# LLM Wiki Agent — Schema & Workflow Instructions

This wiki is maintained entirely by your coding agent. No API key or Python scripts needed — just open this repo in Codex, OpenCode, or any agent that reads this file, and talk to it.

## How to Use

Describe what you want in plain English:
- *"Ingest this file: raw/papers/my-paper.md"*
- *"What does the wiki say about transformer models?"*
- *"Check the wiki for orphan pages and contradictions"*
- *"Build the knowledge graph"*

Or use shorthand triggers:
- `ingest <file>` → runs the Ingest Workflow
- `query: <question>` → runs the Query Workflow
- `lint` → runs the Lint Workflow
- `build graph` → runs the Graph Workflow

---

## Directory Layout

```
raw/          # Immutable source documents — never modify these
wiki/         # Agent owns this layer entirely
  index.md    # Catalog of all pages — update on every ingest
  log.md      # Append-only chronological record
  overview.md # Living synthesis across all sources
  sources/    # One summary page per source document
  entities/   # People, companies, projects, products
  concepts/   # Ideas, frameworks, methods, theories
  syntheses/  # Saved query answers
graph/        # Auto-generated graph data
tools/        # Optional standalone Python scripts (require ANTHROPIC_API_KEY)
```

---

## Page Format

Every wiki page uses this frontmatter:

```yaml
---
title: "Page Title"
type: source | entity | concept | synthesis
tags: []
sources: []       # list of source slugs that inform this page
last_updated: YYYY-MM-DD
---
```

Use `[[PageName]]` wikilinks to link to other wiki pages.

---

## Ingest Workflow

Triggered by: *"ingest <file>"*

Steps (in order):
1. Read the source document fully
2. Read `wiki/index.md` and `wiki/overview.md` for current wiki context
3. Write `wiki/sources/<slug>.md` — use the source page format below
4. Update `wiki/index.md` — add entry under Sources section
5. Update `wiki/overview.md` — revise synthesis if warranted
6. Update/create entity pages for key people, companies, projects mentioned
7. Update/create concept pages for key ideas and frameworks discussed
8. Flag any contradictions with existing wiki content
9. Append to `wiki/log.md`: `## [YYYY-MM-DD] ingest | <Title>`

### Source Page Format

```markdown
---
title: "Source Title"
type: source
tags: []
date: YYYY-MM-DD
source_file: raw/...
---

## Summary
2–4 sentence summary.

## Key Claims
- Claim 1
- Claim 2

## Key Quotes
> "Quote here" — context

## Connections
- [[EntityName]] — how they relate
- [[ConceptName]] — how it connects

## Contradictions
- Contradicts [[OtherPage]] on: ...
```

### Domain-Specific Templates

If the source falls into a specific domain (e.g., personal diary, meeting notes), the agent should use a specialized template instead of the default generic one above:

#### Diary / Journal Template
```markdown
---
title: "YYYY-MM-DD Diary"
type: source
tags: [diary]
date: YYYY-MM-DD
---
## Event Summary
...
## Key Decisions
...
## Energy & Mood
...
## Connections
...
## Shifts & Contradictions
...
```

#### Meeting Notes Template
```markdown
---
title: "Meeting Title"
type: source
tags: [meeting]
date: YYYY-MM-DD
---
## Goal
...
## Key Discussions
...
## Decisions Made
...
## Action Items
...
```

---

## Query Workflow

Triggered by: *"query: <question>"*

Steps:
1. Read `wiki/index.md` to identify relevant pages
2. Read those pages
3. Synthesize an answer with inline citations as `[[PageName]]` wikilinks
4. Ask the user if they want the answer filed as `wiki/syntheses/<slug>.md`

---

## Lint Workflow

Triggered by: *"lint"*

Check for:
- **Orphan pages** — wiki pages with no inbound `[[links]]` from other pages
- **Broken links** — `[[WikiLinks]]` pointing to pages that don't exist
- **Contradictions** — claims that conflict across pages
- **Stale summaries** — pages not updated after newer sources
- **Missing entity pages** — entities mentioned in 3+ pages but lacking their own page
- **Data gaps** — questions the wiki can't answer; suggest new sources

Output a lint report and ask if the user wants it saved to `wiki/lint-report.md`.

---

## Graph Workflow

Triggered by: *"build graph"*

First try: `python tools/build_graph.py --open`

If Python/deps unavailable, build manually:
1. Search for all `[[wikilinks]]` across wiki pages
2. Build nodes (one per page) and edges (one per link)
3. Infer implicit relationships not captured by wikilinks — tag `INFERRED` with confidence score; low confidence → `AMBIGUOUS`
4. Write `graph/graph.json` with `{nodes, edges, built: date}`
5. Write `graph/graph.html` as a self-contained vis.js visualization

---

## Naming Conventions

- Source slugs: `kebab-case` matching source filename
- Entity pages: `TitleCase.md` (e.g. `OpenAI.md`, `SamAltman.md`)
- Concept pages: `TitleCase.md` (e.g. `ReinforcementLearning.md`, `RAG.md`)

## Index Format

```markdown
# Wiki Index

## Overview
- [Overview](overview.md) — living synthesis

## Sources
- [Source Title](sources/slug.md) — one-line summary

## Entities
- [Entity Name](entities/EntityName.md) — one-line description

## Concepts
- [Concept Name](concepts/ConceptName.md) — one-line description

## Syntheses
- [Analysis Title](syntheses/slug.md) — what question it answers
```

## Log Format

`## [YYYY-MM-DD] <operation> | <title>`

Operations: `ingest`, `query`, `lint`, `graph`