DeepWiki MCP Skill

AI-powered documentation and Q&A for any public GitHub repository

Version: 1.0.0 Trit: 0 (Ergodic - coordinates knowledge retrieval) Bundle: research Provider: Cognition (Devin AI) - Official, Free, No Auth Required

Overview

DeepWiki MCP provides programmatic access to AI-generated documentation for any public GitHub repository indexed on DeepWiki.com. It enables:

1. Wiki Structure: Get table of contents for any repo's documentation
2. Wiki Contents: Read AI-generated documentation for specific topics
3. Ask Questions: Get AI-powered answers grounded in repository context

Server Configuration

Base URL

https://mcp.deepwiki.com/

Wire Protocols

Protocol	URL	Best For
SSE	https://mcp.deepwiki.com/sse	Claude, most clients
Streamable HTTP	https://mcp.deepwiki.com/mcp	OpenAI, Cloudflare, Amp

Tools

1. read_wiki_structure

Get the documentation topic tree for a GitHub repository.

{
  "tool": "read_wiki_structure",
  "params": {
    "repo_owner": "AlgebraicJulia",
    "repo_name": "ACSets.jl"
  }
}

Returns: List of documentation topics/sections

2. read_wiki_contents

Read documentation for a specific topic.

{
  "tool": "read_wiki_contents",
  "params": {
    "repo_owner": "AlgebraicJulia",
    "repo_name": "ACSets.jl",
    "topic": "Overview"
  }
}

Returns: AI-generated documentation content

3. ask_question

Ask any question about a repository with AI-powered, context-grounded response.

{
  "tool": "ask_question",
  "params": {
    "repo_owner": "AlgebraicJulia",
    "repo_name": "Catlab.jl",
    "question": "How do wiring diagrams compose?"
  }
}

Returns: AI-powered answer with repository context

Client Configuration

Amp / Codex (.mcp.json)

{
  "mcpServers": {
    "deepwiki": {
      "serverUrl": "https://mcp.deepwiki.com/mcp"
    }
  }
}

Claude Desktop

{
  "mcpServers": {
    "deepwiki": {
      "serverUrl": "https://mcp.deepwiki.com/sse"
    }
  }
}

Claude Code (CLI)

claude mcp add -s user -t http deepwiki https://mcp.deepwiki.com/mcp

Cursor / Windsurf

Add to .cursor/mcp.json:

{
  "mcpServers": {
    "deepwiki": {
      "serverUrl": "https://mcp.deepwiki.com/sse"
    }
  }
}

GF(3) Triad Integration

Trit	Skill	Role
-1	hatchery-papers	Validates academic sources
0	deepwiki-mcp	Coordinates repo knowledge
+1	bmorphism-stars	Generates from starred repos

Conservation: (-1) + (0) + (+1) = 0 ✓

Additional Triads

hatchery-papers (-1) ⊗ deepwiki-mcp (0) ⊗ bmorphism-stars (+1) = 0 ✓  [Research]
persistent-homology (-1) ⊗ deepwiki-mcp (0) ⊗ gay-mcp (+1) = 0 ✓  [Documentation]
sheaf-cohomology (-1) ⊗ deepwiki-mcp (0) ⊗ topos-generate (+1) = 0 ✓  [Knowledge]
three-match (-1) ⊗ deepwiki-mcp (0) ⊗ cider-clojure (+1) = 0 ✓  [Clojure Repos]
polyglot-spi (-1) ⊗ deepwiki-mcp (0) ⊗ gay-mcp (+1) = 0 ✓  [Cross-Lang Docs]

Use Cases

1. Understand New Libraries

"Read the documentation structure for react/react and explain the hooks system"

2. Answer Technical Questions

"How does Catlab.jl implement natural transformations?"

3. Compare Implementations

"Compare how ACSets.jl and Catlab.jl handle graph homomorphisms"

4. Explore Category Theory Libraries

"What topics are covered in AlgebraicJulia/AlgebraicDynamics.jl documentation?"

Indexing Your Repository

To make your public GitHub repo available via DeepWiki MCP:

1. Visit DeepWiki.com
2. Enter your repository URL
3. Wait for indexing to complete
4. Add the DeepWiki badge to your README:

[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/owner/repo)

Related Resources

• DeepWiki.com - Web interface
• Devin Docs - Official documentation
• MCP Specification - Protocol details

ACSet Skill Integration

Both deepwiki-mcp and acsets-algebraic-databases are ERGODIC (trit 0) — they substitute for each other in triads and coordinate knowledge transport.

Qualified Workflow

Phase	deepwiki-mcp	acsets skill	Verification
Discovery	read_wiki_structure	Schema patterns	✓ Catlab.jl has 16 topic pages
Q&A	ask_question	Formal definitions	✓ ACSet = Functor C → Set confirmed
Apply	Code examples	Specter navigation	✓ oapply documented in Catlab
Debug	"Why does X fail?"	Check naturality	✓ HomSearch uses BacktrackingSearch

Verified DeepWiki ↔ ACSets Correspondence

From DeepWiki ask_question("AlgebraicJulia/Catlab.jl", "How do ACSets work..."):

DeepWiki Response	ACSets Skill	Match
"ACSet represents a functor from schema to Set"	C-set = Functor X: C → Set	✓
"ACSetFunctor wraps ACSet for functorial view"	∫G category of elements	✓
"BacktrackingSearch (CSP-based, MRV heuristic)"	homomorphisms(G, complete_graph(k))	✓
"VMSearch (compiled virtual machine)"	Specter zero-overhead navigation	✓

Repository Indexing Status (Verified 2025-12-22)

Repository	DeepWiki Status	Topics
AlgebraicJulia/Catlab.jl	✅ Indexed	16 pages (GATs, CSets, HomSearch, WiringDiagrams...)
AlgebraicJulia/ACSets.jl	❌ Needs indexing	Visit https://deepwiki.com/AlgebraicJulia/ACSets.jl
AlgebraicJulia/AlgebraicDynamics.jl	❌ Needs indexing	Visit https://deepwiki.com/AlgebraicJulia/AlgebraicDynamics.jl
AlgebraicJulia/StructuredDecompositions.jl	❌ Needs indexing	Visit https://deepwiki.com/AlgebraicJulia/StructuredDecompositions.jl
redplanetlabs/agent-o-rama	✅ Indexed	28 pages (Rama PStates, Agent Topologies, Tool Calling...)
discopy/discopy	✅ Indexed	23 pages (Monoidal Categories, Quantum Circuits, QNLP...)

Cross-Skill Examples

Example 1: ACSets + Catlab.jl

# 1. Query DeepWiki for oapply semantics
mcp__deepwiki__ask_question("AlgebraicJulia/Catlab.jl", 
  "How does oapply compose undirected wiring diagrams?")

# 2. Apply via ACSets skill patterns
@present SchUWD(FreeSchema) begin
  Box::Ob; Port::Ob; Junction::Ob; OuterPort::Ob
  box::Hom(Port, Box)
  junction::Hom(Port, Junction)
  outer_junction::Hom(OuterPort, Junction)
end

# 3. oapply = colimit of component diagram (verified by DeepWiki)
composite = oapply(wiring_diagram, components)

Example 2: DisCoPy for Quantum/Categorical Diagrams

# Query DisCoPy documentation
mcp__deepwiki__ask_question("discopy/discopy",
  "How do monoidal categories compose with tensor products?")

# DisCoPy has 23 pages covering:
# - Monoidal, Rigid, Symmetric, Frobenius categories
# - Quantum circuits and gates
# - QNLP (Quantum Natural Language Processing)
# - Tensor network backends

Example 3: Agent-o-rama for Rama Integration

;; Query agent-o-rama patterns
mcp__deepwiki__ask_question("redplanetlabs/agent-o-rama",
  "How do PStates store agent invocation state?")

;; 28 pages covering:
;; - Agent Modules and Topology
;; - PStates and Depots storage
;; - Tool Calling Integration
;; - Human-in-the-Loop Workflows

See Also

• hatchery-papers - Academic paper research
• bmorphism-stars - GitHub stars index
• librarian - Codebase understanding agent
• exa - Web search MCP
• acsets-algebraic-databases - ACSet computational patterns (trit 0, substitutes in triads)

---

Skill Name: deepwiki-mcp Type: Repository Documentation / Q&A Trit: 0 (ERGODIC) GF(3): Coordinates knowledge flow Auth: None required (free) Scope: All public GitHub repos indexed on DeepWiki.com Qualified: 2025-12-22 (verified against acsets skill)

Scientific Skill Interleaving

This skill connects to the K-Dense-AI/claude-scientific-skills ecosystem:

Graph Theory

• networkx [○] via bicomodule
  • Universal graph hub

Bibliography References

• general: 734 citations in bib.duckdb

Cat# Integration

This skill maps to Cat# = Comod(P) as a bicomodule in the equipment structure:

Trit: 0 (ERGODIC)
Home: Prof
Poly Op: ⊗
Kan Role: Adj
Color: #26D826

GF(3) Naturality

The skill participates in triads satisfying:

(-1) + (0) + (+1) ≡ 0 (mod 3)

This ensures compositional coherence in the Cat# equipment structure.