All Commands — Quick Reference

Fresh

Installation

pip install graphifyy              # Install package
graphify install                   # Install skill (Claude Code default)
graphify claude install            # Claude Code explicit
graphify codex install             # Codex / OpenCode
graphify cursor install            # Cursor
graphify vscode install            # VS Code Copilot Chat
graphify install --platform aider  # Aider
graphify gemini install            # Gemini CLI

Build

/graphify .                        # Current directory
/graphify ./path                   # Specific path
/graphify . --mode deep            # Aggressive inference
/graphify . --directed             # Preserve edge direction
/graphify . --update               # Incremental update only
/graphify . --cluster-only         # Re-cluster without re-extraction
/graphify . --no-viz               # Skip HTML, produce report + JSON only
/graphify . --watch                # Auto-rebuild on file changes

Query

/graphify query "question"         # Semantic search
/graphify query "question" --dfs   # DFS path tracing
/graphify path "NodeA" "NodeB"     # Shortest path
/graphify explain "NodeName"       # Full node details

Add External Content

/graphify add https://arxiv.org/abs/...   # arXiv paper
/graphify add <youtube-url>               # YouTube video
/graphify add https://... --author "Name" # With attribution

Export Formats

/graphify . --wiki                             # Markdown per community
/graphify . --obsidian                         # Obsidian vault
/graphify . --svg                              # SVG image
/graphify . --graphml                          # Gephi/yEd format
/graphify . --neo4j                            # Cypher statements
/graphify . --neo4j-push bolt://localhost:7687 # Push to Neo4j
/graphify . --mcp                              # Start MCP server after build

MCP Server

python -m graphify.serve graphify-out/graph.json   # Start from existing graph

Git Hooks

graphify hook install     # Install post-commit + post-checkout hooks
graphify hook uninstall   # Remove hooks
graphify hook status      # Check hook state

Uninstall Platform Hooks

graphify claude uninstall
graphify codex uninstall
graphify cursor uninstall
graphify vscode uninstall
graphify gemini uninstall

Output Files

File	Purpose
graphify-out/graph.html	Interactive browser visualization
graphify-out/graph.json	Persistent queryable graph
graphify-out/GRAPH_REPORT.md	Human-readable audit with God Nodes
graphify-out/cache/	SHA256 change detection — do not delete
graphify-out/wiki/	Markdown articles per cluster (--wiki)
graphify-out/obsidian/	Obsidian vault (--obsidian)
graphify-out/graph.graphml	Gephi/yEd format (--graphml)
graphify-out/cypher.txt	Neo4j Cypher statements (--neo4j)

Edge Types

Type	Meaning
EXTRACTED	Directly found in source — high confidence
INFERRED	Reasonable guess from context — medium confidence
AMBIGUOUS	Found but low confidence — verify before acting