llm-wiki

An autonomous knowledge base that grows as you work.

LLM Wiki is a Claude Code plugin that captures research, ideas, and decisions into an interlinked wiki with semantic search, automatic research, and a Wikipedia-style web UI. Knowledge compounds over time — the more you use it, the smarter it gets.

Inspired by Andrej Karpathy's LLM Wiki pattern: raw sources are immutable, the LLM maintains the wiki layer, and a schema governs behavior.

Core Features

Knowledge Management

Automatic capture — saves research, ideas, decisions, and findings to the wiki as you work
Smart retrieval with research-on-miss — checks wiki first, automatically researches and ingests if not found
Full-text search — TF-IDF keyword search with content-aware scoring and snippet extraction
Block references & transclusion — [[page#heading]] links and ![[page#section]] embeds
Backlink panel with automatic unlinked mention detection
Frontmatter query language — Dataview-like queries: SELECT title, type FROM pages WHERE confidence = "high"
Intelligent freshness — 9-tier staleness system from live (15 min) to permanent (never expires)

Research-on-Miss

Automatic research — /wiki-read researches topics not in the wiki using available tools
Tool discovery — works with whatever tools the user has (WebSearch, WebFetch, Wikipedia API, MCP tools)
Auto-ingestion — saves findings to wiki with proper citations

Web UI Features

Wikipedia-style browsable website with 4 themes (light, dark, terminal, wikipedia)
Interactive knowledge graph (Cytoscape.js) with multiple layouts, clustering, and neighborhood highlighting
Canvas/whiteboard view for spatial page arrangement
Split-pane markdown editor with live preview and AI assist
Live research — click any red link to auto-research the topic
Spaced repetition review interface (FSRS-based scheduling)
Content gap analysis dashboard
WebSocket chat sidebar with RAG-augmented Q&A

Maintenance & Health

Self-maintaining — lints broken links, merges duplicates, upgrades confidence, flags stale content
Daily notes and journal workflows
Smart caching with adaptive TTL and stale-while-revalidate
Circuit breakers for external API resilience
Git integration with auto-commit, attribution, and undo

How It Works

The wiki operates in a simple cycle: when you ask a question, it first checks its knowledge base. If found, it returns a cited answer. If not found, it automatically researches the topic, ingests the findings, and provides an answer—all without breaking your workflow.

sequenceDiagram
    User->>wiki-reader: /wiki-read "What is X?"
    wiki-reader->>wiki-index: Check knowledge base
    alt Found in wiki
        wiki-index-->>wiki-reader: Page exists
        wiki-reader->>User: Cited answer from wiki
    else Not found
        wiki-index-->>wiki-reader: No results
        wiki-reader->>search-orchestrator: Research needed
        search-orchestrator->>search-channel: Fan out queries (web, academic, code, docs)
        search-channel->>research-processor: Raw search results
        research-processor->>wiki-writer: Processed findings
        wiki-writer->>wiki-pages: Create/update page
        wiki-writer->>User: Cited answer with new page
    end

Quick Start

Installation

Install the plugin:

claude plugin install ./llm-wiki

Or copy manually:

cp -r llm-wiki .claude/plugins/

Restart Claude Code — dependencies install automatically on first session.

First Commands

Start using the wiki immediately with any of these:

Command	Purpose
`/wiki-write https://example.com/article`	Ingest a web page
`/wiki-read "What is transformer attention?"`	Ask — researches if not in wiki
`/wiki-serve`	Browse the wiki at `localhost:8420`
`/wiki-maintain`	Health check and optimization

Dependencies

Core dependencies (fastapi, uvicorn, mcp, etc.) are installed automatically via the plugin's SessionStart hook. For optional enhanced features:

pip install trafilatura        # fallback content extraction
pip install numpy sqlite-vec   # vector search and caching

Skills Reference

`/wiki-write` — Add or Update Content

Ingest from URLs, files, or text. Auto-creates .wiki/ on first use.

Mode	Command	Purpose
Ingest	`/wiki-write <url>`	Fetch and ingest web page or paper
Ingest	`/wiki-write <file>`	Ingest local file (markdown, text, PDF)
Ingest	`/wiki-write "text..."`	Ingest inline text directly
Batch	`/wiki-write --batch <dir>`	Ingest all `.md` files in directory
Update	`/wiki-write --update <slug>`	Autonomously update existing page
Refresh	`/wiki-write --refresh-stale`	Find and refresh stale pages

Page types: concept, idea, brainstorming, status, rules, config, skill, memory, reference, or custom types from .wiki/templates/

`/wiki-read` — Search and Query

Ask the wiki questions. Automatically researches if knowledge is missing.

Depth	Command	Behavior
Quick	`/wiki-read quick <question>`	Index scan only, no research fallback (fastest)
Standard	`/wiki-read <question>`	Search wiki + auto-research if missing
Deep	`/wiki-read deep <question>`	Full search + raw sources + multi-channel research

All answers include [[slug]] citations. Contradictions between sources are explicitly noted.

`/wiki-serve` — Web UI

Launch Wikipedia-style browsable website at localhost:8420.

Features:

4 themes (light, dark, terminal, wikipedia)
Interactive knowledge graph (Cytoscape.js)
Split-pane markdown editor with live preview
WebSocket chat with RAG-augmented Q&A
Live research (click red links to auto-research)
Spaced repetition review (FSRS-based)
Content gap analysis dashboard
Canvas/whiteboard spatial view

Stop: /wiki-serve stop

`/wiki-maintain` — Health Maintenance

Comprehensive wiki maintenance and quality control.

Subcommand	Purpose
`/wiki-maintain`	Run all maintenance steps
`/wiki-maintain lint`	Fix broken links, missing frontmatter, orphans
`/wiki-maintain dedup`	Find and merge near-duplicate pages
`/wiki-maintain gaps`	Analyze knowledge gaps and missing coverage

Maintenance steps:

Lint — fix broken [[links]], missing frontmatter, orphan pages
Deduplicate — merge pages with >60% slug token overlap
Confidence upgrade — promote pages based on source count (low->medium->high)
Stale detection — flag pages past their freshness tier TTL
Fact-checking — verify claims on high-confidence pages
Concept synthesis — auto-generate articles connecting 3+ related pages
Index regeneration — rebuild index.md from all pages

`/wiki-view` — Dashboard and Export

Read-only dashboard, statistics, and export capabilities.

Subcommand	Purpose
`/wiki-view`	Dashboard summary (page counts, recent activity, health)
`/wiki-view pages`	List all pages grouped by type
`/wiki-view stats`	Detailed statistics and distributions
`/wiki-view graph`	Knowledge graph visualization (Mermaid)
`/wiki-view graph <slug>`	Graph centered on page (2-hop neighborhood)
`/wiki-view export html`	Export as self-contained HTML
`/wiki-view export md`	Export as single markdown bundle
`/wiki-view export json`	Export as JSON knowledge graph
`/wiki-view artifacts <type>`	Generate study guide, timeline, glossary, or comparison

How Research-on-Miss Works

When you ask a question that's not in the wiki, the entire research pipeline activates automatically. Here's the flow:

sequenceDiagram
    actor User
    participant WR as wiki-reader
    participant Index as wiki index
    participant SO as search-orchestrator
    participant SC as search-channel
    participant RP as research-processor
    participant WW as wiki-writer
    participant BM as backlink-manager

    User->>WR: /wiki-read "What is X?"
    WR->>Index: Check for matching pages
    alt Page found
        Index-->>WR: Return page
        WR-->>User: Cited answer from wiki
    else No match
        Index-->>WR: No results
        WR->>WR: Detect query intent & complexity
        WR->>SO: Trigger research
        SO->>SO: Route to search channels
        SO->>SC: Dispatch to web, academic, code, docs channels
        par Parallel Research
            SC->>SC: Web search
            SC->>SC: Academic search
            SC->>SC: Code search
            SC->>SC: Docs search
        end
        SC-->>RP: Raw results
        RP->>RP: Deduplicate, condense, rank
        RP-->>WW: Processed findings
        WW->>WW: Synthesize findings into page
        WW->>BM: Update backlinks
        BM->>Index: Register page
        WW-->>User: Cited answer with new wiki page
    end

Architecture

System Overview

LLM Wiki consists of 5 entry points (skills), 10 autonomous agents, utilities in the bin/, and a persistent data layer in .wiki/.

flowchart TD
    User([User]) -->|Invokes| Skills
    
    subgraph Skills["5 Entry Points"]
        W["/wiki-write<br/>Ingest & Update"]
        R["/wiki-read<br/>Search & Ask"]
        S["/wiki-serve<br/>Web UI"]
        M["/wiki-maintain<br/>Health Check"]
        V["/wiki-view<br/>Dashboard"]
    end
    
    Skills -->|Route to| Agents
    
    subgraph Agents["10 Autonomous Agents"]
        subgraph write["Write Pipeline"]
            WW["wiki-writer<br/>(Sonnet)"]
            BM["backlink-manager<br/>(Haiku)"]
        end
        
        subgraph read["Read Pipeline"]
            WR["wiki-reader<br/>(Haiku)"]
            SO["search-orchestrator<br/>(Sonnet)"]
            SC["search-channel<br/>(Haiku)"]
        end
        
        subgraph research["Research Pipeline"]
            RL["research-loop<br/>(Sonnet)"]
            RP["research-processor<br/>(Haiku)"]
        end
        
        subgraph quality["Quality Pipeline"]
            WA["wiki-auditor<br/>(Haiku)"]
            FC["fact-checker<br/>(Sonnet)"]
            CE["citation-explorer<br/>(Sonnet)"]
        end
    end
    
    Agents -->|Read/Write| Data
    Agents -->|Use| Bin
    
    subgraph Bin["Utilities (bin/)"]
        Search["search.py<br/>TF-IDF"]
        Cache["cache.py<br/>Vectors"]
        BL["backlinks.py<br/>Links"]
        Gap["gaps.py<br/>Analysis"]
        Git["git.py<br/>Tracking"]
    end
    
    subgraph Data[".wiki/ Data Layer"]
        Pages["pages/<br/>Markdown"]
        Index["index.md<br/>Catalog"]
        Cache2["cache/<br/>SQLite"]
        Raw["raw/<br/>Sources"]
        Schema["SCHEMA.md<br/>Rules"]
    end
    
    S -->|Serves| UI["Web Server<br/>localhost:8420"]
    UI -->|Renders| UIFeatures["4 Themes, Graph,<br/>Editor, Chat, Review"]

Directory Structure

llm-wiki/
  .claude-plugin/              Plugin metadata (plugin.json, marketplace.json)
  agents/                      10 autonomous agents
  bin/                         23 CLI utilities (search, backlinks, gaps, cache, git, ...)
  mcp/                         MCP server for wiki operations
  rules/                       Workflow and integration rules
  skills/                      5 user-facing skills
    serve/                     Web UI server and assets
      scripts/                 FastAPI server, WikiStore, RAG, chat, research workers
      static/                  JavaScript + CSS (4 themes)
      templates/               16 Jinja2 templates

Agent Collaboration During Research

When /wiki-read deep triggers a deep research operation, agents coordinate like this:

sequenceDiagram
    participant OR as search-orchestrator
    participant SC as search-channel
    participant RP as research-processor
    participant WW as wiki-writer
    participant BM as backlink-manager
    participant FC as fact-checker

    OR->>OR: Classify query complexity
    OR->>SC: Fan out to 4 channels (web, academic, code, docs)
    par Parallel Search
        SC->>SC: Execute web search
        SC->>SC: Execute academic search
        SC->>SC: Execute code search
        SC->>SC: Execute docs search
    end
    SC-->>RP: Raw results stream
    RP->>RP: Deduplicate & condense
    RP->>WW: Processed findings
    WW->>WW: Synthesize into wiki page
    WW->>BM: Update backlinks
    BM->>BM: Maintain reverse index
    FC->>FC: Verify claims
    FC->>WW: Flag uncertainties
    WW-->>OR: Complete

Data Flow: From Source to Wiki

How content flows from raw sources into the wiki knowledge base:

flowchart LR
    URL["URL / File / Text"]
    Fetch["fetch.py<br/>(Jina/Trafilatura)"]
    Extract["Extract<br/>Content & Metadata"]
    Writer["wiki-writer<br/>Synthesize"]
    Pages["pages/<br/>Markdown + YAML"]
    Backlinks["backlinks.py<br/>Update index"]
    Search["search.py<br/>Index for TF-IDF"]
    Vector["cache.py<br/>Embeddings"]
    
    URL -->|Parse| Fetch
    Fetch -->|Clean| Extract
    Extract -->|Create page| Writer
    Writer -->|Save| Pages
    Pages -->|Extract links| Backlinks
    Pages -->|Index content| Search
    Pages -->|Embed chunks| Vector
    
    style URL fill:#e1f5ff
    style Fetch fill:#fff3e0
    style Extract fill:#fff3e0
    style Writer fill:#f3e5f5
    style Pages fill:#e8f5e9
    style Backlinks fill:#fce4ec
    style Search fill:#e0f2f1
    style Vector fill:#f1f8e9

Circuit Breaker Resilience

External API calls are protected by circuit breakers that gracefully degrade when services fail:

stateDiagram-v2
    [*] --> Closed
    
    Closed --> Open: Threshold exceeded<br/>(5 failures in 60s)
    Open --> HalfOpen: Timeout<br/>(30s backoff)
    HalfOpen --> Closed: Trial succeeds
    HalfOpen --> Open: Trial fails
    
    Closed --> Closed: Success or<br/>slow failure
    Open --> Open: Requests<br/>rejected
    HalfOpen --> HalfOpen: Testing<br/>recovery
    
    note right of Closed
        Normal operation
        Requests pass through
    end note
    
    note right of Open
        Circuit tripped
        Fast-fail all requests
        Cache responses
    end note
    
    note right of HalfOpen
        Recovery test mode
        Allows one request through
        Monitors outcome
    end note

Data Model

Wiki data lives in .wiki/ — its location is derived from the plugin install scope:

User-level install (~/.claude/plugins/llm-wiki) -> ~/.wiki/
Project-level install (.claude/plugins/llm-wiki) -> .wiki/ at project root

.wiki/
  pages/          Markdown files with YAML frontmatter (source of truth)
  templates/      Custom page type templates (user-defined structures)
  index.md        Auto-generated page catalog
  log.md          Append-only activity log
  overview.md     Current understanding synthesis
  SCHEMA.md       Page format and evaluation rules
  cache/          SQLite databases (search, vectors, backlinks, flashcards, provenance)
  raw/            Immutable source materials
    web/          Fetched web pages
    papers/       Downloaded PDFs
    notes/        User notes and transcripts
    code/         Code snippets and repos

Frontmatter Schema

---
title: "Page Title"
type: concept|entity|source|analysis|idea|status|rules|config|skill|memory
confidence: high|medium|low
sources: [source-slug-1, source-slug-2]
related: [related-slug-1, related-slug-2]
tags: [tag1, tag2]
freshness_tier: standard  # optional override
created: 2025-01-15
updated: 2025-01-15
---

Freshness Tiers

The wiki uses a 9-tier staleness system to determine when content needs refresh. Choose the tier matching your content's shelf life.

Tier	TTL	When to Use	Examples
`live`	15 min	Ultra-current data	stock prices, live scores, server status
`breaking`	1-6 hours	Rapidly evolving topics	breaking news, incident updates
`current`	1-3 days	Time-sensitive	news articles, current events
`fast`	1-4 weeks	Quickly changing fields	AI/LLM/MCP, API changes, benchmarks
`moderate`	1-3 months	Moderate change rate	software versions, frameworks
`standard`	6 months	Evergreen with updates	general knowledge, how-to guides (default)
`academic`	1 year	Stable research	research papers, studies
`evergreen`	5 years	Slowly changing	history, biographies, theorems
`permanent`	never	Immutable	personal notes, ideas, memories

Web UI

Start with /wiki-serve — opens at localhost:8420:

Navigation & Discovery

Home — recent pages, quick stats, search bar, active research tasks
Search — TF-IDF full-text search with snippets and autocomplete
Knowledge graph — interactive Cytoscape.js visualization with force-directed layouts, clustering, filtering
Canvas — spatial whiteboard for arranging pages visually
Backlinks sidebar — reverse links and unlinked mention detection

Content Creation & Editing

Page view — rendered markdown with source annotations, red-link detection, live research
Editor — split-pane markdown + live preview with formatting toolbar and AI assist
Templates — custom page type templates with auto-fill

Learning & Review

Review — FSRS-based spaced repetition flashcard interface for active recall
Research dashboard — background research task queue with SSE progress streaming
Chat sidebar — WebSocket-based RAG-augmented Q&A with cited answers

Analysis & Insights

Stats — page counts, type/confidence distributions, freshness overview
Gaps — content gap analysis: missing pages, depth gaps, freshness gaps, structural holes
Themes — 4 visual themes (light, dark, terminal, wikipedia)

Custom Page Types

Create templates in .wiki/templates/<type-name>.md:

---
title: "{{title}}"
type: meeting-notes
confidence: medium
attendees: []
date: "{{date}}"
created: "{{created}}"
updated: "{{updated}}"
---

# {{title}}

## Attendees

## Discussion

## Action Items

Use with /wiki-write — the wiki-writer agent automatically applies templates based on the type: field.

Agents

Agent	Model	Purpose
`wiki-writer`	Sonnet	Create/update pages — autonomous ingest and update
`wiki-reader`	Haiku	Search wiki, synthesize cited answers, research on miss
`wiki-auditor`	Haiku	Lint, dedup, fix broken links, upgrade confidence
`backlink-manager`	Haiku	Maintain reverse index, update related fields, detect unlinked mentions
`search-orchestrator`	Sonnet	Classify complexity, fan out to channels, rank results
`search-channel`	Haiku	Execute searches per channel (web, academic, code, docs)
`research-loop`	Sonnet	Iterative research with git-based rollback (max 3 iterations)
`research-processor`	Haiku	Condense and deduplicate parallel research results
`fact-checker`	Sonnet	Verify claims against external sources
`citation-explorer`	Sonnet	Academic citation graph snowballing

MCP Tools

The plugin includes an MCP server exposing wiki operations:

Tool	Description
`wiki_search`	TF-IDF full-text search
`wiki_read`	Read a page by slug
`wiki_write`	Create or update a page
`wiki_list`	List pages, optionally filtered by type
`wiki_backlinks`	Get backlinks + unlinked mentions
`wiki_stats`	Page count, type/confidence distributions
`wiki_query`	Dataview-style frontmatter queries
`wiki_gaps`	Content gap analysis
`wiki_daily`	Create/get today's daily note
`wiki_wikipedia_search`	Search Wikipedia via MediaWiki Action API

Compatibility

Obsidian — open .wiki/ as a vault for graph visualization and editing
Any MCP tools — the wiki discovers available tools at runtime (Perplexity, Context7, etc.)
Git — wiki changes are tracked, with auto-commit and rollback support

Credits

Andrej Karpathy's LLM Wiki gist — the original pattern
FSRS — spaced repetition scheduling algorithm
Cytoscape.js — knowledge graph visualization
FastMCP — MCP server framework
FastAPI — web server framework
markdown-it — markdown rendering

Rules (Always-On Behavior)

The plugin includes two always-active rule files that govern behavior:

Write Rules (`rules/wiki-integration.md`)

Write to the wiki when:

You research any topic — save findings as a wiki page
You generate analysis, comparisons, or summaries worth keeping
You solve non-trivial problems — save the solution pattern
The user shares ideas, plans, decisions, or requirements
You discover facts, relationships, or patterns during work
The user says "save this", "remember this", "note this"

Read from the wiki when:

The user asks about a topic — check wiki FIRST before web search
You need context about the project, its decisions, or history
You're about to research something — check if wiki already covers it

Workflow Rules (`rules/workflow.md`)

Ingest is autonomous — never pause for user confirmation
Contradictions are flagged — note both views, never silently overwrite
Backlinks are mandatory — update related: fields on connected pages
Complete frontmatter required — every page needs title, type, confidence, created, updated
Auto-init — create .wiki/ automatically if it doesn't exist
Freshness-aware — 9-tier staleness system governs when content needs refresh

Troubleshooting

Issue	Solution
No wiki found	Run any `/wiki-*` command — `.wiki/` auto-creates
Web UI won't start	Check port 8420 availability; run `/wiki-serve stop` then retry
Search returns no results	Run `/wiki-maintain` to rebuild indexes
Broken links	Run `/wiki-maintain lint` to auto-fix
Stale content	Run `/wiki-write --refresh-stale` to update old pages

License

MIT

Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
.claude-plugin		.claude-plugin
agents		agents
bin		bin
mcp_server		mcp_server
rules		rules
skills		skills
templates		templates
.gitignore		.gitignore
CONTRIBUTING.md		CONTRIBUTING.md
LICENSE		LICENSE
LLM-Wiki-Guide.html		LLM-Wiki-Guide.html
README.md		README.md
requirements.txt		requirements.txt

Folders and files

Latest commit

History

Repository files navigation

llm-wiki

Core Features

Knowledge Management

Research-on-Miss

Web UI Features

Maintenance & Health

How It Works

Quick Start

Installation

First Commands

Dependencies

Skills Reference

/wiki-write — Add or Update Content

/wiki-read — Search and Query

/wiki-serve — Web UI

/wiki-maintain — Health Maintenance

/wiki-view — Dashboard and Export

How Research-on-Miss Works

Architecture

System Overview

Directory Structure

Agent Collaboration During Research

Data Flow: From Source to Wiki

Circuit Breaker Resilience

Data Model

Frontmatter Schema

Freshness Tiers

Web UI

Navigation & Discovery

Content Creation & Editing

Learning & Review

Analysis & Insights

Custom Page Types

Agents

MCP Tools

Compatibility

Credits

Rules (Always-On Behavior)

Write Rules (rules/wiki-integration.md)

Workflow Rules (rules/workflow.md)

Troubleshooting

License

About

Topics

Resources

License

Contributing

Uh oh!

Stars

Watchers

Forks

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Contributors 1

Languages

`/wiki-write` — Add or Update Content

`/wiki-read` — Search and Query

`/wiki-serve` — Web UI

`/wiki-maintain` — Health Maintenance

`/wiki-view` — Dashboard and Export

Write Rules (`rules/wiki-integration.md`)

Workflow Rules (`rules/workflow.md`)