CLI Reference

ontoskills is the product entrypoint. It installs and manages the runtime, compiler, store skills, and local state under ~/.ontoskills/.

Quickstart

# First-time setup
npx ontoskills install mcp

# After bootstrap, use directly
ontoskills --help

Installation commands

`install mcp`

Install the MCP runtime, or install it and bootstrap one or more MCP clients in one command.

ontoskills install mcp
ontoskills install mcp --claude
ontoskills install mcp --codex --cursor
ontoskills install mcp --cursor --vscode --project

Creates:

~/.ontoskills/bin/ontomcp — the MCP server binary
~/.ontoskills/ontologies/core.ttl — core ontology (downloaded from ontoskills.sh)
~/.ontoskills/state/ — lockfiles and metadata

Supported flags:

Flag	Meaning
`--global`	Configure user-wide MCP settings (default)
`--project`	Configure only the current repository/workspace
`--all-clients`	Bootstrap every supported MCP client
`--codex`	Configure Codex
`--claude`	Configure Claude Code
`--qwen`	Configure Qwen Code
`--cursor`	Configure Cursor
`--vscode`	Configure VS Code
`--windsurf`	Configure Windsurf
`--antigravity`	Configure Antigravity (best effort/manual fallback)
`--opencode`	Configure OpenCode

When a client cannot be configured fully, ontoskills still installs ontomcp and prints exact manual steps.

`install core`

Install the OntoCore compiler (optional).

ontoskills install core

Requires Python 3.10+. Creates ~/.ontoskills/core/ with the compiler runtime.

Store commands

`search <query>`

Search for skills in OntoStore.

ontoskills search hello
ontoskills search pdf
ontoskills search "office document"

`install <package-id>`

Install a skill from OntoStore.

ontoskills install mareasw/greeting/hello
ontoskills install mareasw/office/xlsx

The package ID format is: owner/repo/skill

`enable <package-id>`

Re-enable a disabled skill for the MCP runtime.

ontoskills enable mareasw/greeting/hello

Skills are enabled by default on install. Use this to re-enable a previously disabled skill.

`disable <package-id>`

Disable a skill without removing it.

ontoskills disable mareasw/greeting/hello

`remove <package-id>`

Remove an installed skill.

ontoskills remove mareasw/greeting/hello

`list-installed`

List all installed skills.

ontoskills list-installed

Store source commands

`store list`

List configured skill stores.

ontoskills store list

`store add-source <name> <url>`

Add a third-party skill store.

ontoskills store add-source acme https://example.com/skills/index.json

Import commands

`import-source <url>`

Import a raw Git repository containing SKILL.md files.

ontoskills import-source https://github.com/user/skill-repo

Imported skills are stored under ~/.ontoskills/skills/vendor/ and compiled to ~/.ontoskills/ontologies/vendor/.

Compiler commands

These commands require ontocore to be installed.

`init-core`

Initialize the core ontology.

ontoskills init-core

Creates core.ttl with base classes and properties.

`compile [skill]`

Compile skills to ontology modules.

# Compile all skills
ontoskills compile

# Compile specific skill
ontoskills compile my-skill

# With options
ontoskills compile --force          # Bypass cache
ontoskills compile --dry-run        # Preview only
ontoskills compile --skip-security  # Skip LLM security review
ontoskills compile -v               # Verbose output

Option	Description
`-i, --input`	Input directory (default: `skills/`)
`-o, --output`	Output directory (default: `ontoskills/`)
`--dry-run`	Preview without saving
`--skip-security`	Skip LLM security review
`-f, --force`	Force recompilation
`-y, --yes`	Skip confirmation prompts
`-v, --verbose`	Debug logging
`-q, --quiet`	Suppress progress output

`query <sparql>`

Run a SPARQL query against compiled ontologies.

ontoskills query "SELECT ?s WHERE { ?s a oc:Skill }"
ontoskills query "SELECT ?intent WHERE { ?skill oc:resolvesIntent ?intent }"

`list-skills`

List all compiled skills.

ontoskills list-skills

`security-audit`

Run security audit on all skills.

ontoskills security-audit

Management commands

`update [target]`

Update a component or skill.

ontoskills update mcp
ontoskills update core
ontoskills update mareasw/office/xlsx

`rebuild-index`

Rebuild the ontology index.

ontoskills rebuild-index

`doctor`

Diagnose installation issues.

ontoskills doctor

Checks:

MCP binary exists and is executable
Core ontology is valid
Environment variables are set
Index is consistent

Uninstall

`uninstall --all`

Remove the entire managed home.

ontoskills uninstall --all

Warning: This deletes everything under ~/.ontoskills/.

Managed home structure

~/.ontoskills/
├── bin/
│   └── ontomcp           # MCP server binary
├── core/                  # Compiler runtime (if installed)
├── ontologies/            # Compiled ontology packages
│   ├── core.ttl
│   ├── index.ttl
│   ├── system/            # System-level files
│   │   └── index.enabled.ttl  # Enabled skills manifest
│   └── */ontoskill.ttl
├── skills/                # Source skills
│   └── vendor/            # Imported repositories
└── state/                 # Lockfiles and metadata
    ├── registry.sources.json
    └── registry.lock.json

Environment variables

Variable	Description	Default
`ANTHROPIC_API_KEY`	API key for compilation	Required for compiler
`ANTHROPIC_BASE_URL`	API base URL	`https://api.anthropic.com`
`ONTOSKILLS_HOME`	Managed home directory	`~/.ontoskills`

Exit codes

Code	Meaning
0	Success
1	General error
2	Invalid arguments
3	Skill not found
4	Security error
5	Validation error
6	Network error

CLI Reference

Quickstart

Installation commands

install mcp

install core

Store commands

search <query>

install <package-id>

enable <package-id>

disable <package-id>

remove <package-id>

list-installed

Store source commands

store list

store add-source <name> <url>