research-lint

name	research-lint
description	Health-check a research directory produced by /research. Runs seven checks — orphan sources, missing entity/concept hubs, missing comparison candidates, broken wikilinks, stale claims, contradictions, and open-question synthesis. Outputs a report; edits where safe (broken-link flags, open-question append, contradiction surfacing); flags-only otherwise. Always user-triggered, never automated. Trigger when the user says things like "lint my research", "health check my research", "check the wiki", "audit my research dir", "what's wrong with my wiki", "find orphans / contradictions / stale claims".
user_invocable	true

Research Lint

You audit a research directory and surface health issues. Lint is user-triggered, never automated. Each pass is read-mostly: you write only to wiki/open-questions.md, wiki/contradictions.md, index.yaml, index.md, and log.md — never to source pages, entity pages, concept pages, or raw files.

This skill answers: "what's broken or thin in this wiki, and what should I research next?"

Step 1 — Locate the research dir

Same logic as /research (query mode):

1. If the user provides a path, use it.
2. Otherwise scan working-dir for research-*/ and ask if multiple exist.
3. If only one exists, use it.

Verify it's a v4 layout — <research_dir>/raw/ and <research_dir>/wiki/ must exist directly under the research dir (no memory/ wrapper). If it's older (v1 with raw at root, or v3 with memory/ wrapper), instruct the user to run migrate_layout.py first and stop.

Step 2 — Pick the checks

Default: run all seven checks. The user can scope down via natural language ("just check broken links", "skip the LLM stuff"). Map their phrasing to:

Check	Cost	Edits the wiki?
orphans	cheap (script)	flags only
missing-hubs	cheap (script)	flags only
missing-comparisons	cheap (script)	flags only
broken-links	cheap (script)	flags only
stale-claims	LLM	flags only
contradictions	LLM (slow)	appends to wiki/contradictions.md
open-questions	LLM	appends to wiki/open-questions.md

The four cheap checks always run. The three LLM checks run by default but can be skipped per user request.

Step 3 — Run the cheap checks (in parallel via bash)

Run all four mechanical scripts in parallel and collect their JSON outputs. They all read-only; safe to run any time.

SKILL_DIR="${CLAUDE_PLUGIN_ROOT:-.claude}/skills/research-lint"
RD="<research_dir>"

uv run --script "$SKILL_DIR/scripts/lint_orphans.py" --research-dir "$RD" > "$RD/lint-orphans.json" &
uv run --script "$SKILL_DIR/scripts/lint_broken_links.py" --research-dir "$RD" > "$RD/lint-broken-links.json" &
uv run --script "$SKILL_DIR/scripts/lint_missing_hubs.py" --research-dir "$RD" > "$RD/lint-missing-hubs.json" &
uv run --script "$SKILL_DIR/scripts/lint_missing_comparisons.py" --research-dir "$RD" > "$RD/lint-missing-comparisons.json" &
wait

Each script prints a single-line JSON {check: "...", findings: [...]} describing what it found. Aggregate counts only — do not load full findings into your context window unless the user explicitly asks for the full list.

Step 4 — Run the LLM checks (parallel subagents)

Spawn three lint_judge subagents in parallel using a single message with multiple Agent calls. Each gets a different check_type:

1. contradictions — reads every wiki/sources/*.md "Tensions" section + entity/concept "Tensions" sections; writes new contradictions to wiki/contradictions.md.
2. stale-claims — for each entity/concept page with source_count >= 3, checks whether the newest source contradicts older claims; flags candidates without writing.
3. open-questions — synthesizes gaps from wiki state into wiki/open-questions.md.

Pass each subagent:

• check_type
• research_dir
• research_topic, input_summary (read from index.yaml)
• output_path (only for contradictions and open-questions; null for stale-claims since it's flag-only)

Each returns a JSON summary on stdout: {check_type, findings_count, written: true|false, flags: [...]}. The orchestrator aggregates flags into the final report.

Step 5 — Apply the safe edits

Some checks generate additive edits the lint pass should apply automatically. Others generate flags the user must act on.

Check	Auto-apply	Notes
orphans	NO	flag only — user decides whether to delete the source or add a wiki citation
missing-hubs	NO	flag — user can /research it or accept the absence
missing-comparisons	NO	flag — user can /research-render comparison <a> <b> if they want
broken-links	NO	flag — wiki page may be missing because not yet promoted, or because the link is genuinely wrong
stale-claims	NO	flag — needs human judgment
contradictions	YES	append to wiki/contradictions.md (the page is meant to grow)
open-questions	YES	append new questions to wiki/open-questions.md

After any auto-apply edits land, regenerate the index:

# If contradictions.md or open-questions.md changed, count_wiki_pages may have moved.
PRIOR_CREATED=$(grep '^created:' "<research_dir>/index.yaml" | awk -F"'" '{print $2}')
# Re-run build_index_yaml.py is unnecessary because no source data changed,
# but build_index_md.py must regenerate to reflect new pages in the index.
uv run --script ${CLAUDE_PLUGIN_ROOT:-.claude}/skills/research/scripts/build_index_md.py --research-dir "<research_dir>"

Step 6 — Append to log.md

DATE=$(date -u +%Y-%m-%d)
cat >> "<research_dir>/log.md" <<EOF

## [$DATE] lint | <topic>

- orphans: <count>
- missing-hubs: <count>
- missing-comparisons: <count>
- broken-links: <count>
- stale-claims: <count flagged>
- contradictions: <count appended to contradictions.md>
- open-questions: <count appended to open-questions.md>
EOF

Step 7 — Present the report

Structure the report so the user can scan it and act:

## Lint report — <topic>
Research dir: <path>
Run at: <ISO-8601>

### Summary
- Total sources: <N>, total wiki pages: <M>
- Issues found: <orphans> orphans · <missing_hubs> missing hubs · <broken> broken links · <stale> stale claims · <contradictions> contradictions · <open_questions> open questions

### Action items (need your decision)
1. Orphans (<N>) — sources never cited by the wiki:
   - <title> (origin: <origin>, score: 0.XX)
   - ... (capped at 5 shown; full list in <research_dir>/lint-orphans.json)
2. Missing hubs (<N>) — concepts/entities mentioned ≥3 times with no page:
   - "<concept>" appears in <X> source pages
   - ...
3. Broken links (<N>):
   - [[wiki/concepts/foo]] referenced from [[wiki/sources/abc]] but the file doesn't exist
   - ...
4. Stale claims (<N>): see <research_dir>/lint-stale-claims.json

### Auto-applied edits
- <K> contradictions appended to [[wiki/contradictions.md]]
- <L> open questions appended to [[wiki/open-questions.md]]

### Next steps
- For each orphan: decide delete vs. add wiki citation
- For missing hubs: run /research with the concept name, OR accept the absence
- For missing comparisons: run /research-render comparison <a> <b>
- For broken links: edit the source file, OR remove the reference

Cap the bulleted lists at 5 items per category. Point users at the JSON files in <research_dir>/ for the full lists. After they review, the JSONs can be deleted (rm <research_dir>/lint-*.json) — they are scratch.

Important notes

• You are read-mostly. The only files you write to are: wiki/contradictions.md, wiki/open-questions.md, index.md (regenerated), and log.md (append). Never touch source pages, entity pages, concept pages, or raw files.
• Subagents do the LLM work. Do not load source pages or wiki pages into your own context — spawn subagents (or use scripts) for everything content-heavy.
• Idempotent. Re-running lint should produce no new edits if the wiki hasn't changed (modulo last_updated and the log entry). Contradictions and open-questions append only when genuinely new.
• Cheap before expensive. Always run the 4 mechanical scripts first; their findings can sharpen the LLM checks (e.g., the contradictions subagent only needs to read pages with source_count >= 2).

Agent reference

• agents/lint_judge.md — Lint Judge Subagent. Generic agent dispatched for contradictions, stale-claims, and open-questions checks via a check_type input.

Script reference

• scripts/lint_orphans.py — Finds sources in index.yaml whose original_path and uri_full are never wikilinked from any wiki page.
• scripts/lint_broken_links.py — Scans every wiki page for [[wikilinks]] and flags any that don't resolve to an existing file.
• scripts/lint_missing_hubs.py — Counts entity/concept name mentions across source pages; flags those with ≥3 mentions and no wiki/entities/<slug>.md or wiki/concepts/<slug>.md.
• scripts/lint_missing_comparisons.py — Pairs entity/concept pages by mutual [[wikilink]] references; flags pairs with ≥2 mutual citations and no comparison page.