Status: Active
Date: 2026-06-14
Author: Cytognosis Foundation
Audience: engineers, operators
Tags: quick-reference, cli, cyto-skills
@cytognosis/cyto-skills-cli — Quick Reference
One line: cyto-skills is the shell interface to the entire cytoskills ecosystem. List, judge, tag, deploy profiles, sync editors, and manage agent memories.
Full doc: cli.md
Key Concepts
| Term |
Definition |
| Profile |
YAML file under profiles/ defining a bundled skill list for a use case. Supports inheritance. |
| Judge |
Quality scorer (6 axes, 0–100, PASS/WARN/FAIL). Run before committing a new skill. |
| Review |
Collection-level analysis: naming conflicts, Jaccard vocab overlap, split candidates. |
| Tag |
Assigns CSO CURIE terms to a skill via .cyto-tags.yaml sidecar, then promotes to frontmatter. |
| deploy-configs |
Deploys CLAUDE.md / GEMINI.md from configs/core_memory/ to ~/.claude/ / ~/.gemini/antigravity/. |
| sync-skills |
Creates flat symlinks from skills/ to editor-specific directories (antigravity, agents). Dry-run by default. |
| memory-diff |
Detects sections present in deployed memory but missing from source (drift). |
Command Groups
| Group |
Base command |
| Skill discovery |
list, inspect, classify, root |
| Quality |
judge skill/all/cytognosis, review collection/cytognosis |
| Tagging |
tag skill/all/promote/show |
| Ontology |
ontology list/search/expand/mappings/validate |
| Profiles |
profile list/show/deploy |
| Deploy/sync |
deploy-configs, sync-editors, sync-brand, sync-skills, sync-all |
| Agent mgmt |
agent list/install/batch/doctor/doctor-desktop/memory/memory-diff/... |
| Catalog |
catalog list/fetch/diff |
Commands
Skill Discovery
| Command |
What It Does |
cyto-skills list [--root <path>] |
List all discoverable skills with CSO tags |
cyto-skills inspect <skillDir> |
Print name, description, tags, IO, scripts, references |
cyto-skills classify <skillDir> |
Print CSO CURIEs for a skill |
cyto-skills doctor <skillDir> |
Run diagnostics (exits 1 if unhealthy) |
cyto-skills validate <file> |
Validate a JSONL file |
cyto-skills synthesize [--root <path>] |
Find overlapping skill clusters |
Judge
| Command |
What It Does |
cyto-skills judge skill <path> [-v] [--tag] |
Score one skill |
cyto-skills judge all [--root] [--min-score] [--verdict] |
Score all under a root |
cyto-skills judge cytognosis [-v] [--roots] |
Score Cytognosis skills |
Review
| Command |
What It Does |
cyto-skills review collection [--root] |
Naming, overlap, split analysis |
cyto-skills review cytognosis |
Same for cytoskeleton + branding |
Tag
| Command |
What It Does |
cyto-skills tag skill <path> [--dry-run] [--confidence] |
Write .cyto-tags.yaml |
cyto-skills tag all [--root] [--dry-run] |
Tag all SKILL.md files |
cyto-skills tag promote <path> [--dry-run] [--confidence] |
Merge sidecar into frontmatter |
cyto-skills tag show <path> |
Print sidecar contents |
Ontology
| Command |
What It Does |
cyto-skills ontology list [--axis A|B|C|meta] |
List CSO terms |
cyto-skills ontology search <query> |
Full-text search |
cyto-skills ontology expand cso:Python |
Get full IRI |
cyto-skills ontology mappings cso:Python |
Show SSSOM mappings |
cyto-skills ontology validate cso:Python |
Check CURIE validity |
Profiles
| Command |
What It Does |
cyto-skills profile list |
List YAML profiles |
cyto-skills profile show <name> |
Show resolved skill list |
cyto-skills profile deploy <name> [--clean] [--target] [--dry-run] |
Deploy symlinks |
Deploy / Sync
| Command |
What It Does |
cyto-skills deploy-configs [--dry-run] [--target claude|gemini] |
Deploy agent configs |
cyto-skills sync-skills [--execute] [--clean] [--target] |
Sync skill symlinks (dry-run by default) |
cyto-skills sync-all [--clean] |
Deploy all profiles |
cyto-skills sync-editors |
Sync editor settings |
cyto-skills sync-brand |
Sync brand skill |
Agent
| Command |
What It Does |
cyto-skills agent list [agent] |
List installed skills |
cyto-skills agent install <skill> [-a agent] [--dry-run] |
Install skill |
cyto-skills agent batch <group> [-a agent] [--all-agents] |
Batch install group |
cyto-skills agent uninstall <skill> [-a agent] |
Remove skill |
cyto-skills agent doctor [agent] [--fix] |
Health check |
cyto-skills agent doctor-all [--fix] |
Check all agents |
cyto-skills agent doctor-desktop |
Check Claude Desktop |
cyto-skills agent fix-launcher [--dry-run] |
Install version-agnostic launcher |
cyto-skills agent fix-paths <old> <new> [--dry-run] |
Fix stale paths after folder move |
cyto-skills agent purge-cache [--dry-run] |
Purge Electron caches |
cyto-skills agent memory <agent> |
Print memory file |
cyto-skills agent memory-update <agent> <section> [-f file] |
Upsert section |
cyto-skills agent memory-diff [agent] [--json] |
Detect memory drift |
cyto-skills agent memory-harmonize [--backport] [--json] |
Backport deployed sections |
cyto-skills agent memory-revision <section> [-f file] [-c text] |
Update section in source |
cyto-skills agent vault-link <repoPath> [--vault-section] |
Link docs/ to Obsidian |
Catalog
| Command |
What It Does |
cyto-skills catalog list [--root] [--json] |
List third-party sources |
cyto-skills catalog fetch <org/repo> |
Clone / pull a skill repo |
cyto-skills catalog diff [--source] [--json] |
Skills in catalog not installed locally |
Common Patterns
# Full tagging + judging workflow
cyto-skills tag skill skills/my-skill/SKILL.md
cyto-skills tag promote skills/my-skill/SKILL.md
cyto-skills judge skill skills/my-skill -v
# Deploy configs after memory change
cyto-skills agent memory-harmonize --backport
cyto-skills deploy-configs
# Sync skills to all editors
cyto-skills sync-skills --execute
# Install cytognosis group to Claude
cyto-skills agent batch cytognosis -a claude
# Claude Desktop health check
cyto-skills agent doctor-desktop
cyto-skills agent fix-launcher
# Check memory drift for all agents
cyto-skills agent memory-diff
Options at a Glance
| Option |
Commands |
Meaning |
--dry-run |
Most mutating commands |
Preview without writing |
-v, --verbose |
judge skill/all |
Show per-axis breakdown |
--clean |
profile deploy, sync-skills, sync-all |
Remove existing entries first |
--execute |
sync-skills |
Apply (default is dry-run) |
-a, --agent <id> |
agent install/batch/uninstall |
Target agent (default: antigravity) |
--all-agents |
agent batch |
Install to antigravity + claude + agents |
--tag |
judge skill |
Run tagger before scoring |
--json |
catalog list/diff, agent memory-diff/harmonize |
Machine-readable output |
--backport |
agent memory-harmonize |
Apply backport changes |
--root <path> |
list, synthesize, judge all, sync-skills |
Override search/source root |
Error Quick-Fix
| Error / Symptom |
Fix |
No skills found in search roots |
Pass --root pointing to a directory that contains phase subdirs, or set CYTO_SKILLS_ROOT |
Profile 'X' not found |
Run cyto-skills profile list to see available profiles |
Unknown agent: X |
Valid IDs: antigravity, claude, agents, cursor, kiro |
sync-skills does nothing |
Default is dry-run; pass --execute to apply |
| Judge CSO axis is 0 |
Re-run with --tag or run cyto-skills tag skill <path> && cyto-skills tag promote <path> manually |
deploy-configs writes wrong sections |
Run memory-diff first to see what will merge, then deploy |
See Also