Binary: cyto-skills
Source: packages/cli/src/bin/cyto-skills.ts
Framework: Commander.js
All commands support --help for inline usage. The CLI is organized
into eight command groups covering the full cytoskills lifecycle.
cyto-skills listList all discoverable skills across phase repositories.
cyto-skills list [--root <path>]
| Option | Default | Description |
|---|---|---|
--root <path> |
cwd |
Search root directory |
Each skill is printed with its CSO classification tags and
description. Searches the given root and its parent directory.
Exit codes: 0 on success, 1 on load error.
cyto-skills inspect <skillDir>Print frontmatter and paths for a single skill.
cyto-skills inspect ./skills/languages/python-pro
Displays: name, description, tags, directory path, input/output
counts, script files, and reference files.
Exit codes: 0 on success, 1 if skill cannot be loaded.
cyto-skills classify <skillDir>Classify a skill using the CSO taxonomy hierarchy.
cyto-skills classify ./skills/ai-ml/deep-learning
# Skill: deep-learning
# Tags: cso:DeepLearning, cso:MachineLearning
Exit codes: 0 on success, 1 on error.
cyto-skills doctor <skillDir>Run diagnostics on a single skill directory. Checks SKILL.md
presence, frontmatter validity, description quality, tags, triggers,
scripts, references, body content, and IO schema references.
cyto-skills doctor ./skills/cytognosis/brand
Output is a formatted Markdown diagnostic report.
Exit codes: 0 if healthy, 1 if unhealthy.
cyto-skills validate <file>Validate a JSONL file for structural integrity. Checks JSON parse
errors, duplicate UUIDs, and orphaned parent references.
cyto-skills validate session.jsonl
Exit codes: 0 if valid, 1 if issues found.
cyto-skills synthesizeFind overlapping skills and generate consolidation reports.
cyto-skills synthesize [--root <path>]
| Option | Default | Description |
|---|---|---|
--root <path> |
cwd |
Search root directory |
Clusters skills by primary classifier tag. Reports clusters of 2+
skills with proposed merged names and unified trigger counts.
cyto-skills rootPrint the resolved skills/ root directory path.
cyto-skills root
# /home/user/repos/cytognosis/cytoskills/skills
cyto-skills profile listList all available profile YAML files.
cyto-skills profile list
# Available profiles (12):
# coding
# science/ai-scientist
# science/research-scientist
# writing
cyto-skills profile show <name>Show the resolved contents of a profile, including inherited skills.
cyto-skills profile show coding
Displays: name, description, target, inherited profiles, and the
full resolved skill list (with inheritance flattened).
Exit codes: 0 on success, 1 if profile not found.
cyto-skills profile deploy <name>Deploy a profile by creating symlinks in the target directory.
cyto-skills profile deploy coding [--clean] [--target <dir>] [--dry-run]
| Option | Description |
|---|---|
--clean |
Remove all existing entries before deploying |
--target <dir> |
Override the target directory |
--dry-run |
Preview without making changes |
Reports created, skipped (unchanged), and removed symlink counts.
Warns about skills not found in the skill repository.
cyto-skills deploy-configsDeploy agent memory configs (CLAUDE.md, GEMINI.md, KIRO.md) to user
directories using section-aware merge.
cyto-skills deploy-configs [--dry-run] [--skip-git] [--target <name>]
| Option | Description |
|---|---|
--dry-run |
Preview changes without writing |
--skip-git |
Skip git init and commit tracking |
--target <name> |
Deploy only a specific target (claude, gemini, kiro) |
Merge strategy: reads agent-specific config + shared MEMORY.md,
merges with existing target file preserving user-specific sections.
Optionally snapshots before/after via git.
cyto-skills sync-skillsSync skill symlinks to editor-specific directories.
cyto-skills sync-skills [--execute] [--clean] [--target <name>] [--skills-dir <path>]
| Option | Description |
|---|---|
--execute |
Apply changes (default is dry-run) |
--clean |
Remove all existing entries before recreating |
--target <name> |
Sync only a specific target (antigravity, agents) |
--skills-dir <path> |
Override the skills/ directory |
[!IMPORTANT]
Default mode is dry-run. Pass--executeto apply changes.
cyto-skills sync-editorsSync IDE configuration files (settings.json, keybindings.json,
launch.json) and install extensions across all detected IDEs.
cyto-skills sync-editors
Supported IDEs: VS Code, Antigravity, Cursor, Windsurf, Positron.
Reads config from configs/editors/{ide}/.
cyto-skills sync-brandSync the brand skill from the cytognosis branding repository.
cyto-skills sync-brand
Pulls SKILL.tpl.md, guideline .md files, and brand assets from
the branding repo into skills/cytognosis/brand/. The branding repo
location can be overridden with CYTOGNOSIS_BRANDING_DIR.
cyto-skills sync-allDeploy ALL profiles to their respective targets.
cyto-skills sync-all [--clean]
| Option | Description |
|---|---|
--clean |
Clean target before deploying each profile |
cyto-skills ontology listList all Cyto Skill Ontology terms.
cyto-skills ontology list [--axis <A|B|C|meta>]
| Option | Description |
|---|---|
--axis <axis> |
Filter by axis (A, B, C, or meta) |
Shows CURIE, label, and SSSOM mapping count for each term.
cyto-skills ontology search <query>Search CSO terms by keyword against labels and aliases.
cyto-skills ontology search python
# 3 match(es) for "python":
# cso:Python Python [Axis A]
# aliases: CPython, pip, ruff
cyto-skills ontology expand <curie>Expand a CURIE to a full IRI.
cyto-skills ontology expand cso:Python
# https://w3id.org/cytognosis/cso/Python
Exit codes: 0 on success, 1 if prefix unknown.
cyto-skills ontology mappings <curie>Show SSSOM cross-ontology mappings for a CSO term.
cyto-skills ontology mappings cso:Genomics
Exit codes: 0 on success, 1 if CURIE not found.
cyto-skills ontology validate <curie>Check if a CURIE is a valid CSO term.
cyto-skills ontology validate cso:Python
# ✓ cso:Python — Python [Axis A]
Exit codes: 0 if valid, 1 if invalid.
cyto-skills tag skill <skillPath>Tag a single SKILL.md with CSO terms. Writes a .cyto-tags.yaml
sidecar file alongside the skill.
cyto-skills tag skill ./skills/languages/python-pro [--dry-run] [--confidence <0-1>]
| Option | Default | Description |
|---|---|---|
--dry-run |
— | Preview tags without writing sidecar |
--confidence <n> |
0.5 |
Minimum confidence threshold (0-1) |
Accepts either a directory path or a direct SKILL.md path.
cyto-skills tag allTag all SKILL.md files under a directory.
cyto-skills tag all [--root <path>] [--dry-run] [--confidence <n>]
| Option | Default | Description |
|---|---|---|
--root <path> |
cwd |
Root directory to scan |
--dry-run |
— | Preview without writing sidecars |
--confidence <n> |
0.5 |
Minimum confidence threshold |
cyto-skills tag promote <skillPath>Promote high-confidence tags from .cyto-tags.yaml into SKILL.md
frontmatter.
cyto-skills tag promote ./skills/languages/python-pro/SKILL.md [--dry-run] [--confidence <n>]
| Option | Default | Description |
|---|---|---|
--dry-run |
— | Preview without writing |
--confidence <n> |
0.7 |
Minimum confidence to promote |
Exit codes: 0 on success, 1 if no sidecar or no tags above
threshold.
cyto-skills tag show <skillPath>Show current .cyto-tags.yaml sidecar for a skill.
cyto-skills tag show ./skills/languages/python-pro/SKILL.md
cyto-skills judge skill <path>Score a single skill on 6 weighted axes (structure, trigger, content,
CSO, naming, freshness).
cyto-skills judge skill ./skills/languages/python-pro [-v|--verbose]
| Option | Description |
|---|---|
-v, --verbose |
Show per-axis notes and all issues |
Output includes overall score (0-100), verdict (PASS/WARN/FAIL),
visual bar chart, and prioritized recommendations.
Exit codes: 0 if PASS or WARN, 1 if FAIL.
cyto-skills judge allJudge all skills under a root directory.
cyto-skills judge all [--root <path>] [-v] [--min-score <n>] [--verdict <PASS|WARN|FAIL>]
| Option | Description |
|---|---|
--root <path> |
Search root (default: cwd) |
-v, --verbose |
Show per-axis notes |
--min-score <n> |
Only show skills below this score |
--verdict <v> |
Filter by verdict: PASS, WARN, or FAIL |
cyto-skills judge cytognosisJudge all Cytognosis skills across cytoskeleton/skills/ and
branding/skills/.
cyto-skills judge cytognosis [-v|--verbose]
cyto-skills review collectionAnalyze a skill directory for naming issues, overlaps, and split
candidates.
cyto-skills review collection [--root <path>]
Reports: total skills, average score, PASS/WARN/FAIL counts, naming
issues, overlap groups (Jaccard >= 0.35), and split candidates.
cyto-skills review cytognosisReview all Cytognosis skills across cytoskeleton + branding repos.
cyto-skills review cytognosis
cyto-skills agent list [agent]List installed skills for an agent.
cyto-skills agent list antigravity
cyto-skills agent list claude
Supported agents: antigravity, claude, agents, cursor,
kiro.
cyto-skills agent install <skill>Install a skill to an agent's skills directory via symlink.
cyto-skills agent install python-pro [-a antigravity] [--root <path>] [--dry-run]
| Option | Default | Description |
|---|---|---|
-a, --agent <id> |
antigravity |
Target agent |
--root <path> |
— | Additional skill search root |
--dry-run |
— | Preview without changes |
Searches cytoskeleton, branding, and cytoskills skill directories.
cyto-skills agent uninstall <skill>Remove a skill from an agent's skills directory.
cyto-skills agent uninstall python-pro [-a antigravity] [--dry-run]
cyto-skills agent batch <group>Batch install a skill group to one or all agents.
cyto-skills agent batch cytognosis [-a antigravity] [--all-agents] [--dry-run]
| Option | Description |
|---|---|
-a, --agent <id> |
Target agent (default: antigravity) |
--all-agents |
Install to antigravity, claude, and agents |
--dry-run |
Preview without changes |
Built-in groups: cytognosis, coding, science, writing,
meta. Unknown group names are treated as single skill names.
cyto-skills agent doctor [agent]Health-check an agent's skills directory for broken symlinks,
missing SKILL.md, and memory file status.
cyto-skills agent doctor antigravity [--fix]
| Option | Description |
|---|---|
--fix |
Auto-remove broken symlinks |
Exit codes: 0 if all healthy, 1 if broken symlinks found.
cyto-skills agent doctor-allHealth-check all known agents in a single run.
cyto-skills agent doctor-all [--fix]
cyto-skills agent doctor-desktopHealth-check the Claude Desktop / Cowork installation.
cyto-skills agent doctor-desktop
Checks: SDK binary, launcher script, desktop config,
spaces.json paths, session configs. See
module-spec-claude-desktop-doctor.md
for details.
Exit codes: 0 if healthy, 1 if unhealthy.
cyto-skills agent fix-launcherInstall or update the version-agnostic Claude Code launcher script.
cyto-skills agent fix-launcher [--dry-run]
If the launcher is already installed and version-agnostic, reports
no changes needed.
cyto-skills agent fix-paths <oldPath> <newPath>Fix stale folder paths in Cowork spaces and session configs after a
directory move.
cyto-skills agent fix-paths ~/Documents/Claude ~/Claude [--dry-run]
Replaces all occurrences of oldPath with newPath in
spaces.json and all local_*.json session config files. Supports
~ expansion.
[!IMPORTANT]
Restart Claude Desktop after running this command.
cyto-skills agent purge-cachePurge Electron renderer caches to force re-sync from backend.
cyto-skills agent purge-cache [--dry-run]
Removes: IndexedDB, Local Storage, Session Storage, Cache,
Code Cache, GPUCache.
[!IMPORTANT]
Restart Claude Desktop after purging caches.
cyto-skills agent memory <agent>Show the full memory file contents for an agent.
cyto-skills agent memory antigravity
cyto-skills agent memory claude
cyto-skills agent memory-update <agent> <section>Update or append a section in an agent's deployed memory file.
# From file
cyto-skills agent memory-update claude "Custom Rules" -f rules.md
# From stdin
echo "New content" | cyto-skills agent memory-update antigravity "Notes"
| Option | Description |
|---|---|
-f, --file <path> |
Read content from file instead of stdin |
cyto-skills agent memory-diff [agent]Compare source memory (configs/core_memory/) with deployed memory
for drift detection.
# Single agent
cyto-skills agent memory-diff antigravity [--json]
# All agents
cyto-skills agent memory-diff [--json]
| Option | Description |
|---|---|
--json |
Output as JSON |
Reports: identical, deployed-only (drift), source-only (deploy
needed), and modified sections.
Exit codes: 0 if no drift, 1 if drift detected.
cyto-skills agent memory-harmonizeReconcile deployed-only sections by backporting to source files.
cyto-skills agent memory-harmonize [--backport] [--dry-run] [--json]
| Option | Description |
|---|---|
--backport |
Apply the backport changes (default: dry-run) |
--dry-run |
Preview without writing (default behavior) |
--json |
Output as JSON |
Proposes three action types:
backport-shared — universal sections → MEMORY.mdbackport-agent — single-agent sections → agent source fileneeds-review — sections in some but not all agentscyto-skills agent memory-revision <section>Update a memory section in the source files. Determines whether the
section is shared (MEMORY.md) or agent-specific.
cyto-skills agent memory-revision "Code Standards" -f standards.md [--dry-run]
cyto-skills agent memory-revision "Notes" -c "Updated content" [--dry-run]
echo "Content" | cyto-skills agent memory-revision "Section Name"
| Option | Description |
|---|---|
-f, --file <path> |
Read content from file |
-c, --content <text> |
Section content as string |
--dry-run |
Preview without writing |
After updating source, run cyto-skills deploy-configs to
propagate changes to deployed files.
cyto-skills agent vault-link <repoPath>Create or update a symlink from ObsidianVault to a repo's docs/
folder.
cyto-skills agent vault-link ~/repos/cytognosis/cytoskills \
[--vault-section 03-Engineering] \
[--vault-root <path>] \
[--dry-run]
| Option | Default | Description |
|---|---|---|
--vault-section |
03-Engineering |
Vault section subdirectory |
--vault-root |
~/Documents/ObsidianVault |
Vault root path |
--dry-run |
— | Preview without creating symlink |
Exit codes: 0 on success, 1 on error.
cyto-skills catalog listList all configured third-party skill catalog sources.
cyto-skills catalog list [--root <path>] [--json]
| Option | Description |
|---|---|
--root <path> |
Skills root directory (default: cwd) |
--json |
Output as JSON |
Scans third_party/ subdirectory for skill repositories.
cyto-skills catalog fetch <source>Fetch or update a skill repo from a catalog source.
# GitHub shorthand
cyto-skills catalog fetch jeffallan/claude-skills [--root <path>] [--dry-run]
# Full URL
cyto-skills catalog fetch https://github.com/org/repo.git
# Local path
cyto-skills catalog fetch /path/to/local/repo
| Option | Description |
|---|---|
--root <path> |
Skills root directory (default: cwd) |
--dry-run |
Preview without cloning |
Clones new repos or runs git pull --ff-only on existing ones.
Exit codes: 0 on success, 1 on clone/pull failure.
cyto-skills catalog diffShow skills in catalog sources not yet installed locally.
cyto-skills catalog diff [--root <path>] [--source <name>] [--json]
| Option | Description |
|---|---|
--root <path> |
Skills root directory (default: cwd) |
--source <name> |
Limit to a specific catalog source |
--json |
Output as JSON |
All commands support the standard Commander.js flags:
| Flag | Description |
|---|---|
--help |
Display help for the command |
--version |
Display the CLI version (1.0.0) |