Mini Context Graph Skill

The Core Idea

Standard RAG re-discovers knowledge from scratch on every query. This skill is different:

1. Wiki layer — The LLM writes and maintains persistent markdown pages (summaries, entity pages, topic syntheses). Cross-references are already there. The wiki gets richer with every ingest.
2. Graph layer — Entities and relations are extracted once and stored as a navigable knowledge graph. BFS traversal answers structural queries without re-reading sources.
3. Raw source layer — Original documents are stored immutably with chunks. Provenance links tie every graph node and edge back to the exact text that supports it.

The LLM writes; the Python tools handle all bookkeeping.

---

Three Layers

Layer	Where	What the LLM does	What Python does
Raw Sources	data/documents.json	Reads (never modifies)	Stores chunks + metadata
Wiki	wiki/ (markdown)	Writes/updates pages	Manages index.md + log.md
Graph	data/graph.json	Extracts entities + relations	Persists, deduplicates, traverses

---

⚡ Quick Start for Agents

A complete runnable version of this workflow is in scripts/template_agent_workflow.py — copy and adapt it.

from scripts.contextgraph import ContextGraphSkill
from scripts.tools import wiki_store

skill = ContextGraphSkill()

# ===== INGEST WITH FULL RAG + WIKI =====
# 1. Read references/ingestion.md and references/ontology.md first
# 2. Extract entities and relations (LLM reasoning step)
entities = [
    {"name": "memory leak",   "type": "issue",  "supporting_text": "memory leaks cause crashes"},
    {"name": "system crash",  "type": "issue",  "supporting_text": "system crashes due to memory leaks"},
]
relations = [
    {"source": "memory leak", "target": "system crash", "type": "causes",
     "confidence": 1.0, "supporting_text": "System crashes due to memory leaks."},
]

result = skill.ingest_with_content(
    doc_id="doc_001",
    title="System Crash Analysis",
    source="/docs/incident_report.pdf",
    raw_content="System crashes due to memory leaks. Memory leaks occur when objects are not released.",
    entities=entities,
    relations=relations,
)
# result = {"doc_id": "doc_001", "chunk_count": 1, "nodes_added": 2, "edges_added": 1}

# 3. Write a wiki summary page for this document
wiki_store.write_page(
    category="summary",
    title="System Crash Analysis Summary",
    content="""---
title: System Crash Analysis
source_document: doc_001
tags: [summary, incident]
---

# System Crash Analysis

**Source:** incident_report.pdf

## Key Claims

- [[memory-leak]] causes [[system-crash]] (confidence: 1.0)

## Entities

- [[memory-leak]] (issue)
- [[system-crash]] (issue)
""",
    summary="Incident report: memory leaks cause system crashes.",
)

# ===== QUERY WITH EVIDENCE =====
result = skill.query_with_evidence("Why does the system crash?")
# Returns: {"query": ..., "subgraph": ..., "supporting_documents": [...], "evidence_chain": ...}

# ===== WIKI SEARCH (read wiki before answering) =====
pages = wiki_store.search_wiki("memory leak")
# Returns: [{slug, category, path, snippet}, ...]

---

Operations

Ingest

When a user provides a new document:

1. Read references/ingestion.md — entity/relation extraction rules.
2. Read references/ontology.md — type normalization rules.
3. Extract entities and relations using your LLM reasoning.
4. Call skill.ingest_with_content(...) — stores raw content + chunks + graph nodes + provenance.
5. Write a wiki summary page using wiki_store.write_page(category="summary", ...).
6. Update entity pages — for each new/updated entity, write or update wiki_store.write_page(category="entity", ...).
7. Update topic pages if the document touches an existing synthesis topic.
8. A single document ingest will typically touch 3–10 wiki pages.

Query

When a user asks a question:

1. Check the wiki first — wiki_store.search_wiki(query) to find relevant pages. Read them.
2. If the wiki has a good answer, synthesize from wiki pages (fast path).
3. If deeper graph traversal is needed, call skill.query_with_evidence(query).
4. Return the answer with evidence citations from supporting_documents.
5. If the answer is valuable, file it back as a new wiki topic page.

Lint

Periodically health-check the wiki:

from scripts.tools import wiki_store
issues = wiki_store.lint_wiki()
# Returns: {orphan_pages, missing_pages, broken_wikilinks, isolated_pages}

Ask the LLM to review and fix: broken links, orphan pages, stale claims, missing cross-references. See references/lint.md for full lint workflow.

---

Ingestion Constraints

• ❌ Do NOT hallucinate entities not present in the text
• ❌ Do NOT add relations without explicit textual evidence
• ❌ Do NOT add edges with confidence < 0.6
• ✅ Provide supporting_text for every entity and relation — this enables provenance
• ✅ Write a wiki summary page for every ingested document
• ✅ Update existing entity pages when new information arrives
• ✅ Flag contradictions in wiki pages when new data conflicts with old claims

---

Retrieval Constraints

• 🔒 Traversal depth MUST NOT exceed 2 (config: MAX_GRAPH_DEPTH)
• 🔒 Only edges with confidence ≥ 0.6 (config: MIN_CONFIDENCE)
• 🔒 Maximum 50 nodes returned (config: MAX_NODES)
• ❌ Do NOT fabricate nodes or edges not in the graph

---

Full Python API Reference

Method	Purpose	When to Use
skill.ingest_with_content(doc_id, title, source, raw_content, entities, relations)	Full RAG ingest: raw docs + graph + provenance	Every new document
skill.add_node(name, node_type)	Add single entity (no provenance)	Quick additions without a source doc
skill.add_edge(source_name, target_name, relation, confidence)	Add single relation	Quick additions without a source doc
skill.query(query)	Graph-only retrieval → subgraph	Structural queries
skill.query_with_evidence(query)	Graph + provenance → subgraph + source chunks	Queries requiring citations
wiki_store.write_page(category, title, content, summary)	Write/update a wiki page	After every ingest; after answering queries
wiki_store.read_page(category, title)	Read a wiki page	Before answering; for cross-referencing
wiki_store.search_wiki(query)	Keyword search across wiki	Fast path before graph traversal
wiki_store.list_pages(category)	List all wiki pages	Getting an overview
wiki_store.get_log(last_n)	Read recent operations	Understanding wiki history
wiki_store.lint_wiki()	Health check	Periodic maintenance
documents_store.list_documents()	List all ingested raw sources	Audit / provenance checking
documents_store.search_chunks(query)	Chunk-level search	Finding specific evidence

---

Design Philosophy

"The wiki is a persistent, compounding artifact. The cross-references are already there. The synthesis already reflects everything you've read." — Karpathy

Layer	What Happens	Who Owns It
LLM Reasoning	Extraction, synthesis, writing wiki pages	Agent (.md guidance files)
Wiki Persistence	Index, log, file I/O	wiki_store.py
Graph Persistence	Dedup, index, BFS traverse	graph_store.py, retrieval_engine.py
Raw Source Storage	Immutable docs + chunks + provenance	documents_store.py

The human curates sources and asks questions. The LLM writes the wiki, extracts the graph, and answers with citations. Python handles all bookkeeping.