nexus/AGENTS.md

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:

---
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 "

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

---
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

---
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

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

---

Query Workflow

Triggered by: "query: "

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

# 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