t1k-graphify

name	t1k:graphify
description	Build queryable knowledge graphs from code, docs, papers, and images. Use for codebase understanding, architecture analysis, cross-file relationship mapping.
category	dev-tools
keywords	["knowledge-graph","code-analysis","tree-sitter","codebase-understanding","ast","graphify"]
argument-hint	[path] [--mcp|--report|--watch]
effort	high
context	fork
maturity	beta
metadata	{"author":"safishamsi","attribution":"https://github.com/safishamsi/graphify","ported-from":"ck:graphify"}
version	1.115.3
origin	theonekit-core
repository	The1Studio/theonekit-core
module	t1k-maintainer
protected	true

Graphify — Knowledge Graph Builder

Turn any folder of code, docs, papers, or images into a queryable knowledge graph. Uses tree-sitter AST for code (20 languages), Whisper for audio/video, and LLM subagents for documents.

Prerequisites

Python 3.10+ required. This is an optional skill that integrates with the third-party graphifyy package.

Install:

pip install graphifyy
graphify install  # downloads tree-sitter grammars

Optional extras:

pip install 'graphifyy[mcp]'     # MCP server mode
pip install 'graphifyy[all]'     # full install (PDF, video, office, Leiden)
pip install 'graphifyy[neo4j]'   # Neo4j graph database integration
pip install 'graphifyy[leiden]'  # Leiden community detection algorithm

Note: The PyPI package is graphifyy (double-y). Other graphify* packages on PyPI are unaffiliated.

When to Use

• Understanding unfamiliar codebase architecture before planning
• Discovering cross-file relationships and dependency chains
• Finding "god nodes" (most-connected concepts) in large projects
• Navigating by structure instead of grepping every file
• Preparing context-efficient codebase representation (71.5x fewer tokens vs raw files)

Typically precedes: /t1k:plan (understand architecture before planning) Related: /t1k:scout (quick file search), /t1k:repomix (full context dump)

Quick Start

# Build knowledge graph from current directory
graphify .

# Build from specific path
graphify /path/to/project

# Watch mode (auto-rebuild on file changes)
graphify . --watch

Output Artifacts

File	Purpose
graphify-out/graph.html	Interactive visualization with search + community filtering
graphify-out/GRAPH_REPORT.md	God nodes, surprising connections, suggested questions
graphify-out/graph.json	Persistent graph for queries across sessions
graphify-out/cache/	SHA256-based incremental updates (only reprocesses changed files)

MCP Server Mode

Expose the graph as an MCP server for Claude to query directly:

python -m graphify.serve graphify-out/graph.json

MCP Tools Available

Tool	Purpose
query_graph	Search for concepts and relationships
get_node	Get details of a specific node
get_neighbors	Find related concepts
shortest_path	Find connection path between two concepts

Claude Code MCP Setup

Add to .claude/.mcp.json:

{
  "mcpServers": {
    "graphify": {
      "command": "python",
      "args": ["-m", "graphify.serve", "graphify-out/graph.json"]
    }
  }
}

Three-Pass Architecture

1. AST extraction (local, no API) — tree-sitter parses code in 20 languages deterministically
2. Audio/video transcription (local) — Whisper runs on-device for media files
3. Semantic extraction (API) — LLM subagents process docs, papers, images in parallel

Supported Languages (tree-sitter)

Python, JavaScript, TypeScript, Go, Rust, Java, C, C++, Ruby, C#, Kotlin, Scala, PHP, Swift, Lua, Zig, PowerShell, Elixir, Objective-C, Julia

Confidence Tagging

Relationships in the graph are tagged by provenance:

Tag	Meaning
EXTRACTED	Directly from AST (imports, function calls, class inheritance)
INFERRED	LLM-derived with confidence score
AMBIGUOUS	Uncertain — needs human verification

Workflow Integration

Before Planning

# Build graph first, then plan with context
graphify .
# Claude reads GRAPH_REPORT.md → understands architecture → better plans

With Scout

# Graph for high-level structure, scout for specific files
graphify .                        # build graph
/t1k:scout "auth module"          # find specific files

Incremental Updates

Graph rebuilds are incremental — only changed files get reprocessed. Cache at graphify-out/cache/ tracks file hashes.

Privacy

• Code: Processed locally via tree-sitter AST. No file contents leave your machine.
• Audio/Video: Transcribed locally via Whisper.
• Docs/Images: Sent to your configured model provider (Claude/OpenAI) for semantic extraction.

Limitations

• First build on large codebases can be slow (AST parsing + LLM calls)
• Semantic extraction quality depends on the underlying model
• Neo4j integration requires separate setup (pip install 'graphifyy[neo4j]')
• Leiden community detection requires pip install 'graphifyy[leiden]'
• Beta status: This skill depends on a third-party package (graphifyy). API surface may change.

Tool Size Caps (E6)

When invoking the graphify MCP server's query_graph and get_neighbors tools, this skill MUST pass an explicit maxResultSizeChars cap to prevent context blow-up on large graphs:

• query_graph: cap at maxResultSizeChars: 200_000 (~50k tokens). Larger results break Claude's working memory; instead, paginate via cursor.
• get_neighbors: cap at maxResultSizeChars: 50_000 (~12k tokens). Neighbor expansion can fan out exponentially in dense graphs.
• Always include limit AND maxResultSizeChars — limit bounds nodes, but a single node with megabyte-sized properties still blows the budget.

If a query exceeds the cap, the MCP server returns truncated: true; the skill MUST surface this to the user with a hint to refine the query, NOT silently deliver a partial result as if it were complete.