wiki-enrich

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SKILL.md (first lines)

# Wiki Enrich: Fill Paper TODO Sections (Karpathy LLM-Wiki)

Target: **$ARGUMENTS**

## Why this skill exists

`ingest_paper` (called by `/research-lit`, `/arxiv`, `/alphaxiv`, `/deepxiv`, `/semantic-scholar`, `/exa-search`, `/firecrawl-search`) only renders the per-paper scaffold — frontmatter + abstract + **10 fillable** `_TODO._` placeholder sections (plus two protected sections: `## Connections` is graph-summary and `## Abstract (original)` is auto-populated when `--arxiv-id` is given). No downstream skill in ARIS fills those 10 sections; the wiki sits as TODO until someone reads each paper.

This contradicts the Karpathy LLM-wiki design (https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f):

> "You never (or rarely) write the wiki yourself — the LLM writes and maintains all of it. … The tedious part of maintaining a knowledge base is not the reading or the thinking — it's the bookkeeping. … LLMs don't get bored, don't forget to update a cross-reference, and can touch 15 files in one pass."

`/wiki-enrich` is the missing back half of `ingest_paper`: it reads each scaffolded paper page, fetches paper content from external sources via a graceful fallback chain (see Phase 2.3 for the full 5-source chain), and rewrites the 10 fillable TODO sections into 1-3 sentence prose summaries.

## Constants

- **WIKI_ROOT = `research-wiki/`** — Resolved relative to git root. Skill hard-fails if not a directory.
- **TARGET_DEFAULT = `missing`** — When no target is given, enrich only papers with ≥1 TODO section. Other targets: `<slug>` (one paper) or `all` (every paper, even ones already enriched — usually combined with `--force` to overwrite).
- **SOURCE_DEFAULT = `auto`** — Fetch order: alphaxiv overview → alphaxiv abs → deepxiv brief → arXiv API abstract → page abstract fallback. First non-empty wins (full chain documented in Phase 2.3 table). Override with `--source` to pin one source.
- **MAX_PAPERS = 20** — Hard cap per invocation; LLMs touch many files but token budgets are real. Override with `--max N`.
- **FORCE = false** — When `false` (default), skip sections that already have non-TODO content. When `true`, overwrite every fillable section, but **never** touch the two protected sections: `## Connections` (auto-generated from `edges.jsonl`) and `## Abstract (original)` (immutable arXiv-fetched source data).
- **SECTIONS_TO_FILL** — 10 fillable sections + 2 protected. `ingest_paper` (`research_wiki.py:436-473`) scaffolds 11 section headers unconditionally and a 12th — `## Abstract (original)` — only when arXiv returns an abstract for the given `--arxiv-id` (`research_wiki.py:469-473`). Of these, 10 carry a `_TODO._` (or `_TODO: fill in after reading._`) marker and need filling. The other 2 — `## Connections` (position 10 in the enumeration below) and `## Abstract (original)` (position 12, conditional) — are protected by construction: `Connections` is auto-generated from `graph/edges.jsonl`, `Abstract (original)` is immutable source data from the arXiv API. This skill writes to the 10, never the 2.
  1. `One-line thesis` (marker: `_TODO: fill in after reading._`)
  2. `Problem / Gap` (marker: `_TODO._`)
  3. `Method` (marker: `_TODO._`)
  4. `Key Results` (marker: `_TODO._`)
  5. `Assumptions` (marker: `_TODO._`)
  6. `Limitations / Failure Modes` (marker: `_TODO._`)
  7. `Reusable Ingredients` (marker: `_TODO._`)
  8. `Open Questions` (marker: `_TODO._`)
  9. `Claims` (marker: `_TODO._`) — fill with `_No claims tracked yet._` if no `claim:` edges point to this paper; otherwise list them.
  10. `Connections` — **NEVER edit** (auto-generated from `graph/edges.jsonl`).
  11. `Relevance to This Project` (marker: `_TODO._`) — use `RESEARCH_BRIEF.md`, `AGENTS.md` (or legacy `CLAUDE.md`), or `gap_map.md` for project context. If no project context exists, leave as TODO and report it.
  12. `Abstract (original)` — leave alone (already populated by `ingest_paper` when `--arxiv-id` was used).

> 💡 Examples:
> - `/wiki-enrich` — enrich every paper with ≥1 TODO section (most common usage)
> - `/wiki-enrich vllm` — enrich a single paper by slug
> - `/wiki-enrich all --force` — rewrite every paper from scratch (use when you've adopted a new style)
> - `/wiki-enrich --source alphaxiv --max 5` — only use alphaxiv, only do 5 papers
> - `/wiki-enrich missing --max 50` — bigger batch (watch token budget)

## Pre-flight

Resolve `$WIKI_ROOT` and `$WIKI_SCRIPT` (canonical chain — see `shared-references/wiki-helper-resolution.md`):

```bash
cd "$(git rev-parse --show-toplevel 2>/dev/null || pwd)" || exit 1
[ -d research-wiki/ ] || { echo "ERROR: research-wiki/ not found. Run /research-wiki init first." >&2; exit 1; }

ARIS_REPO="${ARIS_REPO:-$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills-codex.txt 2>/dev/null)}"
WIKI_SCRIPT=""
[ -n "$ARIS_REPO" ] && [ -f "$ARIS_REPO/tools/research_wiki.py" ] && WIKI_SCRIPT="$ARIS_REPO/tools/research_wiki.py"
[ -z "$WIKI_SCRIPT" ] && [ -f tools/research_wiki.py ] && WIKI_SCRIPT="tools/research_wiki.py"
[ -z "$WIKI_SCRIPT" ] && [ -f ~/.codex/skills/research-wiki/research_wiki.py ] && WIKI_SCRIPT="$HOME/.codex/skills/research-wiki/research_wiki.py"
[ -n "$WIKI_SCRIPT" ] || { echo "ERROR: research_wiki.py not found." >&2; exit 1; }
```

If either fails, **hard-fail** — this skill manipulates wiki state and must not run blind.

## Workflow

### Phase 1: Parse target + discover candidates

Parse `$ARGUMENTS` for the first positional (target) and flags (`--source`, `--force`, `--max`).

Build the candidate paper list:

```bash
case "$TARGET" in
  all)
    PAPERS=( research-wiki/papers/*.md )
    ;;
  missing|"")
    # only papers with at least one TODO marker line
    PAPERS=( $(grep -lE "^_TODO(\._?|: fill in after reading\._?)$" research-wiki/papers/*.md 2>/dev/null) )
    ;;
  *)
    P="research-wiki/papers/${TARGET}.md"
    [ -f "$P" ] || { echo "ERROR: paper not found: $P" >&2; exit 1; }
    PAPERS=( "$P" )
    ;;
esac
echo "Candidate papers: ${#PAPERS[@]} (cap ${MAX_PAPERS})"
PAPERS=( "${PAPERS[@]:0:${MAX_PAPERS}}" )
```

If the candidate list is empty, print `"✓ Nothing to enrich."` and exit 0. Do not error.

### Phase 2: For each paper — read, fetch, fill

Iterate **one paper at a time**. For each `$PAPER` in `$PAPERS`:

**Step 2.1 — Read the page and project context.** Use the `Read` tool on the full paper file. Extract from the YAML frontmatter:
- `node_id` (e.g. `paper:vllm`) — slug = part after `paper:`
- `arxiv` from `external_ids.arxiv` — empty string if absent
- `title`
- existing `## Abstract (original)` blockquote (if present) — fallback content source

Additionally, on the FIRST paper of the batch (cache for the rest), read project-context files needed for the `Claims` and `Relevance to This Project` sections:
- `research-wiki/graph/edges.jsonl` — scan for `claim:` edges pointing to the current paper's `node_id`
- `RESEARCH_BRIEF.md` (project root) — if present, source for project goals
- `AGENTS.md` (project root, Codex CLI primary) or legacy `CLAUDE.md` — if present, fallback for project context
- `research-wiki/gap_map.md` — if non-empty, source for gap framing

If none of the project-context files exist, the `Relevance to This Project` section will be filled with the literal "context not yet set" line (see Step 2.4 table).

**Step 2.2 — Identify which sections are TODO.**

Match each section header against its marker:
- A header followed by exactly `_TODO._` → fill
- A header followed by `_TODO: fill in after reading._` → fill (One-line thesis)
- A header followed by any other content → skip (unless `--force`)
- `## Connections` → **always skip** (auto-generated)
- `## Abstract (original)` → **always skip** (immutable source data)

If no fillable sections remain, log `"skip: <slug> (already enriched)"` and continue.

**Step 2.3 — Fetch source content.**

From wanshuiyin/Auto-claude-code-research-in-sleep, MIT.

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