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) 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):

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:

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.

The fetch chain runs in order until one returns usable content (>200 chars of text):

Order	Source	How
1	alphaxiv overview (auto default; --source alphaxiv to pin)	WebFetch https://alphaxiv.org/overview/<arxiv_id>.md — LLM-optimized summary, often best for filling sections
2	alphaxiv abs (fallback within alphaxiv)	WebFetch https://alphaxiv.org/abs/<arxiv_id>.md
3	deepxiv brief (--source deepxiv to pin)	python3 "$DEEPXIV_FETCHER" paper-brief <arxiv_id> if helper resolves
4	arXiv API abstract — fresh fetch (--source arxiv to pin)	curl http://export.arxiv.org/api/query?id_list=<arxiv_id> — log label: arxiv-api-abstract
5	Page abstract — fallback (last resort)	Reuse the existing ## Abstract (original) blockquote already present in the page body from a prior ingest_paper run — log label: page-abstract-fallback
—	No arxiv id + no page abstract	Skip this paper, log "skip: <slug> (no arxiv id, no abstract)", continue

When trying alphaxiv: if WebFetch returns 404 / "Paper not found" / a redirect to the homepage, treat as miss and fall through.

When trying deepxiv: resolve $DEEPXIV_FETCHER per shared-references/integration-contract.md. If the helper or deepxiv CLI is missing, fall through silently.

Save the fetched content as $SOURCE_TEXT. Record which source succeeded for the log entry.

Step 2.4 — Generate per-section content.

You (the executor agent) are the LLM doing the grunt work. Given:

• $SOURCE_TEXT (the fetched overview / brief / abstract)
• $TITLE
• the list of fillable section headers

Write each TODO section's body following these rules:

Section	Length	Style	What to extract
One-line thesis	1 sentence, ≤25 words	Declarative	The paper's core contribution in one sentence — what they built / proved / improved
Problem / Gap	1-2 sentences	Declarative	What problem the field had, why prior work fell short
Method	2-4 sentences	Technical, name the technique	Core mechanism — algorithm name + key idea + how it differs from baselines
Key Results	1-3 bullets OR 2-3 sentences	Quantitative	Headline numbers from the abstract / overview (X% improvement, Yx speedup, etc.). Keep units verbatim.
Assumptions	1-3 bullets	Declarative	What the paper takes for granted (workload type, hardware, model class, distribution shape)
Limitations / Failure Modes	1-3 bullets	Honest	What the paper explicitly admits OR what's structurally absent (e.g. "no multi-node evaluation", "assumes uniform request length")
Reusable Ingredients	1-3 bullets	Concrete	Techniques / datasets / insights from this paper that could be ported elsewhere. Highest value for /idea-creator — write carefully.
Open Questions	1-2 bullets	Question form	What the paper does NOT answer but raises
Claims	1 line	Static	If no claim: edges in graph/edges.jsonl reference this paper, write the literal italic line: _No claims tracked yet — populate via /proof-checker._. Else list claim node IDs.
Relevance to This Project	1-2 sentences	Project-contextual	Use RESEARCH_BRIEF.md / AGENTS.md (or legacy CLAUDE.md) / gap_map.md to phrase the connection. If no project context, write the literal italic line: _Project context not yet set — populate RESEARCH_BRIEF.md or gap_map.md to enable this section._ and report.

Rules (Karpathy fidelity):

• Faithful to source. If the paper doesn't say it, don't invent it. Prefer _Not stated in source._ over hallucination.
• No filler. "This paper presents an approach to..." — don't write that. Start with the noun.
• Keep technical terms in English. vLLM, KV cache, prefill, decode, TTFT, etc. stay verbatim.
• Quantitative when possible. If the abstract has numbers, use them; don't paraphrase as "significant".
• Bilingual support. If the project's AGENTS.md declares a language preference (language: zh or language: bilingual), match it. Otherwise default to English (or follow shared-references/output-language.md).

Step 2.5 — Edit the file.

For each fillable section, use the Edit tool to replace the TODO marker with the generated body. Match the exact section header + marker pair to keep edits unique, e.g.:

## Problem / Gap
_TODO._

→

## Problem / Gap
<generated body>

Never touch the YAML frontmatter, ## Connections, or ## Abstract (original).

Step 2.6 — Append log entry.

python3 "$WIKI_SCRIPT" log research-wiki/ "wiki-enrich: enriched paper:<slug> from <source> (filled N/M sections)"

Record which source provided content (alphaxiv-overview, alphaxiv-abs, deepxiv-brief, arxiv-api-abstract, or page-abstract-fallback) so the audit trail is honest about provenance.

Phase 3: Final report

After processing all candidates, print:

✓ wiki-enrich complete

Processed:  N
Enriched:   X (sections filled: total)
Skipped:    Y  (reasons: already enriched / no arxiv id / fetch failed)
Failed:     Z  (with paper + reason)

Source breakdown:
  alphaxiv-overview: A
  alphaxiv-abs:      B
  deepxiv-brief:     C
  arxiv-api-abstract:     D
  page-abstract-fallback: E

Re-ideation suggestion: <if ≥5 papers were enriched, recommend `/idea-creator "topic"` so the freshly-filled `Reusable Ingredients` and `Limitations` feed brainstorming. `query_pack.md` is already rebuilt below — the user does NOT need to call `/research-wiki query` manually.>

Also rebuild query_pack.md once at the end (single python3 "$WIKI_SCRIPT" rebuild_query_pack research-wiki/ call) so /idea-creator sees the new bodies on its next run.

Output Protocols

Follow the shared protocols:

• No MANIFEST.md entry. This skill edits existing scaffolded pages in place rather than generating new artifacts. The audit trail lives in research-wiki/log.md (Step 2.6), with provenance per paper. Adding a wiki-enrich stage to shared-references/output-manifest.md is out of scope for this PR.
• Output Language Protocol — respect the project's language setting.

Key Rules

• Idempotent by default. Re-running without --force only touches still-TODO sections. Safe to invoke as a cron.
• Never touch frontmatter, ## Connections, or ## Abstract (original). Frontmatter is metadata, Connections is graph-generated, Abstract is immutable source data.
• Hard-fail on missing wiki / missing helper. Do not silently create research-wiki/ — if it's missing, the user is in the wrong cwd or hasn't run /research-wiki init.
• Track provenance. Every log entry records which source actually filled the body. If a future audit shows alphaxiv hallucinated for a paper, you can find every page touched by that source.
• Don't auto-trigger /idea-creator. This skill builds the substrate; the user decides when to brainstorm next. Only suggest re-ideation in the final report.
• Gracefully degrade. If WebFetch is rate-limited, fall through to next source. If all sources miss, skip the paper and continue — don't abort the whole batch.
• Karpathy fidelity above completeness. It is better to leave a section as _Not stated in source._ than to hallucinate. The wiki's value is that it doesn't lie.

Composing with Other Skills

/research-lit "topic"               ← ingests papers as scaffolds (Step 6)
/wiki-enrich                        ← THIS — fills paper bodies (you are here)
/research-wiki lint                 ← health-check (orphans, contradictions, dead ideas)
/idea-creator "direction"           ← reads query_pack, ideates on top of enriched wiki
/research-wiki query "topic"        ← rebuild query_pack after big wiki changes

After a fresh /research-pipeline run leaves Stage 1 Phase 1 done but Phase 2 not started (the failure mode that prompted this skill), the recovery path is:

/wiki-enrich              # fill the paper TODOs ingest_paper left behind
/idea-creator "..."        # now ideate with a wiki that actually has content