Prefill

---
description: Seed wiki/foundations/ with domain background knowledge so subsequent /ingest does not create duplicate concept pages for textbook material
argument-hint: "[domain] [--add 'concept name']"
---

# /prefill

> Sediments foundational background (seminal methods, common practice, standard architectures) into `wiki/foundations/` as **terminal** pages.
> Foundations are single-direction by design: other pages link to them, foundations write no reverse links.

## Trigger

Manual: `/prefill [domain]` or `/prefill --add "concept name"`.

## Inputs

- `domain` *(positional, optional)*: research domain — one of `general`, `NLP`, `CV`, `ML Systems`, `Robotics`. If omitted, infer from `wiki/topics/` tags; if `wiki/topics/` is empty, prompt the user.
- `--add "<concept>"`: skip the catalog and seed exactly one foundation by name.

## Outputs

- `wiki/foundations/{slug}.md` — one page per seeded concept
- Updated `wiki/index.md` (foundations section regenerated by `rebuild-index`)
- `wiki/log.md` entry

## Wiki Interaction

### Reads
- `wiki/topics/*.md` — for domain inference (when `domain` is omitted)
- `wiki/foundations/*.md` — to skip already-seeded concepts (idempotent)
- `.claude/skills/prefill/foundations-catalog.yaml` — seed list

### Writes
- `wiki/foundations/{slug}.md` (new only — never overwrite)
- `wiki/index.md` (via `tools/research_wiki.py rebuild-index`)
- `wiki/log.md` (via `tools/research_wiki.py log`)

## Workflow

**Pre-conditions**: working directory contains `wiki/`, `tools/`, `.claude/`. Set `WIKI_ROOT=wiki/`.

### Step 1: Resolve domain

1. If `domain` argument given → use it.
2. Else if `--add` mode → domain is `general` unless the user specified one.
3. Else: read all `wiki/topics/*.md` frontmatter `tags`; if a single dominant domain is detected, use it; otherwise ask the user.

### Step 2: Load seeds

- **Catalog mode**: read `.claude/skills/prefill/foundations-catalog.yaml`. Pick all entries under `domains.{domain}` plus everything under `domains.general` (general foundations apply to every research field).
- **`--add` mode**: synthesize a single seed entry `{slug: <slugified concept>, title: <concept>, summary: ""}`. Use `python3 tools/research_wiki.py slug "<concept>"` to derive the slug.

For each seed, check `wiki/foundations/{slug}.md`. If it already exists, **skip** (do not overwrite, do not warn).

### Step 3: Fetch background from Wikipedia

For each remaining seed, call `tools/fetch_wikipedia.py`:

```bash
python3 tools/fetch_wikipedia.py summary "<title>"
python3 tools/fetch_wikipedia.py sections "<title>"
python3 tools/fetch_wikipedia.py section "<title>" --index <N>   # for relevant sections
```

- The summary call returns `{title, extract, url}`.
- The sections call returns a list of `{index, line, level}` — pick sections whose `line` matches `Variants`, `Types`, `Architecture`, `History`, `Limitations`, `Applications` (case-insensitive substring match).
- Exit code `2` from any call means **page not found** — fall back to LLM knowledge for that seed and set `source_url: ""` in the resulting frontmatter.

### Step 4: Compose the foundation page

Render each seed into the template below. Distinguish Wikipedia-derived content from LLM-supplied content by appending `(LLM analysis)` to sections that have no Wikipedia source material.

```yaml
---
title: "{title}"
slug: "{slug}"
domain: "{domain}"
status: mainstream         # or historical, if the seed is a superseded technique
aliases: []                # list any common aliases the LLM is confident about
first_introduced: "{year if present in Wikipedia summary, else empty}"
date_updated: "{today}"
source_url: "{wikipedia url, or empty if 404}"
---

## Definition
{First paragraph of Wikipedia summary, or LLM-supplied definition.}

## Intuition
{Plain-language explanation built on the definition.}

## Formal notation
{Math/notation extracted from Wikipedia, or LLM-supplied with `(LLM analysis)` tag.}

## Key variants
{Bulleted list distilled from Wikipedia "Variants"/"Types"/"Architecture" sections.}

## Known limitations
{From Wikipedia + LLM judgment.}

## Open problems
{LLM analysis (LLM analysis)}

## Relevance to active research
{LLM analysis (LLM analysis)}
```

Write each file to `wiki/foundations/{slug}.md`.

### Step 5: Refresh navigation and log

```bash
python3 tools/research_wiki.py rebuild-index wiki/
python3 tools/research_wiki.py log wiki/ "prefill | {N} foundations created for {domain}"
```

### Step 6: Report

Print a grouped summary:

```
## Prefill Report — {date}

**Domain**: {domain}
**Created**: {N}  **Skipped (already present)**: {M}

### mainstream
- foundations/gradient-descent — Gradient Descent
- ...

### historical
- foundations/recurrent-neural-networks — Recurrent Neural Networks
```

Remind the user that subsequent `/ingest` runs will dedup against these foundations and create wikilinks (`[[foundation-slug]]`) instead of new concept pages.

## Constraints

- **foundations are terminal**: never write `key_papers`, `related_concepts`, or any outbound reference field on a foundation page. Other pages may link in.
- **never overwrite** an existing `wiki/foundations/{slug}.md` (idempotent re-runs).
- **distinguish sources**: Wikipedia-derived content vs. LLM-derived content must be visually distinct in the page body.
- **catalog is advisory**: the YAML seed list is hand-curated and incomplete. Users may extend it without code changes.
- **only writes to `wiki/foundations/`**: never creates pages under `papers/`, `concepts/`, `topics/`, etc.

## Error Handling

- **`wiki/foundations/` does not exist**: run `python3 tools/research_wiki.py init wiki/` first.
- **Wikipedia 404**: log the missing page, fall back to LLM knowledge for that seed (`source_url: ""`).
- **Network failure**: print which seeds failed and continue with the remainder; do not abort the whole batch.
- **Catalog file missing**: print error pointing to `.claude/skills/prefill/foundations-catalog.yaml`.

## Dependencies

### Tools (via Bash)
- `python3 tools/fetch_wikipedia.py summary|sections|section|wikitext "<title>" [--index N]`
- `python3 tools/research_wiki.py slug "<title>"`
- `python3 tools/research_wiki.py rebuild-index wiki/`
- `python3 tools/research_wiki.py log wiki/ "<message>"`

### Catalog
- `.claude/skills/prefill/foundations-catalog.yaml`