Reference on Ghafoor's Personal Blog

Command Reference

hello@ghafoorsblog.com (AG Sayyed) — Mon, 09 Nov 2026 00:00:00 +0000

Command Reference

Complete CLI reference for all Graphify commands.

🔑 Golden Rule

Signal activity before EVERY command:

1mkdir -p graphify-out && touch graphify-out/.graphify-activity

📋 Commands

`graphify .` — Initial Build

Build the knowledge graph from scratch.

1graphify . [OPTIONS]

Option	Description
`--code-only`	Index code only (no API key needed)
`--no-gitignore`	Ignore .gitignore rules
`--exclude PATTERN`	Additional exclude patterns
`-v, --verbose`	Verbose output

Examples:

1graphify . --code-only # Code-only (fast, free)
2graphify . # Full (needs API key)
3graphify . --no-gitignore # Include gitignored files

`graphify update .` — Rebuild

Incremental rebuild of existing graph.

Configuration

hello@ghafoorsblog.com (AG Sayyed) — Mon, 09 Nov 2026 00:00:00 +0000

Configuration

Graphify configuration file options, environment variables, and runtime settings.

📁 Config File Locations

Location	Scope	Priority
`~/.config/graphify/config.yaml`	Global (all projects)	Low
`.graphify.yaml`	Project root	Medium
`--config PATH`	CLI argument	High

📝 Config File Format (YAML)

 1# ~/.config/graphify/config.yaml
 2
 3# Model settings
 4model:
 5 path: ~/.cache/graphify/model.gguf # Local LLM model path
 6 n_ctx: 8192 # Context window
 7 n_gpu_layers: -1 # -1 = all on GPU; 0 = CPU only
 8 n_threads: 8 # CPU threads for inference
 9 verbose: false # Model debug output
10
11# Extraction settings
12extraction:
13 max_file_size_mb: 10 # Skip files larger than this
14 skip_binary: true # Auto-skip binary files
15 include_patterns: [] # Additional include globs
16 exclude_patterns: [] # Additional exclude globs
17 parallel_workers: 16 # AST extraction workers
18
19# LLM settings (for full graph)
20llm:
21 provider: gemini # gemini, openai, anthropic, moonshot, deepseek
22 api_key_env: GEMINI_API_KEY # Env var name for API key
23 model: gemini-1.5-flash # Model name
24 temperature: 0.1 # Generation temperature
25 max_tokens: 4096 # Max output tokens
26 timeout: 60 # Request timeout (seconds)
27
28# Activity tracking
29activity:
30 enabled: true # Enable activity signaling
31 path: ~/.graphify-stats # Activity data directory
32 auto_signal: true # Auto-touch .graphify-activity
33
34# Output settings
35output:
36 graph_path: graphify-out/graph.json # Graph file location
37 report_path: graphify-out/GRAPH_REPORT.md
38 html_path: graphify-out/graph.html
39 cluster_resolution: 1.0 # Community detection resolution
40 min_community_size: 3 # Min nodes per community
41
42# Logging
43logging:
44 level: INFO # DEBUG, INFO, WARN, ERROR
45 file: '' # Empty = stderr only
46 format: text # text, json

🌍 Environment Variables

Variable	Description	Default
`GEMINI_API_KEY`	Google Gemini API key	—
`GOOGLE_API_KEY`	Alias for Gemini	—
`OPENAI_API_KEY`	OpenAI API key	—
`ANTHROPIC_API_KEY`	Anthropic API key	—
`MOONSHOT_API_KEY`	Moonshot/Kimi API key	—
`DEEPSEEK_API_KEY`	DeepSeek API key	—
`GRAPHIFY_CONFIG`	Custom config file path	`~/.config/graphify/config.yaml`
`GRAPHIFY_CACHE_DIR`	Model/cache directory	`~/.cache/graphify`
`GRAPHIFY_GRAPH_PATH`	Graph output path	`graphify-out/graph.json`
`GRAPHIFY_VERBOSE`	Enable verbose logging	`false`
`GRAPHIFY_CODE_ONLY`	Force code-only mode	`false`

⚙️ CLI Overrides

All config options can be overridden via CLI flags:

Edge Types

hello@ghafoorsblog.com (AG Sayyed) — Mon, 09 Nov 2026 00:00:00 +0000

Edge Types

Reference for all relationship types (edges) in the Graphify knowledge graph.

📊 Edge Type Summary

Edge Type	Direction	Description	Code Example
`imports_from`	A → B	Module A imports module B	`import yaml`
`calls`	A → B	Function A calls function B	`main() → parse_args()`
`contains`	A → B	File/module A contains symbol B	`file.py → mergeParams()`
`references`	A → B	Symbol A references symbol B	`mergeParams() → deepMerge()`
`reads`	A → B	Code A reads file B	`script → config.yaml`
`writes`	A → B	Code A writes file B	`script → output.yaml`

🔍 Detailed Edge Types

`imports_from`

Meaning: Module/file imports another module.

Node IDs Explained

hello@ghafoorsblog.com (AG Sayyed) — Mon, 09 Nov 2026 00:00:00 +0000

Node IDs Explained

Understanding Graphify node identifiers — the keys to querying, explaining, and tracing your codebase.

🔑 What is a Node ID?

A Node ID is a unique identifier for any node in the Graphify knowledge graph. Every file, function, class, variable, and symbol gets a Node ID.

📋 Node ID Formats

Format	Example	Resolves To
File path	`scripts/dictionary/yt-to-content-v2.py`	File node
File + line	`scripts/dictionary/yt-to-content-v2.py:L100`	Symbol at line 100
Symbol name	`mergeParams`	Function/class by name
Qualified symbol	`scripts/dictionary/yt-to-content-v2.py:mergeParams`	Specific symbol in file
Class.method	`Config.load`	Method on class

🎯 Usage in Commands

`graphify explain`

 1# File (shows all symbols, imports, structure)
 2graphify explain scripts/dictionary/yt-to-content-v2.py
 3
 4# Specific function
 5graphify explain mergeParams
 6
 7# Qualified (disambiguates same-name functions)
 8graphify explain scripts/dictionary/yt-to-content-v2.py:mergeParams
 9
10# Line-specific
11graphify explain scripts/dictionary/yt-to-content-v2.py:L100

`graphify path`

1# File to file
2graphify path tasks/content.yaml scripts/dictionary/yt-to-content-v2.py
3
4# Function to file
5graphify path mergeParams scripts/dictionary/yt-to-content-v2.py
6
7# Qualified to file
8graphify path scripts/dictionary/yt-to-content-v2.py:mergeParams tasks/content.yaml

`graphify query`

1# Natural language (Graphify resolves internally)
2graphify query "explain the mergeParams function"
3graphify query "what does scripts/dictionary/yt-to-content-v2.py do?"

🔍 Resolution Rules

1. Exact File Path

scripts/dictionary/yt-to-content-v2.py

→ Resolves to file node if exists in graph.

Troubleshooting

hello@ghafoorsblog.com (AG Sayyed) — Mon, 09 Nov 2026 00:00:00 +0000

Troubleshooting

Common Graphify issues and their solutions.

🚨 Quick Diagnosis

 1# 1. Check installation
 2graphify --version
 3
 4# 2. Check graph exists
 5ls -lh graphify-out/graph.json
 6
 7# 3. Check activity signaling
 8cat graphify-out/.graphify-activity.json
 9
10# 4. Test basic query
11mkdir -p graphify-out && touch graphify-out/.graphify-activity
12graphify query "test"

📋 Common Issues

1. `graphify: command not found`

Cause: graphify not in PATH after uv tool install.

Reference on Ghafoor's Personal Blog

Command Reference

Command Reference

🔑 Golden Rule

📋 Commands

graphify . — Initial Build

graphify update . — Rebuild

Configuration

Configuration

📁 Config File Locations

📝 Config File Format (YAML)

🌍 Environment Variables

⚙️ CLI Overrides

Edge Types

Edge Types

📊 Edge Type Summary

🔍 Detailed Edge Types

imports_from

Node IDs Explained

Node IDs Explained

🔑 What is a Node ID?

📋 Node ID Formats

🎯 Usage in Commands

graphify explain

graphify path

graphify query

🔍 Resolution Rules

1. Exact File Path

Troubleshooting

Troubleshooting

🚨 Quick Diagnosis

📋 Common Issues

1. graphify: command not found

`graphify .` — Initial Build

`graphify update .` — Rebuild

`imports_from`

`graphify explain`

`graphify path`

`graphify query`

1. `graphify: command not found`