parquet]` based on detected `read_parquet()` call at line 42.
**Status:** pending

(... one block per finding ...)

### SUGGESTED

(... same format ...)

### Outcome
- Applied: <N>
- Declined: <M> (reasons below)
- Deferred to PINBOARD.md: <K>

Update each finding's Status: line as the user responds: pending → applied | declined: <reason> | deferred.

Step 6 — Confirmation flow

Present findings one at a time, MUST-FIX first, in this order:

1. Print the finding (with file path, line numbers where relevant, proposed fix).
2. Ask: "Apply this fix? [y/n/skip/defer/explain]"
   • y — apply the fix, update Status to applied.
   • n — ask for a one-line reason, record declined: <reason>.
   • skip — leave Status pending, revisit at end of pass.
   • defer — append to PINBOARD.md (use the pinboard skill if available), Status deferred.
   • explain — give more context on why this is flagged, then re-ask.
3. Move to the next finding.

Batch shortcut: when 3+ consecutive findings share the same check ID (e.g., multiple S4 naming violations), after the first one offer: "Apply this same fix to all remaining S4 findings? [y/n]". If y, apply en bloc and report the count.

When all findings are processed:

• Print the final summary (N applied, M declined, K deferred).
• Finalise the report section in the session log.
• If any MUST-FIX were declined or deferred, surface them as a one-line warning: "⚠ MUST-FIX findings unresolved — paper may not reproduce."

Important Rules

• Never auto-apply any fix without confirmation. Even "safe" ones (e.g., adding a status: active default). The whole skill is propose-and-confirm.
• Never delete code or data. Moves to _Archive/ only. This is a project ground rule.
• Never re-run scripts to "fix" stale outputs. S1 flags staleness; the user decides what to re-run.
• Never compile the paper. M2 is parse-based. LaTeX compile is the user's job.
• Never edit _Archive/ contents. It's the dumping ground.
• Don't duplicate script-registry's logic. Use its builder, read its REGISTRY.md, trust its drift detection. Code Sweep adds checks that span beyond the registry (paper cross-ref, dry-run, orphans, naming, TODOs, env manifest).
• Don't call other skills inline (e.g., the pinboard skill). If the user wants pinboard entries, just write directly to PINBOARD.md using the existing format the project uses.

Known limitations

• Dry-run (M3) only catches errors that surface within 120s on sample data. Scaling bugs, OOM issues, and long-tail failures may slip through.
• Paper cross-ref (M2) doesn't follow conditional \if...\else...\fi branches. Figures inside dead branches will look "missing" — user can decline those findings.
• Orphan detection (S2, S3) assumes registry: declarations are accurate. Stale or incomplete declarations produce false positives. Run M4 (registry sync) first so drift warnings surface before orphan checks.
• Naming patterns (S4) are inferred from existing files if the defaults don't match. If the project mixes conventions, sweep may pick the wrong "standard" — user can decline.

Quick reference — when to invoke

Run Code Sweep:

• Before sharing the code with a coauthor or RA
• Before a paper submission / re-submission
• After a large refactor of Code/
• After a data refresh (raw data updated → check downstream staleness)
• When the user is unsure what state the project is in

Don't run Code Sweep mid-development on a single script — it's a milestone tool, not a per-commit linter.