Command Reference¶

Complete reference for all Graphize CLI commands.

graphize init¶

Initialize a new graph database.

graphize init

Creates the .graphize/ directory with:

manifest.json - Source tracking
nodes/ - Node storage
edges/ - Edge storage
cache/ - Extraction cache

graphize add¶

Add a repository to track.

graphize add <path>

Arguments:

Argument	Description
`path`	Path to Go repository

Examples:

graphize add .
graphize add /path/to/repo
graphize add ../sibling-project

graphize status¶

Show status of tracked sources.

graphize status

Output:

Source path
Git commit hash
Git branch
Last analyzed timestamp
Currency status (current/stale)

graphize analyze¶

Extract graph from tracked sources using AST parsing.

graphize analyze [flags]

Flags:

Flag	Description	Default
`--no-cache`	Disable caching, re-extract all files	false
`--directed`	Treat graph as directed (edges flow from→to)	true

Output:

Number of nodes extracted
Number of edges extracted
Node types breakdown
Edge types breakdown
Cache hit/miss statistics

All edges have EXTRACTED confidence level.

graphize enhance¶

Prepare files for LLM semantic extraction.

graphize enhance [flags]

Flags:

Flag	Description	Default
`--json`	Output as JSON	false
`--force`	Ignore cache, re-extract all files	false
`--chunk-size`	Files per chunk for parallel processing	25
`--include-docs`	Include markdown/text documentation files	false
`--docs-only`	Only analyze documentation files (skip code)	false

Examples:

# Human-readable output
graphize enhance

# JSON for scripting
graphize enhance --json > files.json

# Include documentation files
graphize enhance --include-docs

# Only documentation files
graphize enhance --docs-only

graphize merge¶

Merge semantic edges from LLM extraction into the graph.

graphize merge [flags]

Flags:

Flag	Description	Default
`-i, --input`	Input file with semantic edges	required

Examples:

graphize merge -i agents/graph/semantic-edges.json

Input Format:

{
  "edges": [
    {
      "from": "func_handler.go.HandleRequest",
      "to": "func_db.go.Query",
      "type": "inferred_depends",
      "confidence": "INFERRED",
      "confidence_score": 0.85
    }
  ]
}

graphize rebuild¶

Rebuild graph from sources and merge semantic edges.

graphize rebuild

Equivalent to:

graphize analyze && graphize merge -i agents/graph/semantic-edges.json

graphize query¶

Query the knowledge graph.

graphize query [node-id] [flags]

Arguments:

Argument	Description
`node-id`	Node ID to query (optional)

Flags:

Flag	Description	Default
`--from`	Filter edges by source node
`--type`	Filter edges by type
`--limit`	Maximum results	100
`--depth`	Traversal depth (enables BFS/DFS)	0
`--dfs`	Use depth-first search	false
`--dir`	Direction: out, in, both	both
`--path`	Find path to this node
`--edge-type`	Filter by edge type(s), comma-separated

Examples:

# Show graph summary
graphize query

# Show edges for a node
graphize query func_main

# BFS traverse 3 levels deep
graphize query func_main --depth 3

# DFS traverse
graphize query func_main --dfs --depth 5

# Only outgoing edges
graphize query func_main --dir out

# Only incoming edges
graphize query func_main --dir in

# Find path between nodes
graphize query func_main --path func_handleRequest

# Filter by edge type
graphize query --type calls

graphize diff¶

Compare two graph snapshots.

graphize diff [flags]

Flags:

Flag	Description	Default
`--old`	Path to old graph	required

Examples:

graphize diff --old .graphize.bak
graphize diff --old /path/to/old/graph --graph /path/to/new/graph

Output:

New nodes added
Nodes removed
New edges added
Edges removed

graphize report¶

Generate analysis report for the graph.

graphize report [flags]

Flags:

Flag	Description	Default
`--top`	Number of top items to show	10
`-o, --output`	Output file	stdout
`--health`	Include corpus health assessment	false

Examples:

graphize report
graphize report --top 20 -o GRAPH_REPORT.md
graphize report --health

Report Sections:

Summary (nodes, edges, types)
God Nodes (most connected)
Communities (Louvain detection)
Surprising Connections
Isolated Nodes
Package Statistics
Suggested Questions
Corpus Health (with --health flag)

graphize summary¶

Generate a markdown summary of the graph.

graphize summary [flags]

Flags:

Flag	Description	Default
`-o, --output`	Output file	stdout

graphize export¶

Export graph to various formats.

graphize export <format> [flags]

Formats:

Format	Description
`html`	Interactive Cytoscape.js visualization
`htmlsite`	Multi-page HTML documentation site
`toon`	Token-optimized notation
`json`	Cytoscape.js JSON format
`graphml`	GraphML XML (for Gephi, yEd)
`cypher`	Neo4j Cypher CREATE statements
`obsidian`	Wiki-style Obsidian vault

Common Flags:

Flag	Description	Default
`-o, --output`	Output file or directory	stdout

Examples:

graphize export html -o graph.html
graphize export htmlsite -o ./site
graphize export toon -o GRAPH.toon
graphize export json -o graph.json
graphize export graphml -o graph.graphml
graphize export cypher -o graph.cypher
graphize export obsidian -o ./vault

graphize export cypher¶

Export graph as Neo4j Cypher CREATE statements.

graphize export cypher [flags]

Flags:

Flag	Description	Default
`-o, --output`	Output file	stdout

Generates CREATE statements for all nodes and edges, including:

Node labels and properties
Edge types and properties
Confidence metadata for semantic edges

graphize export htmlsite¶

Export graph as a multi-page HTML documentation site.

graphize export htmlsite [flags]

Flags:

Flag	Description	Default
`-o, --output`	Output directory	required
`-t, --title`	Site title	"Code Graph"
`--dark`	Use dark mode theme	false
`--no-communities`	Skip community pages	false

Output Structure:

site/
├── index.html           # System overview with topology
├── services/            # Per-service subgraphs (multi-service mode)
│   ├── api/index.html
│   └── payments/index.html
└── communities/         # Optional community groupings
    └── 1.html

Modes:

Multi-service mode (system-spec present): Index shows system topology, service pages show per-repo code graphs
Single-repo mode (no system-spec): Index shows full graph, optional community pages

Examples:

# Basic usage
graphize export htmlsite -o ./site

# Dark mode with custom title
graphize export htmlsite -o ./docs --dark --title "Platform Architecture"

# Skip community detection
graphize export htmlsite -o ./site --no-communities

graphize export obsidian¶

Export graph as an Obsidian vault with wikilinks.

graphize export obsidian [flags]

Flags:

Flag	Description	Default
`-o, --output`	Output directory	required
`--top`	Number of top nodes to include	20
`--min-degree`	Minimum degree for node pages	3

Output Structure:

vault/
├── index.md           # Entry point with god nodes
├── communities/       # One page per community
│   ├── community-0.md
│   └── community-1.md
└── nodes/             # One page per significant node
    ├── func_main.md
    └── type_Config.md

Pages are interconnected with [[wikilinks]] for Obsidian navigation.

graphize serve¶

Start MCP server for graph queries.

graphize serve

Starts a Model Context Protocol server over stdio.

Available Tools:

Tool	Description
`query_graph`	Search and traverse the graph
`get_node`	Get details for a specific node
`get_neighbors`	Get neighbors of a node
`get_community`	Get nodes in a community
`graph_summary`	Get overall graph statistics

See MCP Server for integration details.

graphize path¶

Find the shortest path between two nodes.

graphize path <from> <to> [flags]

Arguments:

Argument	Description
`from`	Starting node ID
`to`	Target node ID

Flags:

Flag	Description	Default
`--max-depth`	Maximum search depth	10

Examples:

graphize path func_main func_handleRequest
graphize path type_Config type_Options --max-depth 5

Output:

Shows the path with intermediate nodes and edge types:

func_main
  --[calls]--> func_init
  --[calls]--> func_handleRequest

graphize benchmark¶

Show token reduction statistics comparing raw corpus to TOON output.

graphize benchmark

Output:

Raw corpus size (total bytes of source files)
TOON output size (compressed graph representation)
Compression ratio
Token estimates (raw vs TOON)

graphize explain¶

Get comprehensive context about a specific node.

graphize explain <node-id> [flags]

Arguments:

Argument	Description
`node-id`	Node ID to explain (supports partial matching)

Flags:

Flag	Description	Default
`--depth`	Neighbor traversal depth	1
`--max-edges`	Maximum edges to display	20
`--json`	Output as JSON	false

Examples:

graphize explain func_main
graphize explain func_main --depth 2
graphize explain func_main --json
graphize explain Config  # Partial match

Output:

Node info (ID, type, label, attributes)
Community membership (ID, label, size, bridge status)
Centrality metrics (betweenness score, rank, hub/bridge status)
Incoming and outgoing edges with types and confidence

graphize install¶

Install integrations with AI assistants.

graphize install <platform> [flags]

Platforms:

Platform	Description	Config Location
`claude`	Claude Desktop MCP server	`~/Library/.../claude_desktop_config.json`
`cursor`	Cursor IDE rules	`.cursor/rules/graphize.mdc`
`copilot`	GitHub Copilot skills	`.github/copilot/skills/graphize.md`
`codex`	OpenAI Codex CLI	`hooks.json`
`gemini`	Google Gemini CLI	`.gemini/context/graphize.md`
`aider`	Aider/OpenClaw	`AGENTS.md` section

Flags:

Flag	Description	Default
`--status`	Check installation status	false
`--uninstall`	Remove integration	false
`--force`	Overwrite existing configuration	false
`--dry-run`	Show what would be changed	false
`--json`	Output status as JSON	false

Examples:

# Install Claude Desktop integration
graphize install claude

# Check status of all platforms
graphize install claude --status
graphize install cursor --status

# Remove integration
graphize install aider --uninstall

# Preview changes
graphize install copilot --dry-run

graphize watch¶

Monitor tracked sources for changes and auto-rebuild the graph.

graphize watch [flags]

Flags:

Flag	Description	Default
`--debounce`	Debounce delay for rapid changes	500ms
`--html`	Regenerate HTML visualization on changes	false
`--report`	Regenerate analysis report on changes	false
`--verbose`	Show detailed file change events	false

Examples:

# Basic watch mode
graphize watch

# Also regenerate HTML and report
graphize watch --html --report

# Increase debounce for slower systems
graphize watch --debounce 1s

Press Ctrl+C to stop watching.

graphize hook¶

Manage git hooks for automatic graph updates.

graphize hook install¶

Install git hooks in the repository.

graphize hook install

Installs:

post-commit: Auto-run graphize analyze after commits
post-checkout: Check if graph is stale after checkout

graphize hook uninstall¶

Remove graphize git hooks.

graphize hook uninstall

graphize hook status¶

Check git hook installation status.

graphize hook status

graphize init-agents¶

Initialize agent framework directories.

graphize init-agents

Creates:

agents/
├── specs/       # multi-agent-spec definitions
├── plugins/     # assistantkit-generated plugins
└── graph/       # Graph artifacts

graphize completion¶

Generate shell completion scripts.

graphize completion <shell>

Shells:

bash
zsh
fish
powershell

Examples:

# Bash
graphize completion bash > /etc/bash_completion.d/graphize

# Zsh
graphize completion zsh > "${fpath[1]}/_graphize"

# Fish
graphize completion fish > ~/.config/fish/completions/graphize.fish