RAG Tree Knowledge Graph Wiki

A personal research wiki built with Cursor Agent and Obsidian. Cursor writes and maintains interlinked markdown pages; Obsidian is where you browse, follow links, and explore the graph.

Instead of re-deriving answers from raw documents on every question, the agent compiles knowledge once into a persistent wiki — summaries, concept pages, cross-references, and an evolving synthesis that gets richer with every source you add.

How it works

Layer	Who owns it	Purpose
raw/	You	Immutable sources (articles, papers, notes). Agent reads, never edits.
wiki/	Cursor Agent	Summaries, concepts, systems, comparisons — all interlinked.
index.md	Agent (updated on ingest)	Catalog of every wiki page. Agent reads this first when answering questions.
log.md	Agent (append-only)	Timeline of ingests, queries, and lint passes.
AGENTS.md	Co-evolved	Master instructions that make the agent a disciplined wiki maintainer.

Open this folder as your Cursor workspace and as your Obsidian vault — both tools read the same files.

Architecture

Derived from index.md after the initial ingest: 37 wiki pages from 21 sources — 10 concepts, 3 systems, 2 comparisons.

Enterprise AI stack

How raw sources become compounding knowledge (synthesized in wiki/overview.md):

flowchart TB
  raw["raw/<br/>21 immutable sources"]
  knowledge["Organizational knowledge<br/>Asset complementarity"]
  context["Context pipeline<br/>Retrieve · classify · prune · layer"]
  harness["Agent harness<br/>Skills · hooks · disclosure · subagents"]
  security["Deterministic constraints<br/>Typed actions · invariants · gates"]
  wiki["Wiki synthesis<br/>Compounding knowledge (this vault)"]

  raw --> knowledge --> context --> harness --> security --> wiki

  style wiki fill:#599CE7,stroke:#599CE7,color:#191c22

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Wiki knowledge graph

How index.md organizes the vault:

flowchart TB
  index["index.md<br/>Content catalog"]
  overview["Overview<br/>Evolving thesis"]
  concepts["Concepts<br/>10 pages"]
  systems["Systems<br/>3 implementations"]
  comparisons["Comparisons<br/>2 analyses"]
  sources["Sources<br/>21 summaries"]

  index --> overview
  overview --> concepts
  overview --> systems
  overview --> comparisons
  sources --> concepts
  sources --> systems
  concepts --> comparisons

  style index fill:#599CE7,stroke:#599CE7,color:#191c22

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Concept domains

Retrieval	Runtime	Security
RAG	Agent harness	Deterministic constraints
Context organization	Skills	Agentic cognitive security
Syntax → semantics	Incremental disclosure
Organizational knowledge	Intent architecture

Reference implementations: cognitiveShield · Anthropic multi-agent harness · DSPM for RAG

Quick start (Cursor)

1. Open the vault

File → Open Folder → rag-tree-knowledge-graph

Point Obsidian at the same directory if you want graph view and live preview.

2. Add sources

Drop files into raw/ — markdown, text, clipped articles (Obsidian Web Clipper works well).

3. Ingest

In Agent mode, prompt:

Ingest raw/my-article.md

Or batch:

Ingest raw/*.txt

The agent will read the source, create a summary page in wiki/sources/, update concept pages, refresh cross-links, update index.md, and append to log.md.

Use @-mentions for explicit context:

Ingest @raw/my-article.md using @AGENTS.md

4. Query the wiki

Ask questions against the compiled knowledge, not just raw files:

@index.md How does cognitiveShield relate to RAG security?

Good answers can be filed back into the wiki — ask the agent to save durable analyses as new pages.

5. Lint (periodic health check)

Lint the wiki — contradictions, stale claims, orphans, missing cross-refs.

6. Browse in Obsidian

Open Graph view to see how pages connect. Start from wiki/overview.md for the current synthesis.

Directory layout

rag-tree-knowledge-graph/
  AGENTS.md                 # Agent identity and protocols
  README.md                 # This file
  cursor-obsidian.md        # Full pattern description
  index.md                  # Page catalog
  log.md                    # Activity log
  raw/                      # Your sources (immutable)
  wiki/
    overview.md             # Evolving synthesis
    concepts/               # RAG, harnesses, security, etc.
    systems/                # Specific architectures and tools
    comparisons/            # Side-by-side analyses
    sources/                # One page per ingested source
  .cursor/rules/
    wiki-pages.mdc          # Page format and wikilink conventions

Cursor tips

• Agent mode — ingest, write pages, update the index.
• Plan mode — design layout or revise AGENTS.md before big changes.
• @-mentions — @AGENTS.md, @index.md, @wiki/, @raw/foo.md give the agent precise context.
• Git — the wiki is plain markdown; commit when you want version history.

Current state

This vault is seeded with research on RAG, agent harnesses, cognitive security, and context architecture. See wiki/overview.md and index.md for what's already compiled.

For the full pattern (architecture, operations, Obsidian tips), read cursor-obsidian.md.